Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 20 15:15:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/07_2023/7cpj_30431_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/07_2023/7cpj_30431.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/07_2023/7cpj_30431_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/07_2023/7cpj_30431_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/07_2023/7cpj_30431_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/07_2023/7cpj_30431.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/07_2023/7cpj_30431.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/07_2023/7cpj_30431_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/07_2023/7cpj_30431_updated.pdb" } resolution = 3.3 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= 0.013 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 4639 5.49 5 S 155 5.16 5 C 73469 2.51 5 N 27181 2.21 5 O 40497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 77": "OE1" <-> "OE2" Residue "b PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b ASP 126": "OD1" <-> "OD2" Residue "b ASP 152": "OD1" <-> "OD2" Residue "b ASP 158": "OD1" <-> "OD2" Residue "b ASP 164": "OD1" <-> "OD2" Residue "b ASP 196": "OD1" <-> "OD2" Residue "b ASP 203": "OD1" <-> "OD2" Residue "b ASP 204": "OD1" <-> "OD2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 82": "OD1" <-> "OD2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "c GLU 165": "OE1" <-> "OE2" Residue "c ASP 182": "OD1" <-> "OD2" Residue "d TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 14": "OE1" <-> "OE2" Residue "d ASP 17": "OD1" <-> "OD2" Residue "d TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 98": "OD1" <-> "OD2" Residue "d TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 173": "OD1" <-> "OD2" Residue "d GLU 186": "OE1" <-> "OE2" Residue "e PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 141": "OD1" <-> "OD2" Residue "e GLU 150": "OE1" <-> "OE2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "f GLU 5": "OE1" <-> "OE2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 69": "OE1" <-> "OE2" Residue "f PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 82": "OD1" <-> "OD2" Residue "g ASP 32": "OD1" <-> "OD2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 145": "OE1" <-> "OE2" Residue "h ASP 8": "OD1" <-> "OD2" Residue "h ASP 47": "OD1" <-> "OD2" Residue "h TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 35": "OE1" <-> "OE2" Residue "i PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ASP 75": "OD1" <-> "OD2" Residue "j GLU 81": "OE1" <-> "OE2" Residue "j ASP 91": "OD1" <-> "OD2" Residue "k TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 93": "OE1" <-> "OE2" Residue "l GLU 24": "OE1" <-> "OE2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l ASP 102": "OD1" <-> "OD2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 53": "OD1" <-> "OD2" Residue "n GLU 25": "OE1" <-> "OE2" Residue "n GLU 86": "OE1" <-> "OE2" Residue "o GLU 13": "OE1" <-> "OE2" Residue "o PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p ASP 53": "OD1" <-> "OD2" Residue "q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 19": "OE1" <-> "OE2" Residue "r TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 71": "OD1" <-> "OD2" Residue "s ASP 11": "OD1" <-> "OD2" Residue "t GLU 39": "OE1" <-> "OE2" Residue "t PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 7": "OE1" <-> "OE2" Residue "u PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 191": "OD1" <-> "OD2" Residue "F TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 45": "OD1" <-> "OD2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ASP 143": "OD1" <-> "OD2" Residue "F PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ASP 46": "OD1" <-> "OD2" Residue "G TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 59": "OD1" <-> "OD2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H ASP 98": "OD1" <-> "OD2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 46": "OD1" <-> "OD2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ASP 19": "OD1" <-> "OD2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 80": "OD1" <-> "OD2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ASP 91": "OD1" <-> "OD2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 106": "OD1" <-> "OD2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M GLU 115": "OE1" <-> "OE2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ASP 58": "OD1" <-> "OD2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 117": "OD1" <-> "OD2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P GLU 10": "OE1" <-> "OE2" Residue "P PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ASP 23": "OD1" <-> "OD2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "Q ASP 101": "OD1" <-> "OD2" Residue "R PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "U PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 45": "OD1" <-> "OD2" Residue "W PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 64": "OD1" <-> "OD2" Residue "X TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "5 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 70": "OE1" <-> "OE2" Residue "5 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 98": "OE1" <-> "OE2" Residue "5 PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 10": "OE1" <-> "OE2" Residue "6 GLU 11": "OE1" <-> "OE2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 145941 Number of models: 1 Model: "" Number of chains: 58 Chain: "a" Number of atoms: 33030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33030 Classifications: {'RNA': 1539} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 94, 'rna2p_pyr': 52, 'rna3p': 11, 'rna3p_pur': 773, 'rna3p_pyr': 608} Link IDs: {'rna2p': 147, 'rna3p': 1391} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 7 Chain: "b" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1141 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 504 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "s" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 495 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 62276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62276 Classifications: {'RNA': 2900} Modifications used: {'p5*END': 1, 'rna2p': 7, 'rna2p_pur': 228, 'rna2p_pyr': 107, 'rna3p': 17, 'rna3p_pur': 1438, 'rna3p_pyr': 1103} Link IDs: {'rna2p': 342, 'rna3p': 2557} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 62, 'rna3p_pyr': 51} Link IDs: {'rna2p': 7, 'rna3p': 112} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "6" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "9" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 31} Link IDs: {'rna2p': 13, 'rna3p': 63} Chain: "x" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Chain: "9" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Time building chain proxies: 49.74, per 1000 atoms: 0.34 Number of scatterers: 145941 At special positions: 0 Unit cell: (248.43, 235.2, 249.9, 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 155 16.00 P 4639 15.00 O 40497 8.00 N 27181 7.00 C 73469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 64.09 Conformation dependent library (CDL) restraints added in 5.4 seconds 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10936 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 184 helices and 69 sheets defined 39.2% alpha, 17.4% beta 1543 base pairs and 2401 stacking pairs defined. Time for finding SS restraints: 60.85 Creating SS restraints... Processing helix chain 'b' and resid 41 through 63 Proline residue: b 47 - end of helix Processing helix chain 'b' and resid 72 through 87 removed outlier: 6.468A pdb=" N SER b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 3.525A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 Processing helix chain 'b' and resid 164 through 169 removed outlier: 4.113A pdb=" N HIS b 169 " --> pdb=" O ALA b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 179 removed outlier: 3.725A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 Processing helix chain 'c' and resid 5 through 11 removed outlier: 4.195A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 Processing helix chain 'c' and resid 71 through 77 Processing helix chain 'c' and resid 80 through 95 Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.643A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 Processing helix chain 'd' and resid 6 through 15 removed outlier: 4.248A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 Processing helix chain 'd' and resid 67 through 82 removed outlier: 5.076A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 Processing helix chain 'd' and resid 97 through 105 removed outlier: 3.865A pdb=" N GLY d 105 " --> pdb=" O VAL d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 120 removed outlier: 5.320A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 163 removed outlier: 5.244A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 4.073A pdb=" N LEU d 190 " --> pdb=" O GLU d 186 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER d 191 " --> pdb=" O ARG d 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 186 through 191' Processing helix chain 'd' and resid 195 through 205 Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.786A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.552A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 156 Processing helix chain 'e' and resid 159 through 165 Processing helix chain 'f' and resid 11 through 18 Processing helix chain 'f' and resid 19 through 33 Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 19 through 30 Processing helix chain 'g' and resid 34 through 54 Processing helix chain 'g' and resid 56 through 69 removed outlier: 6.330A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 3.919A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 Processing helix chain 'g' and resid 131 through 149 removed outlier: 3.958A pdb=" N GLU g 145 " --> pdb=" O HIS g 141 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN g 147 " --> pdb=" O MET g 143 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS g 148 " --> pdb=" O ALA g 144 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA g 149 " --> pdb=" O GLU g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 111 through 119 Processing helix chain 'i' and resid 33 through 38 Processing helix chain 'i' and resid 43 through 55 removed outlier: 5.168A pdb=" N VAL i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) Proline residue: i 50 - end of helix removed outlier: 4.329A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL i 54 " --> pdb=" O PRO i 50 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP i 55 " --> pdb=" O LEU i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 87 removed outlier: 4.460A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 90 through 101 removed outlier: 3.582A pdb=" N ARG i 94 " --> pdb=" O ASP i 90 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS i 99 " --> pdb=" O SER i 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.122A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.708A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 4.516A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 59 removed outlier: 3.972A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) Proline residue: k 59 - end of helix No H-bonds generated for 'chain 'k' and resid 53 through 59' Processing helix chain 'k' and resid 60 through 77 removed outlier: 4.832A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU k 75 " --> pdb=" O ASP k 71 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY k 77 " --> pdb=" O VAL k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 5.674A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 10 Proline residue: l 10 - end of helix Processing helix chain 'l' and resid 112 through 117 removed outlier: 4.638A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 21 removed outlier: 4.720A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 Processing helix chain 'm' and resid 48 through 63 removed outlier: 3.584A pdb=" N ILE m 52 " --> pdb=" O SER m 48 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 Processing helix chain 'm' and resid 84 through 93 Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 2 through 23 removed outlier: 5.515A pdb=" N ALA n 21 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS n 22 " --> pdb=" O LYS n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 32 removed outlier: 4.393A pdb=" N ILE n 30 " --> pdb=" O LEU n 26 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER n 31 " --> pdb=" O LYS n 27 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP n 32 " --> pdb=" O ALA n 28 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 51 removed outlier: 4.001A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 4.013A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 15 Processing helix chain 'o' and resid 23 through 46 removed outlier: 4.422A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N HIS o 45 " --> pdb=" O HIS o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 Processing helix chain 'o' and resid 74 through 85 Processing helix chain 'p' and resid 53 through 64 Processing helix chain 'p' and resid 68 through 79 Processing helix chain 'r' and resid 11 through 16 removed outlier: 4.679A pdb=" N GLU r 15 " --> pdb=" O ARG r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 5.241A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 Processing helix chain 'r' and resid 47 through 65 Processing helix chain 's' and resid 11 through 25 Processing helix chain 's' and resid 69 through 75 removed outlier: 4.280A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA s 74 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Proline residue: s 75 - end of helix No H-bonds generated for 'chain 's' and resid 69 through 75' Processing helix chain 't' and resid 6 through 41 removed outlier: 4.875A pdb=" N ALA t 10 " --> pdb=" O ALA t 6 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 64 Proline residue: t 55 - end of helix Processing helix chain 't' and resid 67 through 86 removed outlier: 5.748A pdb=" N ALA t 71 " --> pdb=" O HIS t 67 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA t 72 " --> pdb=" O LYS t 68 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 22 removed outlier: 3.823A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 31 removed outlier: 5.364A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 61 removed outlier: 3.695A pdb=" N THR u 42 " --> pdb=" O GLU u 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 15 removed outlier: 7.137A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 4.147A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLU C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 29 through 34' Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.612A pdb=" N ILE C 134 " --> pdb=" O PRO C 130 " (cutoff:3.500A) Proline residue: C 135 - end of helix No H-bonds generated for 'chain 'C' and resid 130 through 135' Processing helix chain 'C' and resid 206 through 214 removed outlier: 4.222A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 4.104A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASN C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 225' Processing helix chain 'C' and resid 259 through 267 removed outlier: 6.258A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 267' Processing helix chain 'C' and resid 196 through 201 removed outlier: 4.391A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 98 through 105 removed outlier: 4.412A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS D 105 " --> pdb=" O PHE D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 105' Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 120 through 126 removed outlier: 4.159A pdb=" N TRP D 125 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 41 removed outlier: 5.513A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 7.048A pdb=" N THR E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 165 removed outlier: 4.877A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N HIS E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 1 through 20 removed outlier: 5.020A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.809A pdb=" N LYS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 61 removed outlier: 4.274A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 3.780A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Proline residue: F 108 - end of helix Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.590A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 Proline residue: F 138 - end of helix Processing helix chain 'G' and resid 1 through 7 removed outlier: 4.392A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Proline residue: G 7 - end of helix Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 136 through 152 removed outlier: 4.766A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 49 removed outlier: 5.624A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 72 removed outlier: 3.868A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 4.132A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 4.531A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 49 removed outlier: 4.964A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 4.335A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 113 removed outlier: 4.269A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 4.050A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.320A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.560A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.290A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.620A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.260A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 86 removed outlier: 4.318A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLU L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 86' Processing helix chain 'L' and resid 91 through 99 removed outlier: 4.227A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 5.474A pdb=" N ARG L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.992A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 56 removed outlier: 4.383A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 71 removed outlier: 4.570A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.717A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.395A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 62 removed outlier: 4.031A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 1 through 12 removed outlier: 4.511A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.599A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 103' Processing helix chain 'Q' and resid 5 through 21 removed outlier: 4.169A pdb=" N LYS Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.174A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 Processing helix chain 'Q' and resid 38 through 72 removed outlier: 4.457A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 102 through 117 Processing helix chain 'S' and resid 13 through 25 removed outlier: 4.669A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 Processing helix chain 'S' and resid 65 through 70 removed outlier: 4.306A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 1 through 11 removed outlier: 4.419A pdb=" N GLU T 5 " --> pdb=" O MET T 1 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 51 removed outlier: 4.227A pdb=" N PHE T 51 " --> pdb=" O VAL T 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 4.013A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ALA U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.725A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.696A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 Processing helix chain 'X' and resid 51 through 62 removed outlier: 3.947A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 Processing helix chain 'Y' and resid 1 through 7 removed outlier: 4.328A pdb=" N LEU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 23 Processing helix chain 'Y' and resid 25 through 35 Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.556A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 Processing helix chain '0' and resid 8 through 18 removed outlier: 4.926A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 30 Proline residue: 1 30 - end of helix Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 24 removed outlier: 4.276A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 Processing helix chain '3' and resid 6 through 13 removed outlier: 3.808A pdb=" N LYS 3 11 " --> pdb=" O ARG 3 7 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 36 removed outlier: 4.611A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ALA 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 31 through 36' Processing helix chain '3' and resid 37 through 45 Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 50 through 62 removed outlier: 5.021A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '4' and resid 30 through 35 removed outlier: 4.393A pdb=" N LYS 4 34 " --> pdb=" O GLU 4 30 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN 4 35 " --> pdb=" O PRO 4 31 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 30 through 35' Processing helix chain '5' and resid 3 through 21 removed outlier: 4.361A pdb=" N LYS 5 20 " --> pdb=" O SER 5 16 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 48 removed outlier: 3.615A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 69 removed outlier: 3.968A pdb=" N VAL 5 64 " --> pdb=" O LEU 5 60 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU 5 65 " --> pdb=" O ARG 5 61 " (cutoff:3.500A) Proline residue: 5 68 - end of helix Processing helix chain '5' and resid 94 through 106 removed outlier: 3.760A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 71 through 78 removed outlier: 3.511A pdb=" N ASP 5 74 " --> pdb=" O CYS 5 71 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA 5 75 " --> pdb=" O LEU 5 72 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE 5 76 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY 5 78 " --> pdb=" O ALA 5 75 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 53 removed outlier: 4.986A pdb=" N GLN 6 48 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR 6 53 " --> pdb=" O ARG 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 65 removed outlier: 4.696A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 30 through 33 Processing sheet with id= 2, first strand: chain 'b' and resid 66 through 70 removed outlier: 4.174A pdb=" N PHE b 197 " --> pdb=" O VAL b 182 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 52 through 58 Processing sheet with id= 4, first strand: chain 'c' and resid 163 through 169 removed outlier: 3.584A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'd' and resid 140 through 144 removed outlier: 3.884A pdb=" N ASP d 140 " --> pdb=" O PHE d 181 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL d 142 " --> pdb=" O GLY d 179 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N MET d 177 " --> pdb=" O ILE d 144 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 12 through 15 removed outlier: 6.699A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE e 29 " --> pdb=" O LYS e 22 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.094A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU e 123 " --> pdb=" O GLN e 96 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'e' and resid 32 through 39 removed outlier: 4.549A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 38 through 43 removed outlier: 5.882A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'g' and resid 71 through 76 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'h' and resid 22 through 28 removed outlier: 6.209A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER h 28 " --> pdb=" O PRO h 56 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU h 51 " --> pdb=" O GLU h 57 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 73 through 76 removed outlier: 6.641A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.604A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS i 26 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.863A pdb=" N LEU j 42 " --> pdb=" O LEU j 71 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 16, first strand: chain 'k' and resid 30 through 34 Processing sheet with id= 17, first strand: chain 'l' and resid 28 through 31 removed outlier: 5.037A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'l' and resid 35 through 40 removed outlier: 4.510A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'p' and resid 4 through 10 removed outlier: 5.860A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'q' and resid 6 through 10 removed outlier: 6.897A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'q' and resid 18 through 29 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 's' and resid 29 through 33 removed outlier: 3.703A pdb=" N LEU s 30 " --> pdb=" O THR s 47 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C' and resid 1 through 4 removed outlier: 3.943A pdb=" N ALA C 1 " --> pdb=" O VAL C 19 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 74 through 77 removed outlier: 4.560A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 79 through 82 removed outlier: 5.513A pdb=" N ASN C 89 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.902A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D' and resid 3 through 6 Processing sheet with id= 28, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.672A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D' and resid 79 through 84 removed outlier: 5.867A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'E' and resid 1 through 6 removed outlier: 4.146A pdb=" N LEU E 5 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.423A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'F' and resid 64 through 68 removed outlier: 3.730A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLY F 125 " --> pdb=" O THR F 157 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'G' and resid 21 through 26 removed outlier: 6.188A pdb=" N GLN G 21 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU G 36 " --> pdb=" O GLN G 21 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'G' and resid 40 through 45 removed outlier: 4.282A pdb=" N ALA G 45 " --> pdb=" O THR G 48 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'G' and resid 94 through 97 removed outlier: 7.237A pdb=" N ASN G 100 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'G' and resid 128 through 135 removed outlier: 5.912A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'H' and resid 3 through 6 removed outlier: 6.802A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'H' and resid 76 through 81 Processing sheet with id= 39, first strand: chain 'H' and resid 114 through 117 removed outlier: 5.656A pdb=" N GLU H 114 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.994A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.169A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.264A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'K' and resid 38 through 41 Processing sheet with id= 44, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.773A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.366A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.071A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'O' and resid 49 through 52 removed outlier: 4.024A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'P' and resid 48 through 52 removed outlier: 3.668A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG P 52 " --> pdb=" O HIS P 55 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'P' and resid 57 through 63 Processing sheet with id= 50, first strand: chain 'R' and resid 11 through 15 Processing sheet with id= 51, first strand: chain 'R' and resid 18 through 23 removed outlier: 3.798A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 53, first strand: chain 'R' and resid 68 through 78 No H-bonds generated for sheet with id= 53 Processing sheet with id= 54, first strand: chain 'S' and resid 3 through 8 removed outlier: 4.515A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'S' and resid 81 through 88 removed outlier: 3.844A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'T' and resid 28 through 33 removed outlier: 6.502A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'U' and resid 39 through 44 No H-bonds generated for sheet with id= 57 Processing sheet with id= 58, first strand: chain 'U' and resid 82 through 85 Processing sheet with id= 59, first strand: chain 'V' and resid 69 through 72 Processing sheet with id= 60, first strand: chain 'W' and resid 47 through 50 removed outlier: 4.387A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'W' and resid 63 through 67 Processing sheet with id= 62, first strand: chain 'X' and resid 10 through 18 No H-bonds generated for sheet with id= 62 Processing sheet with id= 63, first strand: chain 'X' and resid 34 through 40 Processing sheet with id= 64, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.278A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '1' and resid 18 through 23 removed outlier: 6.228A pdb=" N HIS 1 18 " --> pdb=" O SER 1 12 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '3' and resid 21 through 24 removed outlier: 5.304A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '4' and resid 13 through 19 removed outlier: 8.358A pdb=" N ASN 4 13 " --> pdb=" O SER 4 28 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '5' and resid 22 through 28 removed outlier: 4.297A pdb=" N LEU 5 23 " --> pdb=" O GLU 5 87 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU 5 87 " --> pdb=" O LEU 5 23 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '6' and resid 20 through 25 removed outlier: 4.671A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS 6 16 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N HIS 6 30 " --> pdb=" O GLU 6 11 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR 6 13 " --> pdb=" O HIS 6 30 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU 6 32 " --> pdb=" O THR 6 13 " (cutoff:3.500A) 1879 hydrogen bonds defined for protein. 5529 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3883 hydrogen bonds 6064 hydrogen bond angles 0 basepair planarities 1543 basepair parallelities 2401 stacking parallelities Total time for adding SS restraints: 238.72 Time building geometry restraints manager: 69.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 11974 1.28 - 1.42: 65213 1.42 - 1.55: 71759 1.55 - 1.68: 9284 1.68 - 1.81: 277 Bond restraints: 158507 Sorted by residual: bond pdb=" C5 5MU A1939 " pdb=" C6 5MU A1939 " ideal model delta sigma weight residual 1.155 1.443 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.604 0.198 2.00e-02 2.50e+03 9.80e+01 bond pdb=" N1 H2U A2449 " pdb=" C2 H2U A2449 " ideal model delta sigma weight residual 1.482 1.302 0.180 2.00e-02 2.50e+03 8.09e+01 bond pdb=" C8 G7M a 527 " pdb=" N7 G7M a 527 " ideal model delta sigma weight residual 1.348 1.515 -0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" C2 H2U A2449 " pdb=" N3 H2U A2449 " ideal model delta sigma weight residual 1.483 1.317 0.166 2.00e-02 2.50e+03 6.90e+01 ... (remaining 158502 not shown) Histogram of bond angle deviations from ideal: 95.71 - 106.93: 31496 106.93 - 118.16: 119828 118.16 - 129.38: 81569 129.38 - 140.60: 4093 140.60 - 151.83: 4 Bond angle restraints: 236990 Sorted by residual: angle pdb=" C1' OMG A2251 " pdb=" N9 OMG A2251 " pdb=" C8 OMG A2251 " ideal model delta sigma weight residual 142.82 106.86 35.96 3.00e+00 1.11e-01 1.44e+02 angle pdb=" C1' OMG A2251 " pdb=" N9 OMG A2251 " pdb=" C4 OMG A2251 " ideal model delta sigma weight residual 108.29 143.41 -35.12 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C1' G7M A2069 " pdb=" N9 G7M A2069 " pdb=" C8 G7M A2069 " ideal model delta sigma weight residual 94.96 128.27 -33.31 3.00e+00 1.11e-01 1.23e+02 angle pdb=" C1' G7M a 527 " pdb=" N9 G7M a 527 " pdb=" C8 G7M a 527 " ideal model delta sigma weight residual 94.96 127.51 -32.55 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C1' G7M a1405 " pdb=" N9 G7M a1405 " pdb=" C8 G7M a1405 " ideal model delta sigma weight residual 94.96 125.81 -30.85 3.00e+00 1.11e-01 1.06e+02 ... (remaining 236985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 81064 35.80 - 71.60: 3285 71.60 - 107.40: 267 107.40 - 143.19: 26 143.19 - 178.99: 25 Dihedral angle restraints: 84667 sinusoidal: 67720 harmonic: 16947 Sorted by residual: dihedral pdb=" CA THR q 69 " pdb=" C THR q 69 " pdb=" N LYS q 70 " pdb=" CA LYS q 70 " ideal model delta harmonic sigma weight residual -180.00 -125.62 -54.38 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA LEU l 101 " pdb=" C LEU l 101 " pdb=" N ASP l 102 " pdb=" CA ASP l 102 " ideal model delta harmonic sigma weight residual 180.00 -126.04 -53.96 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA HIS 3 30 " pdb=" C HIS 3 30 " pdb=" N ILE 3 31 " pdb=" CA ILE 3 31 " ideal model delta harmonic sigma weight residual 180.00 -129.80 -50.20 0 5.00e+00 4.00e-02 1.01e+02 ... (remaining 84664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 27035 0.079 - 0.158: 2887 0.158 - 0.236: 226 0.236 - 0.315: 33 0.315 - 0.394: 12 Chirality restraints: 30193 Sorted by residual: chirality pdb=" C3' G A2391 " pdb=" C4' G A2391 " pdb=" O3' G A2391 " pdb=" C2' G A2391 " both_signs ideal model delta sigma weight residual False -2.74 -2.35 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C3' G a 380 " pdb=" C4' G a 380 " pdb=" O3' G a 380 " pdb=" C2' G a 380 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C3' C a1399 " pdb=" C4' C a1399 " pdb=" O3' C a1399 " pdb=" C2' C a1399 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 30190 not shown) Planarity restraints: 12798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1516 " -0.083 2.00e-02 2.50e+03 6.14e-01 8.49e+03 pdb=" C4' 2MG a1516 " -0.444 2.00e-02 2.50e+03 pdb=" O4' 2MG a1516 " -0.606 2.00e-02 2.50e+03 pdb=" C3' 2MG a1516 " 0.596 2.00e-02 2.50e+03 pdb=" O3' 2MG a1516 " 0.688 2.00e-02 2.50e+03 pdb=" C2' 2MG a1516 " 0.153 2.00e-02 2.50e+03 pdb=" O2' 2MG a1516 " -1.025 2.00e-02 2.50e+03 pdb=" C1' 2MG a1516 " -0.215 2.00e-02 2.50e+03 pdb=" N9 2MG a1516 " 0.936 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2445 " -0.065 2.00e-02 2.50e+03 5.96e-01 7.99e+03 pdb=" C4' 2MG A2445 " -0.459 2.00e-02 2.50e+03 pdb=" O4' 2MG A2445 " -0.658 2.00e-02 2.50e+03 pdb=" C3' 2MG A2445 " 0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG A2445 " 0.624 2.00e-02 2.50e+03 pdb=" C2' 2MG A2445 " 0.202 2.00e-02 2.50e+03 pdb=" O2' 2MG A2445 " -0.942 2.00e-02 2.50e+03 pdb=" C1' 2MG A2445 " -0.207 2.00e-02 2.50e+03 pdb=" N9 2MG A2445 " 0.919 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1207 " -0.064 2.00e-02 2.50e+03 5.93e-01 7.92e+03 pdb=" C4' 2MG a1207 " -0.439 2.00e-02 2.50e+03 pdb=" O4' 2MG a1207 " -0.597 2.00e-02 2.50e+03 pdb=" C3' 2MG a1207 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG a1207 " 0.643 2.00e-02 2.50e+03 pdb=" C2' 2MG a1207 " 0.179 2.00e-02 2.50e+03 pdb=" O2' 2MG a1207 " -0.990 2.00e-02 2.50e+03 pdb=" C1' 2MG a1207 " -0.216 2.00e-02 2.50e+03 pdb=" N9 2MG a1207 " 0.889 2.00e-02 2.50e+03 ... (remaining 12795 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 10 2.07 - 2.77: 32076 2.77 - 3.48: 196137 3.48 - 4.19: 473538 4.19 - 4.90: 651801 Nonbonded interactions: 1353562 Sorted by model distance: nonbonded pdb=" C ILE A3001 " pdb=" N PRO 9 101 " model vdw 1.356 3.350 nonbonded pdb=" O3' A 9 76 " pdb=" C PRO 9 101 " model vdw 1.397 3.270 nonbonded pdb=" O4 U a 409 " pdb=" O6 G a 433 " model vdw 1.944 2.432 nonbonded pdb=" N2 G A 883 " pdb=" O2 C A 893 " model vdw 1.971 2.496 nonbonded pdb=" O6 G 9 49 " pdb=" O4 U 9 65 " model vdw 1.997 2.432 ... (remaining 1353557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 16.120 Check model and map are aligned: 1.560 Set scattering table: 0.980 Process input model: 513.940 Find NCS groups from input model: 2.920 Set up NCS constraints: 0.350 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: 0.030 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 539.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.010 0.288 158507 Z= 0.586 Angle : 0.920 35.959 236990 Z= 0.463 Chirality : 0.050 0.394 30193 Planarity : 0.019 0.614 12798 Dihedral : 15.911 178.993 73731 Min Nonbonded Distance : 1.356 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.82 % Favored : 85.70 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.37 % 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: -4.55 (0.09), residues: 5847 helix: -2.51 (0.09), residues: 1928 sheet: -2.59 (0.15), residues: 974 loop : -3.58 (0.09), residues: 2945 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1307 time to evaluate : 6.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 1318 average time/residue: 1.3633 time to fit residues: 3027.4634 Evaluate side-chains 1077 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1068 time to evaluate : 5.704 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 1.0022 time to fit residues: 25.0599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 873 optimal weight: 7.9990 chunk 783 optimal weight: 3.9990 chunk 434 optimal weight: 4.9990 chunk 267 optimal weight: 9.9990 chunk 528 optimal weight: 10.0000 chunk 418 optimal weight: 30.0000 chunk 810 optimal weight: 10.0000 chunk 313 optimal weight: 7.9990 chunk 492 optimal weight: 20.0000 chunk 603 optimal weight: 10.0000 chunk 938 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN c 189 HIS ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 58 GLN d 88 ASN d 195 ASN e 76 ASN e 88 HIS ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 30 ASN ** i 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN k 23 HIS k 27 ASN k 39 ASN m 13 HIS ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN o 27 GLN o 36 ASN o 45 HIS p 26 ASN q 8 GLN q 30 HIS r 51 GLN s 51 HIS s 68 HIS ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN C 45 ASN C 89 ASN C 127 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN D 164 GLN E 41 GLN E 115 GLN F 51 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN I 18 ASN ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN K 3 GLN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN M 17 ASN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN O 61 GLN P 11 GLN P 40 GLN P 65 ASN Q 71 ASN R 82 HIS S 7 HIS S 31 GLN T 15 HIS U 45 GLN U 65 GLN W 8 ASN W 72 ASN Y 58 ASN 1 25 ASN 5 88 HIS ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.080 158507 Z= 0.368 Angle : 0.769 14.537 236990 Z= 0.405 Chirality : 0.042 0.353 30193 Planarity : 0.007 0.138 12798 Dihedral : 15.341 178.831 62126 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.58 % Favored : 88.11 % Rotamer Outliers : 3.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -3.54 (0.09), residues: 5847 helix: -1.36 (0.10), residues: 1943 sheet: -2.30 (0.15), residues: 983 loop : -3.12 (0.10), residues: 2921 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1098 time to evaluate : 6.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 179 outliers final: 128 residues processed: 1194 average time/residue: 1.3768 time to fit residues: 2849.8020 Evaluate side-chains 1163 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1035 time to evaluate : 6.085 Switching outliers to nearest non-outliers outliers start: 128 outliers final: 0 residues processed: 128 average time/residue: 1.0967 time to fit residues: 273.4807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 521 optimal weight: 10.0000 chunk 291 optimal weight: 9.9990 chunk 781 optimal weight: 1.9990 chunk 639 optimal weight: 9.9990 chunk 259 optimal weight: 0.9990 chunk 940 optimal weight: 0.9990 chunk 1016 optimal weight: 6.9990 chunk 837 optimal weight: 1.9990 chunk 932 optimal weight: 6.9990 chunk 320 optimal weight: 6.9990 chunk 754 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 41 ASN b 189 ASN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN i 125 GLN j 70 HIS j 99 GLN ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN p 40 ASN q 8 GLN ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 ASN C 152 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN E 115 GLN I 104 GLN K 29 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 HIS O 61 GLN P 40 GLN Q 71 ASN W 72 ASN Y 27 ASN 4 35 GLN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.102 158507 Z= 0.162 Angle : 0.631 14.608 236990 Z= 0.341 Chirality : 0.035 0.348 30193 Planarity : 0.006 0.125 12798 Dihedral : 14.829 178.732 62126 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.46 % Favored : 90.25 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.60 (0.10), residues: 5847 helix: -0.39 (0.11), residues: 1922 sheet: -1.89 (0.16), residues: 982 loop : -2.64 (0.10), residues: 2943 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1161 time to evaluate : 6.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 51 residues processed: 1225 average time/residue: 1.3389 time to fit residues: 2859.7453 Evaluate side-chains 1091 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1040 time to evaluate : 6.175 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 1.1118 time to fit residues: 113.9326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 929 optimal weight: 7.9990 chunk 707 optimal weight: 6.9990 chunk 488 optimal weight: 50.0000 chunk 104 optimal weight: 20.0000 chunk 448 optimal weight: 10.0000 chunk 631 optimal weight: 9.9990 chunk 944 optimal weight: 0.0030 chunk 999 optimal weight: 10.0000 chunk 493 optimal weight: 20.0000 chunk 894 optimal weight: 0.0770 chunk 269 optimal weight: 8.9990 overall best weight: 4.8154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 GLN n 62 ASN ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 8 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN G 63 GLN K 89 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN O 61 GLN P 40 GLN Q 71 ASN R 11 GLN R 86 GLN U 98 ASN W 72 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 158507 Z= 0.290 Angle : 0.676 14.643 236990 Z= 0.360 Chirality : 0.038 0.354 30193 Planarity : 0.006 0.134 12798 Dihedral : 14.810 179.964 62126 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.31 % Favored : 89.40 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.46 (0.10), residues: 5847 helix: -0.25 (0.12), residues: 1934 sheet: -1.81 (0.16), residues: 1005 loop : -2.58 (0.10), residues: 2908 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1229 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1060 time to evaluate : 7.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 169 outliers final: 105 residues processed: 1153 average time/residue: 1.3376 time to fit residues: 2717.0342 Evaluate side-chains 1109 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1004 time to evaluate : 6.072 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 0 residues processed: 105 average time/residue: 1.0781 time to fit residues: 222.2632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 832 optimal weight: 8.9990 chunk 567 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 744 optimal weight: 6.9990 chunk 412 optimal weight: 10.0000 chunk 852 optimal weight: 0.0470 chunk 690 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 510 optimal weight: 10.0000 chunk 897 optimal weight: 20.0000 chunk 252 optimal weight: 9.9990 overall best weight: 7.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 GLN f 68 GLN ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 125 GLN j 56 HIS ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 127 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN O 61 GLN P 40 GLN Q 71 ASN R 86 GLN S 31 GLN W 72 ASN ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.094 158507 Z= 0.406 Angle : 0.760 15.125 236990 Z= 0.399 Chirality : 0.042 0.347 30193 Planarity : 0.007 0.139 12798 Dihedral : 15.011 178.757 62126 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.15 % Favored : 88.56 % Rotamer Outliers : 3.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.50 (0.10), residues: 5847 helix: -0.33 (0.11), residues: 1933 sheet: -1.85 (0.16), residues: 1006 loop : -2.56 (0.10), residues: 2908 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1035 time to evaluate : 6.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 149 outliers final: 99 residues processed: 1132 average time/residue: 1.2973 time to fit residues: 2568.7535 Evaluate side-chains 1096 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 997 time to evaluate : 6.125 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 0 residues processed: 99 average time/residue: 1.1023 time to fit residues: 211.3424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 336 optimal weight: 5.9990 chunk 900 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 586 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 1000 optimal weight: 0.9980 chunk 830 optimal weight: 2.9990 chunk 463 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 330 optimal weight: 6.9990 chunk 525 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN g 67 ASN g 129 ASN i 36 GLN ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 8 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN O 61 GLN Q 71 ASN R 86 GLN S 61 ASN W 72 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 158507 Z= 0.239 Angle : 0.658 14.636 236990 Z= 0.353 Chirality : 0.037 0.351 30193 Planarity : 0.006 0.129 12798 Dihedral : 14.781 179.796 62126 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.18 % Favored : 89.55 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.21 (0.11), residues: 5847 helix: -0.06 (0.12), residues: 1928 sheet: -1.68 (0.16), residues: 1005 loop : -2.41 (0.11), residues: 2914 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1051 time to evaluate : 6.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 66 residues processed: 1105 average time/residue: 1.3389 time to fit residues: 2603.3648 Evaluate side-chains 1068 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1002 time to evaluate : 5.496 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.9571 time to fit residues: 128.1272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 964 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 570 optimal weight: 10.0000 chunk 730 optimal weight: 10.0000 chunk 566 optimal weight: 10.0000 chunk 842 optimal weight: 9.9990 chunk 558 optimal weight: 10.0000 chunk 996 optimal weight: 10.0000 chunk 623 optimal weight: 9.9990 chunk 607 optimal weight: 10.0000 chunk 460 optimal weight: 10.0000 overall best weight: 9.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN Q 58 GLN Q 71 ASN ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN U 68 ASN U 98 ASN W 72 ASN 0 41 HIS ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.110 158507 Z= 0.550 Angle : 0.865 15.164 236990 Z= 0.445 Chirality : 0.048 0.382 30193 Planarity : 0.008 0.146 12798 Dihedral : 15.204 179.241 62126 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.28 % Favored : 87.43 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.56 (0.10), residues: 5847 helix: -0.42 (0.11), residues: 1940 sheet: -1.78 (0.16), residues: 1017 loop : -2.62 (0.10), residues: 2890 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 988 time to evaluate : 6.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 89 residues processed: 1061 average time/residue: 1.3788 time to fit residues: 2577.8079 Evaluate side-chains 1056 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 967 time to evaluate : 6.253 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 1.1159 time to fit residues: 193.9550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 616 optimal weight: 10.0000 chunk 397 optimal weight: 10.0000 chunk 595 optimal weight: 50.0000 chunk 300 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 633 optimal weight: 3.9990 chunk 678 optimal weight: 10.0000 chunk 492 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 783 optimal weight: 0.5980 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN M 22 GLN O 61 GLN Q 71 ASN R 86 GLN S 61 ASN W 72 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 158507 Z= 0.288 Angle : 0.699 14.878 236990 Z= 0.373 Chirality : 0.039 0.345 30193 Planarity : 0.006 0.132 12798 Dihedral : 14.904 179.460 62126 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.54 % Favored : 89.19 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.28 (0.11), residues: 5847 helix: -0.14 (0.12), residues: 1933 sheet: -1.70 (0.16), residues: 986 loop : -2.45 (0.11), residues: 2928 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1016 time to evaluate : 6.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 52 residues processed: 1052 average time/residue: 1.3025 time to fit residues: 2398.2463 Evaluate side-chains 1039 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 987 time to evaluate : 5.530 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 1.0682 time to fit residues: 111.3182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 906 optimal weight: 3.9990 chunk 954 optimal weight: 7.9990 chunk 871 optimal weight: 0.8980 chunk 928 optimal weight: 2.9990 chunk 558 optimal weight: 10.0000 chunk 404 optimal weight: 10.0000 chunk 729 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 839 optimal weight: 9.9990 chunk 878 optimal weight: 0.9990 chunk 925 optimal weight: 0.4980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 125 GLN ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 8 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN G 63 GLN K 88 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN O 61 GLN Q 71 ASN R 86 GLN W 72 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 158507 Z= 0.159 Angle : 0.622 14.300 236990 Z= 0.337 Chirality : 0.035 0.348 30193 Planarity : 0.006 0.124 12798 Dihedral : 14.622 179.867 62126 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.75 % Favored : 89.96 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.96 (0.11), residues: 5847 helix: 0.16 (0.12), residues: 1929 sheet: -1.58 (0.16), residues: 978 loop : -2.26 (0.11), residues: 2940 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1024 time to evaluate : 6.139 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: 40 outliers final: 20 residues processed: 1043 average time/residue: 1.3059 time to fit residues: 2382.5437 Evaluate side-chains 1000 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 980 time to evaluate : 6.229 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 1.0869 time to fit residues: 47.7830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 609 optimal weight: 10.0000 chunk 982 optimal weight: 4.9990 chunk 599 optimal weight: 50.0000 chunk 465 optimal weight: 10.0000 chunk 682 optimal weight: 10.0000 chunk 1030 optimal weight: 10.0000 chunk 948 optimal weight: 0.9990 chunk 820 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 633 optimal weight: 10.0000 chunk 502 optimal weight: 10.0000 overall best weight: 7.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 77 ASN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN o 39 GLN ** o 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 63 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN O 61 GLN O 104 GLN Q 71 ASN R 86 GLN W 72 ASN ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.095 158507 Z= 0.406 Angle : 0.757 15.075 236990 Z= 0.396 Chirality : 0.042 0.355 30193 Planarity : 0.007 0.140 12798 Dihedral : 14.849 179.075 62126 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.36 % Favored : 88.35 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.17 (0.11), residues: 5847 helix: -0.07 (0.12), residues: 1935 sheet: -1.64 (0.16), residues: 965 loop : -2.37 (0.11), residues: 2947 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 998 time to evaluate : 6.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 28 residues processed: 1022 average time/residue: 1.3021 time to fit residues: 2340.1082 Evaluate side-chains 1003 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 975 time to evaluate : 6.164 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 1.0446 time to fit residues: 63.1698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 651 optimal weight: 10.0000 chunk 873 optimal weight: 1.9990 chunk 251 optimal weight: 0.7980 chunk 756 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 chunk 821 optimal weight: 0.8980 chunk 343 optimal weight: 3.9990 chunk 843 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 HIS q 8 GLN t 12 GLN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN K 88 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN Q 71 ASN ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN U 98 ASN W 72 ASN Y 25 GLN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107795 restraints weight = 234111.421| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 0.90 r_work: 0.3076 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 158507 Z= 0.172 Angle : 0.628 14.419 236990 Z= 0.340 Chirality : 0.035 0.343 30193 Planarity : 0.006 0.123 12798 Dihedral : 14.565 179.681 62126 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.34 % Favored : 90.41 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.94 (0.11), residues: 5847 helix: 0.16 (0.12), residues: 1934 sheet: -1.60 (0.16), residues: 969 loop : -2.22 (0.11), residues: 2944 =============================================================================== Job complete usr+sys time: 37292.86 seconds wall clock time: 653 minutes 38.30 seconds (39218.30 seconds total)