Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 17:25:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8l_0371/04_2023/6n8l_0371.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8l_0371/04_2023/6n8l_0371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8l_0371/04_2023/6n8l_0371.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8l_0371/04_2023/6n8l_0371.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8l_0371/04_2023/6n8l_0371.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8l_0371/04_2023/6n8l_0371.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 3479 5.49 5 S 122 5.16 5 C 68274 2.51 5 N 23904 2.21 5 O 34147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "v ARG 63": "NH1" <-> "NH2" Residue "v ARG 73": "NH1" <-> "NH2" Residue "v ARG 113": "NH1" <-> "NH2" Residue "v ARG 162": "NH1" <-> "NH2" Residue "v TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 303": "NH1" <-> "NH2" Residue "v ARG 330": "NH1" <-> "NH2" Residue "v ARG 342": "NH1" <-> "NH2" Residue "v ARG 356": "NH1" <-> "NH2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "a TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 117": "NH1" <-> "NH2" Residue "a ARG 139": "NH1" <-> "NH2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "b TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 510": "NH1" <-> "NH2" Residue "b ARG 613": "NH1" <-> "NH2" Residue "b ARG 615": "NH1" <-> "NH2" Residue "b ARG 624": "NH1" <-> "NH2" Residue "b ARG 647": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "f PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "g ARG 60": "NH1" <-> "NH2" Residue "I ARG 3": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 166": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H ARG 173": "NH1" <-> "NH2" Residue "h TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "k ARG 3": "NH1" <-> "NH2" Residue "k ARG 39": "NH1" <-> "NH2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "L ARG 171": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 77": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "p ARG 36": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "u TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 23": "NH1" <-> "NH2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u ARG 43": "NH1" <-> "NH2" Residue "u ARG 44": "NH1" <-> "NH2" Residue "u ARG 56": "NH1" <-> "NH2" Residue "u ARG 75": "NH1" <-> "NH2" Residue "u ARG 80": "NH1" <-> "NH2" Residue "u ARG 83": "NH1" <-> "NH2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "u ARG 111": "NH1" <-> "NH2" Residue "u ARG 113": "NH1" <-> "NH2" Residue "u ARG 122": "NH1" <-> "NH2" Residue "u ARG 135": "NH1" <-> "NH2" Residue "O PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P ARG 126": "NH1" <-> "NH2" Residue "P ARG 181": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "R ARG 62": "NH1" <-> "NH2" Residue "R ARG 104": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 108": "NH1" <-> "NH2" Residue "T ARG 139": "NH1" <-> "NH2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "W ARG 31": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "X ARG 33": "NH1" <-> "NH2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 125": "NH1" <-> "NH2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "y TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 85": "NH1" <-> "NH2" Residue "y ARG 100": "NH1" <-> "NH2" Residue "Z PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 84": "NH1" <-> "NH2" Residue "Z PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 135": "NH1" <-> "NH2" Residue "z ARG 6": "NH1" <-> "NH2" Residue "z ARG 19": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 158": "NH1" <-> "NH2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "q ARG 18": "NH1" <-> "NH2" Residue "q ARG 71": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 129926 Number of models: 1 Model: "" Number of chains: 48 Chain: "v" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2783 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 348} Chain breaks: 4 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 Chain: "s" 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: "A" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1863 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 233} Chain: "a" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 742 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "B" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3081 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Chain: "b" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2749 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain: "c" 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: "d" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 873 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1270 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "e" 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: "F" 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: "f" 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: "G" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1798 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 12, 'TRANS': 217} Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "I" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1056 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1493 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain: "h" 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: "i" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "j" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "k" 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: "L" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1491 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 178} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "l" 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: "M" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1059 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "p" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "N" 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: "u" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1256 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1409 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain breaks: 1 Chain: "Q" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1191 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "R" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1241 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "S" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1425 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "T" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 476 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 5, 'TRANS': 55} Chain: "U" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 826 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "V" 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: "W" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1053 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "X" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "Y" 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: "y" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1698 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" 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: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 444 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "D" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1983 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 240} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "J" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1304 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 159} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "q" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 783 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "o" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "1" Number of atoms: 68471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3201, 68471 Classifications: {'RNA': 3201} Modifications used: {'rna2p_pur': 335, 'rna2p_pyr': 229, 'rna3p_pur': 1440, 'rna3p_pyr': 1197} Link IDs: {'rna2p': 564, 'rna3p': 2636} Chain breaks: 3 Chain: "2" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "3" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3333 Classifications: {'RNA': 157} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 13, 'rna3p_pur': 62, 'rna3p_pyr': 66} Link IDs: {'rna2p': 29, 'rna3p': 127} Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N VAL O 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 13 " occ=0.50 residue: pdb=" N HIS O 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HIS O 14 " occ=0.50 ... (remaining 185 not shown) Time building chain proxies: 48.80, per 1000 atoms: 0.38 Number of scatterers: 129926 At special positions: 0 Unit cell: (236.5, 214.5, 261.8, 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 122 16.00 P 3479 15.00 O 34147 8.00 N 23904 7.00 C 68274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS v 19 " - pdb=" SG CYS v 22 " distance=2.04 Simple disulfide: pdb=" SG CYS v 19 " - pdb=" SG CYS v 35 " distance=2.04 Simple disulfide: pdb=" SG CYS v 22 " - pdb=" SG CYS v 35 " distance=2.04 Simple disulfide: pdb=" SG CYS v 22 " - pdb=" SG CYS v 38 " distance=2.05 Simple disulfide: pdb=" SG CYS v 58 " - pdb=" SG CYS v 143 " distance=2.03 Simple disulfide: pdb=" SG CYS v 61 " - pdb=" SG CYS v 143 " distance=2.02 Simple disulfide: pdb=" SG CYS v 61 " - pdb=" SG CYS v 146 " distance=2.02 Simple disulfide: pdb=" SG CYS v 143 " - pdb=" SG CYS v 146 " distance=2.05 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 47 " distance=2.03 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 81 " distance=2.03 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 81 " distance=2.02 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 84 " distance=2.03 Simple disulfide: pdb=" SG CYS j 22 " - pdb=" SG CYS j 37 " distance=2.02 Simple disulfide: pdb=" SG CYS p 39 " - pdb=" SG CYS p 57 " distance=2.03 Simple disulfide: pdb=" SG CYS p 42 " - pdb=" SG CYS p 59 " distance=2.02 Simple disulfide: pdb=" SG CYS u 6 " - pdb=" SG CYS u 9 " distance=2.03 Simple disulfide: pdb=" SG CYS u 6 " - pdb=" SG CYS u 32 " distance=2.07 Simple disulfide: pdb=" SG CYS u 9 " - pdb=" SG CYS u 32 " distance=2.03 Simple disulfide: pdb=" SG CYS u 9 " - pdb=" SG CYS u 36 " distance=2.00 Simple disulfide: pdb=" SG CYS u 32 " - pdb=" SG CYS u 36 " distance=2.58 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 50.21 Conformation dependent library (CDL) restraints added in 6.9 seconds 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13308 Finding SS restraints... Secondary structure from input PDB file: 243 helices and 70 sheets defined 37.9% alpha, 13.9% beta 763 base pairs and 1796 stacking pairs defined. Time for finding SS restraints: 34.05 Creating SS restraints... Processing helix chain 'v' and resid 77 through 88 removed outlier: 3.839A pdb=" N LEU v 82 " --> pdb=" O SER v 78 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA v 83 " --> pdb=" O ARG v 79 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS v 85 " --> pdb=" O LEU v 81 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG v 87 " --> pdb=" O ALA v 83 " (cutoff:3.500A) Processing helix chain 'v' and resid 147 through 152 removed outlier: 3.768A pdb=" N THR v 152 " --> pdb=" O SER v 149 " (cutoff:3.500A) Processing helix chain 'v' and resid 168 through 181 removed outlier: 3.698A pdb=" N GLN v 176 " --> pdb=" O LEU v 172 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU v 179 " --> pdb=" O GLU v 175 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS v 181 " --> pdb=" O LEU v 177 " (cutoff:3.500A) Processing helix chain 'v' and resid 204 through 218 removed outlier: 3.782A pdb=" N VAL v 208 " --> pdb=" O LYS v 204 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE v 213 " --> pdb=" O LYS v 209 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA v 216 " --> pdb=" O ASP v 212 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL v 217 " --> pdb=" O PHE v 213 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL v 218 " --> pdb=" O LEU v 214 " (cutoff:3.500A) Processing helix chain 'v' and resid 260 through 265 Processing helix chain 'v' and resid 297 through 302 Processing helix chain 'v' and resid 311 through 315 removed outlier: 3.587A pdb=" N GLN v 314 " --> pdb=" O ASP v 311 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU v 315 " --> pdb=" O VAL v 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 311 through 315' Processing helix chain 'v' and resid 343 through 347 removed outlier: 4.228A pdb=" N GLY v 347 " --> pdb=" O THR v 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 343 through 347' Processing helix chain 'v' and resid 381 through 386 Processing helix chain 'v' and resid 388 through 392 Processing helix chain 's' and resid 4 through 14 removed outlier: 3.539A pdb=" N UNK s 11 " --> pdb=" O UNK s 7 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N UNK s 12 " --> pdb=" O UNK s 8 " (cutoff:3.500A) Processing helix chain 's' and resid 66 through 71 Processing helix chain 's' and resid 80 through 86 Processing helix chain 's' and resid 90 through 99 removed outlier: 3.502A pdb=" N UNK s 96 " --> pdb=" O UNK s 92 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N UNK s 99 " --> pdb=" O UNK s 95 " (cutoff:3.500A) Processing helix chain 's' and resid 111 through 116 Processing helix chain 's' and resid 120 through 125 removed outlier: 4.015A pdb=" N UNK s 124 " --> pdb=" O UNK s 120 " (cutoff:3.500A) Processing helix chain 's' and resid 138 through 146 removed outlier: 4.286A pdb=" N UNK s 142 " --> pdb=" O UNK s 138 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N UNK s 146 " --> pdb=" O UNK s 142 " (cutoff:3.500A) Processing helix chain 's' and resid 171 through 175 removed outlier: 3.920A pdb=" N UNK s 174 " --> pdb=" O UNK s 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 11 removed outlier: 3.737A pdb=" N LYS A 10 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 11 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.543A pdb=" N ASP A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 177' Processing helix chain 'A' and resid 181 through 190 removed outlier: 3.533A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 92 removed outlier: 4.136A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN a 89 " --> pdb=" O ASP a 85 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU a 91 " --> pdb=" O ARG a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 108 Processing helix chain 'a' and resid 131 through 142 removed outlier: 3.528A pdb=" N GLU a 135 " --> pdb=" O SER a 131 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA a 141 " --> pdb=" O LYS a 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 3.559A pdb=" N LYS B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.593A pdb=" N ALA B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 154 removed outlier: 3.661A pdb=" N ILE B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 188 through 197 removed outlier: 3.643A pdb=" N TRP B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'b' and resid 379 through 385 removed outlier: 3.748A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 405 removed outlier: 3.801A pdb=" N ILE b 402 " --> pdb=" O LEU b 398 " (cutoff:3.500A) Processing helix chain 'b' and resid 440 through 445 removed outlier: 3.629A pdb=" N PHE b 444 " --> pdb=" O ASN b 440 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 465 removed outlier: 3.703A pdb=" N ALA b 455 " --> pdb=" O ALA b 451 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU b 459 " --> pdb=" O ALA b 455 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU b 461 " --> pdb=" O GLU b 457 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU b 463 " --> pdb=" O GLU b 459 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN b 465 " --> pdb=" O GLU b 461 " (cutoff:3.500A) Processing helix chain 'b' and resid 482 through 512 removed outlier: 3.534A pdb=" N ASP b 487 " --> pdb=" O ALA b 483 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP b 488 " --> pdb=" O SER b 484 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS b 490 " --> pdb=" O VAL b 486 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP b 495 " --> pdb=" O GLU b 491 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN b 498 " --> pdb=" O ALA b 494 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN b 509 " --> pdb=" O ALA b 505 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER b 512 " --> pdb=" O ARG b 508 " (cutoff:3.500A) Processing helix chain 'b' and resid 528 through 539 removed outlier: 3.923A pdb=" N GLU b 533 " --> pdb=" O GLY b 529 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET b 535 " --> pdb=" O MET b 531 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU b 538 " --> pdb=" O HIS b 534 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY b 539 " --> pdb=" O MET b 535 " (cutoff:3.500A) Processing helix chain 'b' and resid 542 through 550 removed outlier: 4.020A pdb=" N LYS b 548 " --> pdb=" O ALA b 544 " (cutoff:3.500A) Processing helix chain 'b' and resid 595 through 608 removed outlier: 3.704A pdb=" N ARG b 599 " --> pdb=" O ASP b 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER b 600 " --> pdb=" O GLY b 596 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS b 607 " --> pdb=" O ASP b 603 " (cutoff:3.500A) Processing helix chain 'b' and resid 610 through 616 removed outlier: 3.600A pdb=" N ASN b 614 " --> pdb=" O ARG b 610 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG b 615 " --> pdb=" O ARG b 611 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS b 616 " --> pdb=" O GLU b 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 610 through 616' Processing helix chain 'b' and resid 631 through 636 removed outlier: 4.217A pdb=" N PHE b 635 " --> pdb=" O SER b 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 43 removed outlier: 3.877A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.557A pdb=" N ALA C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 153 through 157 Processing helix chain 'C' and resid 161 through 173 removed outlier: 3.519A pdb=" N ALA C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 removed outlier: 3.871A pdb=" N VAL C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.551A pdb=" N LYS C 257 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 removed outlier: 3.964A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.571A pdb=" N GLN C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 325 removed outlier: 3.559A pdb=" N LEU C 324 " --> pdb=" O ASN C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 337 removed outlier: 4.625A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 360 removed outlier: 3.792A pdb=" N THR C 356 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 18 removed outlier: 3.624A pdb=" N LEU c 16 " --> pdb=" O GLN c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 37 removed outlier: 3.962A pdb=" N LYS c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER c 33 " --> pdb=" O SER c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 61 removed outlier: 3.512A pdb=" N MET c 61 " --> pdb=" O GLU c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 74 through 79 removed outlier: 3.838A pdb=" N GLY c 78 " --> pdb=" O ASN c 74 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR c 79 " --> pdb=" O ASN c 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 74 through 79' Processing helix chain 'd' and resid 24 through 27 Processing helix chain 'd' and resid 28 through 45 removed outlier: 3.503A pdb=" N VAL d 33 " --> pdb=" O ALA d 29 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS d 43 " --> pdb=" O PHE d 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'd' and resid 61 through 63 No H-bonds generated for 'chain 'd' and resid 61 through 63' Processing helix chain 'E' and resid 97 through 101 removed outlier: 4.253A pdb=" N LYS E 100 " --> pdb=" O ASN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.800A pdb=" N ALA E 107 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.622A pdb=" N VAL E 141 " --> pdb=" O ASP E 137 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 removed outlier: 3.519A pdb=" N SER E 160 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA E 161 " --> pdb=" O GLN E 157 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.778A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 72 removed outlier: 3.519A pdb=" N LYS F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE F 43 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.789A pdb=" N VAL F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 130 removed outlier: 3.541A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 removed outlier: 3.590A pdb=" N ILE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 171 removed outlier: 4.435A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 177 removed outlier: 3.740A pdb=" N GLY F 177 " --> pdb=" O GLY F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'F' and resid 235 through 244 removed outlier: 3.878A pdb=" N LYS F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 42 Processing helix chain 'f' and resid 43 through 45 No H-bonds generated for 'chain 'f' and resid 43 through 45' Processing helix chain 'G' and resid 53 through 69 removed outlier: 3.511A pdb=" N GLN G 61 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 96 removed outlier: 3.593A pdb=" N ALA G 88 " --> pdb=" O ARG G 84 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU G 89 " --> pdb=" O ASN G 85 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 120 removed outlier: 3.936A pdb=" N THR G 110 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.902A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 222 removed outlier: 3.587A pdb=" N LEU G 211 " --> pdb=" O ASP G 207 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR G 217 " --> pdb=" O LYS G 213 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA G 220 " --> pdb=" O SER G 216 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN G 221 " --> pdb=" O THR G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 230 removed outlier: 3.910A pdb=" N LYS G 230 " --> pdb=" O TYR G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 252 removed outlier: 4.033A pdb=" N ASN G 252 " --> pdb=" O LYS G 248 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 63 removed outlier: 3.775A pdb=" N TYR g 62 " --> pdb=" O PRO g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 70 removed outlier: 3.512A pdb=" N HIS g 69 " --> pdb=" O SER g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 111 removed outlier: 3.680A pdb=" N ARG g 88 " --> pdb=" O CYS g 84 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE g 90 " --> pdb=" O LYS g 86 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA g 92 " --> pdb=" O ARG g 88 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU g 96 " --> pdb=" O ALA g 92 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE g 100 " --> pdb=" O GLU g 96 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL g 101 " --> pdb=" O GLU g 97 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU g 110 " --> pdb=" O LYS g 106 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA g 111 " --> pdb=" O GLU g 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 9 removed outlier: 3.711A pdb=" N LYS I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG I 8 " --> pdb=" O TYR I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 26 removed outlier: 3.541A pdb=" N TYR I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP I 24 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 36 removed outlier: 3.553A pdb=" N VAL I 31 " --> pdb=" O THR I 27 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN I 36 " --> pdb=" O GLN I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 69 removed outlier: 3.682A pdb=" N LYS I 65 " --> pdb=" O ALA I 61 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS I 67 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 80 removed outlier: 3.659A pdb=" N ARG I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS I 78 " --> pdb=" O LYS I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 93 removed outlier: 4.296A pdb=" N SER I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 111 removed outlier: 3.667A pdb=" N ARG I 104 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 130 removed outlier: 3.935A pdb=" N GLU I 115 " --> pdb=" O SER I 111 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA I 121 " --> pdb=" O GLU I 117 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU I 125 " --> pdb=" O ALA I 121 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP I 128 " --> pdb=" O LYS I 124 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER I 129 " --> pdb=" O GLU I 125 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 130 " --> pdb=" O HIS I 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.659A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL H 82 " --> pdb=" O MET H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 120 Processing helix chain 'H' and resid 150 through 164 removed outlier: 3.728A pdb=" N GLN H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN H 157 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN H 162 " --> pdb=" O ALA H 158 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 10 removed outlier: 3.772A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 35 removed outlier: 3.657A pdb=" N GLU h 27 " --> pdb=" O ASP h 23 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS h 32 " --> pdb=" O LEU h 28 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL h 33 " --> pdb=" O ALA h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 43 through 70 removed outlier: 3.607A pdb=" N VAL h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL h 57 " --> pdb=" O CYS h 53 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG h 67 " --> pdb=" O ARG h 63 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN h 68 " --> pdb=" O GLU h 64 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 81 Processing helix chain 'h' and resid 85 through 90 removed outlier: 3.619A pdb=" N ARG h 89 " --> pdb=" O THR h 85 " (cutoff:3.500A) Processing helix chain 'h' and resid 101 through 111 removed outlier: 3.671A pdb=" N LYS h 106 " --> pdb=" O GLU h 102 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE h 109 " --> pdb=" O ARG h 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA h 110 " --> pdb=" O LYS h 106 " (cutoff:3.500A) Processing helix chain 'i' and resid 25 through 29 removed outlier: 3.513A pdb=" N TYR i 28 " --> pdb=" O LYS i 25 " (cutoff:3.500A) Processing helix chain 'i' and resid 36 through 49 removed outlier: 4.067A pdb=" N GLU i 46 " --> pdb=" O SER i 42 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE i 47 " --> pdb=" O LEU i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 77 removed outlier: 3.540A pdb=" N ARG i 56 " --> pdb=" O PRO i 52 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG i 62 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN i 63 " --> pdb=" O ASP i 59 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY i 65 " --> pdb=" O ILE i 61 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N GLU i 66 " --> pdb=" O ARG i 62 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N LYS i 67 " --> pdb=" O ASN i 63 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG i 68 " --> pdb=" O SER i 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA i 69 " --> pdb=" O GLY i 65 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS i 71 " --> pdb=" O LYS i 67 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS i 75 " --> pdb=" O LYS i 71 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU i 77 " --> pdb=" O ALA i 73 " (cutoff:3.500A) Processing helix chain 'i' and resid 80 through 98 removed outlier: 4.254A pdb=" N ALA i 85 " --> pdb=" O THR i 81 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN i 92 " --> pdb=" O GLU i 88 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE i 93 " --> pdb=" O GLU i 89 " (cutoff:3.500A) Processing helix chain 'j' and resid 51 through 56 Processing helix chain 'j' and resid 66 through 68 No H-bonds generated for 'chain 'j' and resid 66 through 68' Processing helix chain 'j' and resid 69 through 77 removed outlier: 3.684A pdb=" N ARG j 73 " --> pdb=" O HIS j 69 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 15 removed outlier: 3.823A pdb=" N GLU k 13 " --> pdb=" O LYS k 9 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU k 14 " --> pdb=" O GLN k 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR k 15 " --> pdb=" O PHE k 11 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 68 removed outlier: 3.500A pdb=" N LYS k 63 " --> pdb=" O ALA k 59 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN k 67 " --> pdb=" O LYS k 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 removed outlier: 3.544A pdb=" N LYS L 32 " --> pdb=" O GLN L 28 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL L 33 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA L 38 " --> pdb=" O SER L 34 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 66 removed outlier: 3.590A pdb=" N ASN L 66 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 84 Processing helix chain 'L' and resid 86 through 94 removed outlier: 3.573A pdb=" N ALA L 90 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.888A pdb=" N SER L 121 " --> pdb=" O LYS L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 145 removed outlier: 3.864A pdb=" N THR L 144 " --> pdb=" O SER L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 179 removed outlier: 3.716A pdb=" N LYS L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE L 179 " --> pdb=" O SER L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 193 removed outlier: 3.604A pdb=" N ARG L 183 " --> pdb=" O PHE L 179 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU L 189 " --> pdb=" O LYS L 185 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA L 191 " --> pdb=" O ALA L 187 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA L 193 " --> pdb=" O GLU L 189 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 19 removed outlier: 3.702A pdb=" N LYS l 12 " --> pdb=" O ARG l 8 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS l 15 " --> pdb=" O GLN l 11 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 3.619A pdb=" N ILE l 27 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG l 30 " --> pdb=" O ILE l 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 89 removed outlier: 3.716A pdb=" N LYS M 83 " --> pdb=" O ALA M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 96 removed outlier: 3.670A pdb=" N ALA M 95 " --> pdb=" O CYS M 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA M 96 " --> pdb=" O GLU M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 109 removed outlier: 3.728A pdb=" N LYS M 101 " --> pdb=" O SER M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 135 removed outlier: 3.526A pdb=" N MET M 121 " --> pdb=" O ARG M 117 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR M 129 " --> pdb=" O LYS M 125 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR M 130 " --> pdb=" O GLN M 126 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS M 133 " --> pdb=" O TYR M 129 " (cutoff:3.500A) Processing helix chain 'p' and resid 8 through 14 removed outlier: 3.814A pdb=" N GLY p 12 " --> pdb=" O GLY p 9 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 21 through 35 removed outlier: 3.661A pdb=" N VAL p 26 " --> pdb=" O LEU p 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS p 27 " --> pdb=" O ARG p 23 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU p 29 " --> pdb=" O GLN p 25 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN p 32 " --> pdb=" O LYS p 28 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS p 34 " --> pdb=" O GLU p 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 91 removed outlier: 4.000A pdb=" N VAL p 79 " --> pdb=" O ALA p 75 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR p 82 " --> pdb=" O THR p 78 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET p 89 " --> pdb=" O ARG p 85 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL p 90 " --> pdb=" O LEU p 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.551A pdb=" N GLN N 11 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG N 12 " --> pdb=" O GLU N 8 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 33 removed outlier: 3.799A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG N 31 " --> pdb=" O VAL N 27 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 50 Processing helix chain 'N' and resid 75 through 79 removed outlier: 4.026A pdb=" N GLY N 78 " --> pdb=" O VAL N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 106 removed outlier: 3.596A pdb=" N THR N 101 " --> pdb=" O SER N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 152 removed outlier: 3.737A pdb=" N ILE N 151 " --> pdb=" O TYR N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 157 removed outlier: 3.962A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 172 Processing helix chain 'N' and resid 186 through 195 removed outlier: 3.874A pdb=" N GLN N 194 " --> pdb=" O THR N 190 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 removed outlier: 3.674A pdb=" N GLN u 42 " --> pdb=" O LYS u 38 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 57 Processing helix chain 'u' and resid 66 through 72 removed outlier: 3.609A pdb=" N THR u 70 " --> pdb=" O SER u 67 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE u 71 " --> pdb=" O THR u 68 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA u 72 " --> pdb=" O LEU u 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 82 through 112 removed outlier: 3.669A pdb=" N VAL u 86 " --> pdb=" O ASN u 82 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU u 98 " --> pdb=" O ALA u 94 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA u 106 " --> pdb=" O LYS u 102 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN u 110 " --> pdb=" O ALA u 106 " (cutoff:3.500A) Processing helix chain 'u' and resid 114 through 129 removed outlier: 3.516A pdb=" N LYS u 118 " --> pdb=" O GLY u 114 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE u 120 " --> pdb=" O LYS u 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP u 123 " --> pdb=" O ASP u 119 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS u 125 " --> pdb=" O LEU u 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU u 126 " --> pdb=" O ARG u 122 " (cutoff:3.500A) Processing helix chain 'u' and resid 132 through 149 removed outlier: 3.655A pdb=" N ILE u 136 " --> pdb=" O GLU u 132 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU u 138 " --> pdb=" O LEU u 134 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL u 139 " --> pdb=" O ARG u 135 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU u 140 " --> pdb=" O ILE u 136 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE u 141 " --> pdb=" O ARG u 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 28 removed outlier: 3.663A pdb=" N VAL O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN O 26 " --> pdb=" O VAL O 22 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 40 removed outlier: 3.819A pdb=" N GLU O 40 " --> pdb=" O ARG O 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 37 through 40' Processing helix chain 'O' and resid 46 through 59 removed outlier: 3.845A pdb=" N ASN O 50 " --> pdb=" O GLU O 46 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU O 52 " --> pdb=" O PHE O 48 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE O 57 " --> pdb=" O LYS O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 69 removed outlier: 3.538A pdb=" N GLY O 69 " --> pdb=" O LYS O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 92 through 99 Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 removed outlier: 3.717A pdb=" N ARG O 128 " --> pdb=" O LEU O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 138 through 145 removed outlier: 3.573A pdb=" N THR O 143 " --> pdb=" O GLY O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 186 removed outlier: 3.756A pdb=" N LYS O 155 " --> pdb=" O ASP O 151 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL O 162 " --> pdb=" O ALA O 158 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS O 170 " --> pdb=" O GLU O 166 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE O 174 " --> pdb=" O LYS O 170 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS O 177 " --> pdb=" O ALA O 173 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA O 183 " --> pdb=" O ALA O 179 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR O 184 " --> pdb=" O SER O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 198 removed outlier: 3.513A pdb=" N GLN O 193 " --> pdb=" O ASP O 189 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU O 194 " --> pdb=" O VAL O 190 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA O 195 " --> pdb=" O ALA O 191 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA O 196 " --> pdb=" O LYS O 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 35 removed outlier: 3.673A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR P 32 " --> pdb=" O ASN P 28 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 52 removed outlier: 3.772A pdb=" N LYS P 46 " --> pdb=" O THR P 42 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU P 49 " --> pdb=" O GLN P 45 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN P 50 " --> pdb=" O LYS P 46 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 75 removed outlier: 3.665A pdb=" N LYS P 74 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 71 through 75' Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.813A pdb=" N VAL P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY P 93 " --> pdb=" O LYS P 89 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA P 100 " --> pdb=" O GLN P 96 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS P 105 " --> pdb=" O ASN P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 132 through 134 No H-bonds generated for 'chain 'P' and resid 132 through 134' Processing helix chain 'P' and resid 169 through 183 removed outlier: 3.722A pdb=" N ILE P 176 " --> pdb=" O GLN P 172 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 40 removed outlier: 3.750A pdb=" N LYS Q 27 " --> pdb=" O ASN Q 23 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG Q 38 " --> pdb=" O THR Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 53 removed outlier: 3.812A pdb=" N VAL Q 47 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 71 Processing helix chain 'Q' and resid 107 through 118 removed outlier: 3.662A pdb=" N ILE Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL Q 115 " --> pdb=" O ARG Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'R' and resid 4 through 16 removed outlier: 3.652A pdb=" N ALA R 12 " --> pdb=" O LYS R 8 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER R 13 " --> pdb=" O ARG R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 33 removed outlier: 3.654A pdb=" N ILE R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA R 33 " --> pdb=" O THR R 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 28 through 33' Processing helix chain 'R' and resid 37 through 47 removed outlier: 3.760A pdb=" N LYS R 43 " --> pdb=" O ASN R 39 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN R 47 " --> pdb=" O LYS R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 72 Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 112 removed outlier: 3.662A pdb=" N LEU R 102 " --> pdb=" O ARG R 98 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG R 103 " --> pdb=" O LEU R 99 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU R 106 " --> pdb=" O LEU R 102 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS R 108 " --> pdb=" O ARG R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 129 removed outlier: 3.949A pdb=" N LYS R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY R 129 " --> pdb=" O LYS R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 155 removed outlier: 3.512A pdb=" N LEU R 138 " --> pdb=" O HIS R 134 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS R 141 " --> pdb=" O ALA R 137 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU R 155 " --> pdb=" O ARG R 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.593A pdb=" N ALA S 37 " --> pdb=" O ASN S 33 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS S 38 " --> pdb=" O GLU S 34 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER S 39 " --> pdb=" O VAL S 35 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP S 42 " --> pdb=" O LYS S 38 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN S 46 " --> pdb=" O TRP S 42 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 114 removed outlier: 3.659A pdb=" N VAL S 103 " --> pdb=" O ARG S 99 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU S 104 " --> pdb=" O VAL S 100 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP S 109 " --> pdb=" O THR S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 140 through 144 removed outlier: 3.525A pdb=" N PHE S 143 " --> pdb=" O VAL S 140 " (cutoff:3.500A) Processing helix chain 'T' and resid 100 through 122 removed outlier: 3.992A pdb=" N LYS T 110 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG T 116 " --> pdb=" O ASN T 112 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA T 121 " --> pdb=" O ALA T 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 25 removed outlier: 3.737A pdb=" N ASN U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 41 removed outlier: 3.846A pdb=" N LYS U 35 " --> pdb=" O ALA U 31 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU U 37 " --> pdb=" O TYR U 33 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE U 38 " --> pdb=" O ALA U 34 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP U 39 " --> pdb=" O LYS U 35 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS U 40 " --> pdb=" O TYR U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 87 removed outlier: 3.692A pdb=" N THR U 80 " --> pdb=" O LEU U 76 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS U 81 " --> pdb=" O LYS U 77 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS U 85 " --> pdb=" O LYS U 81 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 126 removed outlier: 3.894A pdb=" N LEU V 125 " --> pdb=" O GLU V 121 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 132 removed outlier: 3.621A pdb=" N ALA V 130 " --> pdb=" O TRP V 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 32 removed outlier: 3.924A pdb=" N ASP W 28 " --> pdb=" O GLU W 24 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU W 29 " --> pdb=" O ARG W 25 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL W 30 " --> pdb=" O ILE W 26 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG W 31 " --> pdb=" O PHE W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 32 through 37 removed outlier: 4.192A pdb=" N THR W 36 " --> pdb=" O GLU W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 59 removed outlier: 3.516A pdb=" N GLU W 55 " --> pdb=" O PRO W 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 89 through 95 removed outlier: 4.027A pdb=" N SER W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS W 94 " --> pdb=" O TYR W 90 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 89 through 95' Processing helix chain 'W' and resid 108 through 119 removed outlier: 4.416A pdb=" N VAL W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS W 113 " --> pdb=" O VAL W 109 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 62 Processing helix chain 'X' and resid 69 through 78 removed outlier: 4.207A pdb=" N LYS X 75 " --> pdb=" O THR X 71 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP X 78 " --> pdb=" O LYS X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 104 removed outlier: 3.885A pdb=" N LYS X 100 " --> pdb=" O LYS X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 140 removed outlier: 3.784A pdb=" N ILE X 135 " --> pdb=" O ASP X 131 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG X 138 " --> pdb=" O ASP X 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 21 removed outlier: 3.663A pdb=" N LYS Y 17 " --> pdb=" O ARG Y 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 31 removed outlier: 4.277A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU Y 30 " --> pdb=" O GLN Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 removed outlier: 3.560A pdb=" N ALA Y 41 " --> pdb=" O LYS Y 37 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN Y 42 " --> pdb=" O GLU Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 123 removed outlier: 3.545A pdb=" N LYS Y 116 " --> pdb=" O ASP Y 112 " (cutoff:3.500A) Processing helix chain 'y' and resid 33 through 42 removed outlier: 3.633A pdb=" N ALA y 37 " --> pdb=" O ASN y 33 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 removed outlier: 3.793A pdb=" N MET y 62 " --> pdb=" O ILE y 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 122 through 133 removed outlier: 3.877A pdb=" N LEU y 128 " --> pdb=" O GLU y 124 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER y 130 " --> pdb=" O GLU y 126 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 178 removed outlier: 3.573A pdb=" N GLU y 171 " --> pdb=" O VAL y 167 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU y 172 " --> pdb=" O GLN y 168 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU y 176 " --> pdb=" O GLU y 172 " (cutoff:3.500A) Processing helix chain 'y' and resid 192 through 197 removed outlier: 3.561A pdb=" N GLY y 196 " --> pdb=" O VAL y 192 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET y 197 " --> pdb=" O VAL y 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 192 through 197' Processing helix chain 'y' and resid 211 through 223 removed outlier: 3.542A pdb=" N SER y 220 " --> pdb=" O SER y 216 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 66 removed outlier: 4.207A pdb=" N ALA Z 63 " --> pdb=" O ALA Z 59 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS Z 64 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 98 through 102 removed outlier: 3.634A pdb=" N GLU Z 102 " --> pdb=" O GLU Z 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 123 removed outlier: 3.905A pdb=" N GLU Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA Z 110 " --> pdb=" O GLN Z 106 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU Z 120 " --> pdb=" O LYS Z 116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 132 removed outlier: 3.874A pdb=" N PHE Z 131 " --> pdb=" O ASN Z 127 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 20 removed outlier: 4.058A pdb=" N VAL z 16 " --> pdb=" O ASN z 12 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS z 17 " --> pdb=" O ALA z 13 " (cutoff:3.500A) Processing helix chain 'z' and resid 20 through 56 removed outlier: 3.945A pdb=" N LYS z 24 " --> pdb=" O GLY z 20 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL z 26 " --> pdb=" O PHE z 22 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN z 31 " --> pdb=" O ASP z 27 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG z 32 " --> pdb=" O ALA z 28 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS z 36 " --> pdb=" O ARG z 32 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS z 38 " --> pdb=" O SER z 34 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU z 41 " --> pdb=" O LEU z 37 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU z 47 " --> pdb=" O LYS z 43 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP z 48 " --> pdb=" O GLN z 44 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU z 53 " --> pdb=" O LEU z 49 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN z 55 " --> pdb=" O LYS z 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 16 removed outlier: 3.555A pdb=" N SER D 14 " --> pdb=" O SER D 10 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE D 16 " --> pdb=" O TYR D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 removed outlier: 3.562A pdb=" N GLU D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 4.023A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR D 38 " --> pdb=" O LYS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 removed outlier: 3.792A pdb=" N GLY D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 112 removed outlier: 3.572A pdb=" N ALA D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 170 removed outlier: 4.231A pdb=" N ALA D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 200 removed outlier: 3.626A pdb=" N SER D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 211 removed outlier: 3.822A pdb=" N GLU D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 222 Processing helix chain 'D' and resid 223 through 229 Processing helix chain 'D' and resid 235 through 250 removed outlier: 3.584A pdb=" N ILE D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 273 removed outlier: 4.124A pdb=" N LYS D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 285 removed outlier: 3.530A pdb=" N ARG D 282 " --> pdb=" O SER D 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 42 removed outlier: 3.813A pdb=" N VAL J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 85 removed outlier: 4.044A pdb=" N GLU J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU J 78 " --> pdb=" O PRO J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 112 removed outlier: 3.521A pdb=" N LEU J 112 " --> pdb=" O HIS J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 141 removed outlier: 3.611A pdb=" N ARG J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 166 removed outlier: 4.044A pdb=" N THR J 159 " --> pdb=" O THR J 155 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL J 160 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 169 No H-bonds generated for 'chain 'J' and resid 167 through 169' Processing helix chain 'q' and resid 41 through 46 Processing helix chain 'o' and resid 12 through 17 Processing helix chain 'o' and resid 36 through 57 removed outlier: 3.610A pdb=" N ASN o 42 " --> pdb=" O LYS o 38 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS o 45 " --> pdb=" O ARG o 41 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY o 49 " --> pdb=" O HIS o 45 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS o 52 " --> pdb=" O HIS o 48 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU o 54 " --> pdb=" O THR o 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'v' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'v' and resid 187 through 192 removed outlier: 6.930A pdb=" N PHE v 200 " --> pdb=" O ILE v 188 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE v 190 " --> pdb=" O ASP v 198 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP v 198 " --> pdb=" O ILE v 190 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU v 192 " --> pdb=" O GLY v 196 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY v 196 " --> pdb=" O GLU v 192 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR v 158 " --> pdb=" O TYR v 244 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL v 246 " --> pdb=" O THR v 158 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLN v 160 " --> pdb=" O VAL v 246 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER v 243 " --> pdb=" O SER v 225 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS v 223 " --> pdb=" O SER v 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'v' and resid 256 through 258 Processing sheet with id=AA4, first strand: chain 'v' and resid 352 through 357 removed outlier: 3.595A pdb=" N SER v 357 " --> pdb=" O ALA v 336 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP v 337 " --> pdb=" O VAL v 323 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N VAL v 323 " --> pdb=" O ASP v 337 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR v 339 " --> pdb=" O LEU v 321 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR v 372 " --> pdb=" O LEU v 397 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU v 397 " --> pdb=" O TYR v 372 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 's' and resid 28 through 29 Processing sheet with id=AA6, first strand: chain 's' and resid 199 through 200 removed outlier: 3.875A pdb=" N UNK s 200 " --> pdb=" O UNK s 208 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N UNK s 208 " --> pdb=" O UNK s 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 71 through 77 removed outlier: 3.584A pdb=" N GLN A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 62 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL A 45 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ARG A 64 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLY A 43 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 101 through 103 removed outlier: 5.997A pdb=" N ILE A 136 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG A 149 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 138 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A 145 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 72 through 73 Processing sheet with id=AB1, first strand: chain 'a' and resid 145 through 147 removed outlier: 6.674A pdb=" N VAL a 125 " --> pdb=" O GLU a 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.873A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE B 359 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA B 217 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE B 278 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N THR B 276 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 221 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER B 274 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS B 281 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY B 52 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASP B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LYS B 50 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 99 through 106 removed outlier: 7.104A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B 89 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG B 159 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLY B 91 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 157 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 99 through 106 removed outlier: 7.104A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS B 201 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AB6, first strand: chain 'C' and resid 6 through 9 removed outlier: 3.662A pdb=" N VAL C 8 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.371A pdb=" N LEU C 150 " --> pdb=" O TRP C 250 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL C 207 " --> pdb=" O ALA C 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB9, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.802A pdb=" N THR c 24 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE c 92 " --> pdb=" O THR c 24 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 9 through 15 removed outlier: 6.214A pdb=" N ARG d 50 " --> pdb=" O VAL d 93 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 77 through 79 removed outlier: 3.506A pdb=" N LYS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'e' and resid 72 through 76 removed outlier: 6.482A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 74 through 76 Processing sheet with id=AC5, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.565A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR F 115 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY F 137 " --> pdb=" O PHE F 85 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AC7, first strand: chain 'f' and resid 8 through 18 removed outlier: 10.045A pdb=" N VAL f 9 " --> pdb=" O ILE f 32 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE f 32 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLY f 11 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ILE f 30 " --> pdb=" O GLY f 11 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N HIS f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N SER f 28 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N SER f 15 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N ASN f 26 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN f 17 " --> pdb=" O ASN f 24 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL f 80 " --> pdb=" O THR f 74 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N THR f 74 " --> pdb=" O VAL f 80 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ARG f 82 " --> pdb=" O THR f 72 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR f 72 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 150 through 153 removed outlier: 3.789A pdb=" N LEU G 150 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'g' and resid 21 through 24 Processing sheet with id=AD1, first strand: chain 'I' and resid 50 through 51 removed outlier: 3.676A pdb=" N LYS I 56 " --> pdb=" O CYS I 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 11 removed outlier: 6.957A pdb=" N ILE H 4 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN H 8 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL H 55 " --> pdb=" O GLN H 8 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 17 through 21 removed outlier: 3.513A pdb=" N LYS H 21 " --> pdb=" O ILE H 24 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 132 through 136 removed outlier: 3.652A pdb=" N LYS H 89 " --> pdb=" O HIS H 183 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS H 183 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG H 91 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL H 181 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL H 93 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE H 179 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AD6, first strand: chain 'h' and resid 116 through 118 Processing sheet with id=AD7, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AD8, first strand: chain 'k' and resid 3 through 4 removed outlier: 4.940A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA k 23 " --> pdb=" O ASN k 76 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 22 through 24 removed outlier: 6.821A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AE2, first strand: chain 'M' and resid 14 through 15 removed outlier: 3.638A pdb=" N PHE S 150 " --> pdb=" O VAL M 15 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 53 through 59 removed outlier: 5.246A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'p' and resid 47 through 50 removed outlier: 3.667A pdb=" N LYS p 48 " --> pdb=" O THR p 56 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR p 56 " --> pdb=" O LYS p 48 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE p 54 " --> pdb=" O GLY p 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 37 through 38 removed outlier: 7.709A pdb=" N TYR N 127 " --> pdb=" O ASN N 122 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN N 122 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N TYR N 129 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TRP N 120 " --> pdb=" O TYR N 129 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU N 131 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER N 118 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'u' and resid 28 through 30 removed outlier: 3.553A pdb=" N TYR V 94 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU V 93 " --> pdb=" O TRP V 85 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 6 through 10 removed outlier: 6.120A pdb=" N VAL O 7 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL O 36 " --> pdb=" O VAL O 7 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE O 9 " --> pdb=" O VAL O 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AE9, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.670A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AF2, first strand: chain 'P' and resid 128 through 130 removed outlier: 3.564A pdb=" N ASN P 137 " --> pdb=" O THR P 129 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AF4, first strand: chain 'Q' and resid 121 through 122 removed outlier: 6.118A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL Q 81 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 23 through 24 removed outlier: 3.670A pdb=" N TRP R 23 " --> pdb=" O VAL R 51 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL R 51 " --> pdb=" O TRP R 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'S' and resid 58 through 63 removed outlier: 6.768A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 88 through 96 removed outlier: 3.637A pdb=" N HIS S 88 " --> pdb=" O TYR S 81 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR S 81 " --> pdb=" O HIS S 88 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASN S 74 " --> pdb=" O GLU S 128 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLU S 128 " --> pdb=" O ASN S 74 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY S 76 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL S 126 " --> pdb=" O GLY S 76 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 54 through 58 removed outlier: 7.037A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 22 through 25 removed outlier: 6.860A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 114 through 118 removed outlier: 5.892A pdb=" N SER V 133 " --> pdb=" O ILE V 114 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N GLY V 116 " --> pdb=" O SER V 133 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL V 135 " --> pdb=" O GLY V 116 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 66 through 67 removed outlier: 3.641A pdb=" N LEU W 43 " --> pdb=" O GLY W 101 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL W 42 " --> pdb=" O ALA W 219 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS W 44 " --> pdb=" O VAL W 217 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL W 217 " --> pdb=" O HIS W 44 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP W 222 " --> pdb=" O THR W 227 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR W 227 " --> pdb=" O ASP W 222 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 121 through 123 removed outlier: 3.865A pdb=" N SER W 211 " --> pdb=" O ASP W 123 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 63 through 66 removed outlier: 3.698A pdb=" N GLN X 65 " --> pdb=" O GLN X 85 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AG6, first strand: chain 'Y' and resid 79 through 82 removed outlier: 3.749A pdb=" N SER Y 72 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU Y 57 " --> pdb=" O ILE Y 106 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILE Y 106 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 86 through 88 Processing sheet with id=AG8, first strand: chain 'y' and resid 3 through 4 removed outlier: 6.171A pdb=" N THR y 3 " --> pdb=" O THR y 206 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU y 203 " --> pdb=" O ASN y 200 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'y' and resid 17 through 19 Processing sheet with id=AH1, first strand: chain 'y' and resid 64 through 65 removed outlier: 3.554A pdb=" N ALA y 64 " --> pdb=" O LEU y 71 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU y 71 " --> pdb=" O ALA y 64 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'y' and resid 108 through 110 Processing sheet with id=AH3, first strand: chain 'y' and resid 152 through 154 removed outlier: 3.639A pdb=" N VAL y 182 " --> pdb=" O GLY y 159 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.633A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA Z 44 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE Z 25 " --> pdb=" O ALA Z 44 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE Z 46 " --> pdb=" O VAL Z 23 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL Z 23 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL Z 10 " --> pdb=" O TYR Z 85 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR Z 85 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL Z 12 " --> pdb=" O THR Z 83 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR Z 83 " --> pdb=" O VAL Z 12 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 73 through 79 removed outlier: 3.549A pdb=" N VAL D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 64 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA D 77 " --> pdb=" O CYS D 62 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N CYS D 62 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR D 79 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 60 " --> pdb=" O TYR D 79 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP D 59 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL D 53 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 46 through 48 removed outlier: 3.665A pdb=" N VAL J 67 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS J 16 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL J 130 " --> pdb=" O LYS J 16 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'q' and resid 7 through 11 1680 hydrogen bonds defined for protein. 4749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1817 hydrogen bonds 3032 hydrogen bond angles 0 basepair planarities 763 basepair parallelities 1796 stacking parallelities Total time for adding SS restraints: 177.79 Time building geometry restraints manager: 54.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 27978 1.33 - 1.47: 55119 1.47 - 1.60: 53056 1.60 - 1.73: 3383 1.73 - 1.86: 187 Bond restraints: 139723 Sorted by residual: bond pdb=" CA PHE B 130 " pdb=" C PHE B 130 " ideal model delta sigma weight residual 1.524 1.458 0.066 1.40e-02 5.10e+03 2.22e+01 bond pdb=" CB VAL q 69 " pdb=" CG1 VAL q 69 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.70e+00 bond pdb=" CA PHE q 36 " pdb=" C PHE q 36 " ideal model delta sigma weight residual 1.522 1.564 -0.042 1.43e-02 4.89e+03 8.75e+00 bond pdb=" CA ARG D 179 " pdb=" C ARG D 179 " ideal model delta sigma weight residual 1.522 1.483 0.039 1.40e-02 5.10e+03 7.64e+00 bond pdb=" N LYS k 33 " pdb=" CA LYS k 33 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.54e+00 ... (remaining 139718 not shown) Histogram of bond angle deviations from ideal: 96.43 - 104.52: 15525 104.52 - 112.60: 81039 112.60 - 120.69: 66546 120.69 - 128.77: 39264 128.77 - 136.86: 3349 Bond angle restraints: 205723 Sorted by residual: angle pdb=" C ASN b 515 " pdb=" N LYS b 516 " pdb=" CA LYS b 516 " ideal model delta sigma weight residual 122.44 112.82 9.62 1.19e+00 7.06e-01 6.53e+01 angle pdb=" N ALA a 66 " pdb=" CA ALA a 66 " pdb=" C ALA a 66 " ideal model delta sigma weight residual 114.56 105.50 9.06 1.27e+00 6.20e-01 5.09e+01 angle pdb=" C ASN F 157 " pdb=" N LYS F 158 " pdb=" CA LYS F 158 " ideal model delta sigma weight residual 121.54 135.09 -13.55 1.91e+00 2.74e-01 5.04e+01 angle pdb=" CA CYS v 146 " pdb=" CB CYS v 146 " pdb=" SG CYS v 146 " ideal model delta sigma weight residual 114.40 129.92 -15.52 2.30e+00 1.89e-01 4.55e+01 angle pdb=" C THR J 154 " pdb=" N THR J 155 " pdb=" CA THR J 155 " ideal model delta sigma weight residual 121.54 134.12 -12.58 1.91e+00 2.74e-01 4.33e+01 ... (remaining 205718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 73876 35.99 - 71.97: 2450 71.97 - 107.96: 206 107.96 - 143.94: 14 143.94 - 179.93: 67 Dihedral angle restraints: 76613 sinusoidal: 56044 harmonic: 20569 Sorted by residual: dihedral pdb=" CA PHE b 528 " pdb=" C PHE b 528 " pdb=" N GLY b 529 " pdb=" CA GLY b 529 " ideal model delta harmonic sigma weight residual 180.00 121.67 58.33 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA THR q 79 " pdb=" C THR q 79 " pdb=" N ARG q 80 " pdb=" CA ARG q 80 " ideal model delta harmonic sigma weight residual -180.00 -125.65 -54.35 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA VAL J 171 " pdb=" C VAL J 171 " pdb=" N LEU J 172 " pdb=" CA LEU J 172 " ideal model delta harmonic sigma weight residual 180.00 125.70 54.30 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 76610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 25123 0.112 - 0.225: 706 0.225 - 0.337: 65 0.337 - 0.450: 6 0.450 - 0.562: 1 Chirality restraints: 25901 Sorted by residual: chirality pdb=" C4' G 12770 " pdb=" C5' G 12770 " pdb=" O4' G 12770 " pdb=" C3' G 12770 " both_signs ideal model delta sigma weight residual False -2.50 -1.93 -0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C3' G 11097 " pdb=" C4' G 11097 " pdb=" O3' G 11097 " pdb=" C2' G 11097 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CB ILE X 63 " pdb=" CA ILE X 63 " pdb=" CG1 ILE X 63 " pdb=" CG2 ILE X 63 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 25898 not shown) Planarity restraints: 13168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 140 " 0.082 5.00e-02 4.00e+02 1.26e-01 2.54e+01 pdb=" N PRO D 141 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS v 278 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C LYS v 278 " -0.067 2.00e-02 2.50e+03 pdb=" O LYS v 278 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE v 279 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG q 71 " 0.111 9.50e-02 1.11e+02 5.95e-02 1.49e+01 pdb=" NE ARG q 71 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG q 71 " 0.062 2.00e-02 2.50e+03 pdb=" NH1 ARG q 71 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG q 71 " -0.017 2.00e-02 2.50e+03 ... (remaining 13165 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 18321 2.74 - 3.28: 108650 3.28 - 3.82: 244546 3.82 - 4.36: 301418 4.36 - 4.90: 433480 Nonbonded interactions: 1106415 Sorted by model distance: nonbonded pdb=" O THR q 54 " pdb=" O2' U 1 44 " model vdw 2.200 2.440 nonbonded pdb=" O2' A 3 126 " pdb=" OP2 U 3 128 " model vdw 2.201 2.440 nonbonded pdb=" O2' G 1 978 " pdb=" O2 U 1 979 " model vdw 2.204 2.440 nonbonded pdb=" O GLY D 71 " pdb=" O2' G 2 7 " model vdw 2.206 2.440 nonbonded pdb=" OE2 GLU B 74 " pdb=" OH TYR B 283 " model vdw 2.231 2.440 ... (remaining 1106410 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.110 Extract box with map and model: 20.600 Check model and map are aligned: 1.440 Set scattering table: 0.850 Process input model: 403.120 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.300 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:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 434.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 : 0.007 0.103 139723 Z= 0.449 Angle : 0.929 15.515 205723 Z= 0.499 Chirality : 0.047 0.562 25901 Planarity : 0.006 0.126 13168 Dihedral : 15.300 179.928 63245 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.31 % Favored : 92.24 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.56 % 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: -4.50 (0.08), residues: 6774 helix: -4.39 (0.05), residues: 2169 sheet: -1.50 (0.16), residues: 901 loop : -2.49 (0.08), residues: 3704 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2000 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1963 time to evaluate : 6.753 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 outliers start: 37 outliers final: 11 residues processed: 1988 average time/residue: 1.2786 time to fit residues: 4214.7685 Evaluate side-chains 1145 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1134 time to evaluate : 6.718 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.8700 time to fit residues: 26.2379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 875 optimal weight: 10.0000 chunk 785 optimal weight: 50.0000 chunk 436 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 530 optimal weight: 2.9990 chunk 419 optimal weight: 0.0470 chunk 812 optimal weight: 30.0000 chunk 314 optimal weight: 10.0000 chunk 494 optimal weight: 7.9990 chunk 604 optimal weight: 8.9990 chunk 941 optimal weight: 10.0000 overall best weight: 5.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 108 HIS v 349 ASN A 38 HIS A 79 ASN A 140 ASN A 209 HIS a 67 HIS a 120 ASN B 121 ASN b 413 ASN b 415 ASN b 470 ASN b 498 ASN C 48 GLN C 59 GLN C 110 ASN d 57 GLN ** d 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN E 172 HIS F 172 ASN F 186 HIS F 244 ASN G 38 GLN G 85 ASN G 123 GLN G 145 ASN I 73 HIS ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN H 183 HIS h 34 GLN h 59 ASN i 91 ASN L 19 GLN L 120 GLN L 162 ASN l 50 ASN M 27 GLN N 37 HIS ** u 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 45 ASN u 101 GLN O 55 HIS ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 HIS Q 10 HIS Q 152 HIS S 63 GLN S 122 HIS S 157 GLN U 87 ASN W 232 ASN X 94 GLN Y 120 GLN y 86 ASN y 106 ASN ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 45 ASN J 95 ASN J 101 ASN J 109 HIS ** J 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 20 HIS q 38 GLN ** q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 90 HIS o 11 ASN o 42 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 139723 Z= 0.324 Angle : 0.697 19.298 205723 Z= 0.358 Chirality : 0.040 0.385 25901 Planarity : 0.006 0.130 13168 Dihedral : 15.746 179.245 49572 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.20 % Favored : 92.49 % Rotamer Outliers : 3.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.27 % 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: -3.14 (0.09), residues: 6774 helix: -2.32 (0.09), residues: 2260 sheet: -1.20 (0.16), residues: 935 loop : -2.16 (0.09), residues: 3579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1494 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1277 time to evaluate : 6.746 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 outliers start: 217 outliers final: 130 residues processed: 1410 average time/residue: 1.1943 time to fit residues: 2939.8208 Evaluate side-chains 1223 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1093 time to evaluate : 6.732 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 130 outliers final: 1 residues processed: 130 average time/residue: 0.9884 time to fit residues: 255.3725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 523 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 783 optimal weight: 10.0000 chunk 641 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 943 optimal weight: 10.0000 chunk 1019 optimal weight: 10.0000 chunk 840 optimal weight: 10.0000 chunk 935 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 756 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 GLN a 120 ASN C 316 ASN d 57 GLN G 28 HIS g 18 ASN I 73 HIS ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN k 67 GLN l 20 ASN M 27 GLN M 119 GLN ** u 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 GLN P 137 ASN R 121 HIS V 81 GLN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 GLN ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 178 GLN ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN o 45 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 139723 Z= 0.390 Angle : 0.697 23.147 205723 Z= 0.357 Chirality : 0.041 0.357 25901 Planarity : 0.006 0.124 13168 Dihedral : 15.741 179.997 49572 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.90 % Favored : 91.84 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.24 % 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: -2.47 (0.09), residues: 6774 helix: -1.26 (0.10), residues: 2253 sheet: -1.19 (0.16), residues: 957 loop : -2.03 (0.09), residues: 3564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1394 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1195 time to evaluate : 6.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 199 outliers final: 97 residues processed: 1336 average time/residue: 1.1442 time to fit residues: 2678.0561 Evaluate side-chains 1184 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1087 time to evaluate : 6.735 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 0 residues processed: 97 average time/residue: 0.9419 time to fit residues: 182.1103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 932 optimal weight: 10.0000 chunk 709 optimal weight: 10.0000 chunk 489 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 450 optimal weight: 7.9990 chunk 633 optimal weight: 5.9990 chunk 946 optimal weight: 10.0000 chunk 1002 optimal weight: 10.0000 chunk 494 optimal weight: 10.0000 chunk 897 optimal weight: 10.0000 chunk 270 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 281 ASN ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 ASN b 633 HIS C 260 GLN ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN H 162 GLN k 67 GLN M 27 GLN M 41 GLN ** u 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 ASN R 39 ASN S 46 GLN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 223 ASN Y 120 GLN ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 128 GLN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 82 GLN o 11 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.085 139723 Z= 0.378 Angle : 0.683 19.313 205723 Z= 0.350 Chirality : 0.040 0.355 25901 Planarity : 0.005 0.121 13168 Dihedral : 15.701 179.961 49572 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.10 % Favored : 91.61 % Rotamer Outliers : 3.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.24 % 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: -2.14 (0.09), residues: 6774 helix: -0.75 (0.11), residues: 2255 sheet: -1.19 (0.16), residues: 920 loop : -1.93 (0.10), residues: 3599 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1168 time to evaluate : 6.888 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 outliers start: 204 outliers final: 126 residues processed: 1272 average time/residue: 1.1164 time to fit residues: 2477.6683 Evaluate side-chains 1219 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1093 time to evaluate : 6.784 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 0 residues processed: 126 average time/residue: 0.8754 time to fit residues: 218.8823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 834 optimal weight: 10.0000 chunk 569 optimal weight: 40.0000 chunk 14 optimal weight: 10.0000 chunk 746 optimal weight: 10.0000 chunk 413 optimal weight: 4.9990 chunk 855 optimal weight: 10.0000 chunk 692 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 511 optimal weight: 5.9990 chunk 899 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 215 ASN ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN A 83 HIS a 120 ASN B 256 HIS ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN H 162 GLN k 67 GLN M 27 GLN M 119 GLN u 37 HIS ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN P 137 ASN S 46 GLN S 89 ASN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN V 132 ASN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 GLN y 83 HIS ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 128 GLN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 82 GLN o 11 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.114 139723 Z= 0.453 Angle : 0.727 17.158 205723 Z= 0.371 Chirality : 0.042 0.356 25901 Planarity : 0.006 0.120 13168 Dihedral : 15.794 179.065 49572 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.80 % Favored : 90.91 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.26 % 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: -2.08 (0.10), residues: 6774 helix: -0.60 (0.11), residues: 2249 sheet: -1.17 (0.16), residues: 939 loop : -1.98 (0.10), residues: 3586 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1115 time to evaluate : 6.870 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 outliers start: 166 outliers final: 97 residues processed: 1224 average time/residue: 1.1352 time to fit residues: 2430.1218 Evaluate side-chains 1156 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1059 time to evaluate : 6.104 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 0 residues processed: 97 average time/residue: 0.8987 time to fit residues: 171.9858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 337 optimal weight: 0.8980 chunk 902 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 588 optimal weight: 0.9980 chunk 247 optimal weight: 0.9990 chunk 1003 optimal weight: 10.0000 chunk 832 optimal weight: 8.9990 chunk 464 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 331 optimal weight: 10.0000 chunk 526 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 281 ASN ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN a 120 ASN G 77 GLN H 163 GLN k 67 GLN M 27 GLN p 33 GLN O 122 GLN Q 45 ASN R 39 ASN S 89 ASN V 81 GLN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 GLN ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 HIS ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 128 GLN ** z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.106 139723 Z= 0.194 Angle : 0.586 15.805 205723 Z= 0.304 Chirality : 0.036 0.342 25901 Planarity : 0.005 0.116 13168 Dihedral : 15.427 179.777 49572 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.10 % Favored : 92.71 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.20 % 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 (0.10), residues: 6774 helix: -0.16 (0.11), residues: 2273 sheet: -0.90 (0.16), residues: 943 loop : -1.80 (0.10), residues: 3558 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1218 time to evaluate : 6.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 50 residues processed: 1270 average time/residue: 1.1418 time to fit residues: 2529.3245 Evaluate side-chains 1142 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1092 time to evaluate : 6.799 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 50 outliers final: 1 residues processed: 50 average time/residue: 0.9140 time to fit residues: 95.3651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 967 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 571 optimal weight: 5.9990 chunk 732 optimal weight: 10.0000 chunk 567 optimal weight: 6.9990 chunk 844 optimal weight: 10.0000 chunk 560 optimal weight: 20.0000 chunk 999 optimal weight: 20.0000 chunk 625 optimal weight: 9.9990 chunk 609 optimal weight: 9.9990 chunk 461 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 66 GLN v 281 ASN ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN a 120 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 HIS H 162 GLN k 67 GLN L 12 ASN L 19 GLN l 4 GLN M 27 GLN M 119 GLN u 5 GLN O 182 ASN O 193 GLN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 ASN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN ** V 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 GLN ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 128 GLN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.091 139723 Z= 0.462 Angle : 0.731 14.612 205723 Z= 0.371 Chirality : 0.042 0.369 25901 Planarity : 0.006 0.118 13168 Dihedral : 15.732 179.881 49572 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.20 % Favored : 90.55 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.10), residues: 6774 helix: -0.29 (0.11), residues: 2249 sheet: -1.08 (0.16), residues: 935 loop : -1.91 (0.10), residues: 3590 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1077 time to evaluate : 6.828 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 outliers start: 134 outliers final: 88 residues processed: 1147 average time/residue: 1.2469 time to fit residues: 2522.6160 Evaluate side-chains 1134 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1046 time to evaluate : 6.776 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 88 outliers final: 1 residues processed: 88 average time/residue: 1.0277 time to fit residues: 181.1864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 618 optimal weight: 1.9990 chunk 399 optimal weight: 3.9990 chunk 596 optimal weight: 5.9990 chunk 301 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 635 optimal weight: 5.9990 chunk 680 optimal weight: 1.9990 chunk 494 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 785 optimal weight: 40.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 167 HIS ** v 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN a 120 ASN b 498 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 67 GLN l 4 GLN ** l 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN M 119 GLN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 ASN R 39 ASN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 GLN Y 120 GLN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.158 139723 Z= 0.237 Angle : 0.609 13.962 205723 Z= 0.315 Chirality : 0.037 0.324 25901 Planarity : 0.005 0.116 13168 Dihedral : 15.453 179.686 49572 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.38 % Favored : 92.41 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.18 % 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: -1.57 (0.10), residues: 6774 helix: -0.05 (0.11), residues: 2270 sheet: -0.95 (0.16), residues: 937 loop : -1.75 (0.10), residues: 3567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1188 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1127 time to evaluate : 6.885 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 outliers start: 61 outliers final: 36 residues processed: 1157 average time/residue: 1.1325 time to fit residues: 2290.1602 Evaluate side-chains 1112 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1076 time to evaluate : 6.807 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 36 outliers final: 1 residues processed: 36 average time/residue: 0.9700 time to fit residues: 73.0375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 909 optimal weight: 10.0000 chunk 957 optimal weight: 40.0000 chunk 873 optimal weight: 10.0000 chunk 931 optimal weight: 10.0000 chunk 560 optimal weight: 20.0000 chunk 405 optimal weight: 5.9990 chunk 731 optimal weight: 10.0000 chunk 285 optimal weight: 6.9990 chunk 841 optimal weight: 30.0000 chunk 880 optimal weight: 20.0000 chunk 928 optimal weight: 10.0000 overall best weight: 8.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 142 GLN v 281 ASN ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 ASN B 3 HIS B 273 HIS b 498 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 GLN k 10 GLN k 67 GLN L 19 GLN ** l 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 ASN S 46 GLN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 GLN ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 128 GLN z 12 ASN o 11 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.134 139723 Z= 0.498 Angle : 0.752 13.891 205723 Z= 0.381 Chirality : 0.043 0.450 25901 Planarity : 0.006 0.134 13168 Dihedral : 15.758 179.593 49572 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.43 % Favored : 90.32 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.10), residues: 6774 helix: -0.25 (0.11), residues: 2252 sheet: -1.13 (0.16), residues: 965 loop : -1.91 (0.10), residues: 3557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1066 time to evaluate : 6.900 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 outliers start: 88 outliers final: 64 residues processed: 1104 average time/residue: 1.1484 time to fit residues: 2221.2490 Evaluate side-chains 1112 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1048 time to evaluate : 6.778 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 64 outliers final: 1 residues processed: 64 average time/residue: 0.9427 time to fit residues: 123.6641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 611 optimal weight: 0.9980 chunk 984 optimal weight: 10.0000 chunk 601 optimal weight: 6.9990 chunk 467 optimal weight: 0.9990 chunk 684 optimal weight: 0.9980 chunk 1033 optimal weight: 10.0000 chunk 950 optimal weight: 10.0000 chunk 822 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 635 optimal weight: 4.9990 chunk 504 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 167 HIS v 281 ASN ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN a 120 ASN B 319 ASN b 498 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 10 GLN M 27 GLN M 119 GLN N 182 ASN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 ASN S 63 GLN S 89 ASN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 GLN Z 128 GLN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.188 139723 Z= 0.202 Angle : 0.603 13.857 205723 Z= 0.311 Chirality : 0.036 0.328 25901 Planarity : 0.005 0.117 13168 Dihedral : 15.400 179.098 49572 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.35 % Favored : 92.46 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.10), residues: 6774 helix: 0.09 (0.11), residues: 2262 sheet: -0.93 (0.17), residues: 943 loop : -1.72 (0.10), residues: 3569 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1115 time to evaluate : 6.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 1128 average time/residue: 1.2801 time to fit residues: 2537.4067 Evaluate side-chains 1092 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1081 time to evaluate : 6.760 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 1.0482 time to fit residues: 29.6272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 653 optimal weight: 9.9990 chunk 876 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 758 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 228 optimal weight: 8.9990 chunk 823 optimal weight: 10.0000 chunk 344 optimal weight: 0.0010 chunk 846 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 overall best weight: 4.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 ASN B 319 ASN b 498 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 GLN H 162 GLN k 10 GLN L 19 GLN M 119 GLN N 182 ASN u 24 ASN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 ASN R 27 ASN S 63 GLN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 GLN Z 128 GLN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.080451 restraints weight = 285127.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.082790 restraints weight = 120734.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.084215 restraints weight = 75917.971| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.173 139723 Z= 0.303 Angle : 0.637 13.605 205723 Z= 0.326 Chirality : 0.038 0.287 25901 Planarity : 0.005 0.122 13168 Dihedral : 15.438 179.877 49572 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.40 % Favored : 91.39 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.18 % 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: 6774 helix: 0.10 (0.11), residues: 2270 sheet: -0.95 (0.17), residues: 927 loop : -1.75 (0.10), residues: 3577 =============================================================================== Job complete usr+sys time: 35328.66 seconds wall clock time: 616 minutes 12.28 seconds (36972.28 seconds total)