Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 14:36:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqg_11363/04_2023/6zqg_11363_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqg_11363/04_2023/6zqg_11363.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqg_11363/04_2023/6zqg_11363_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqg_11363/04_2023/6zqg_11363_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqg_11363/04_2023/6zqg_11363_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqg_11363/04_2023/6zqg_11363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqg_11363/04_2023/6zqg_11363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqg_11363/04_2023/6zqg_11363_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqg_11363/04_2023/6zqg_11363_updated.pdb" } resolution = 3.5 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= 0.002 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1423 5.49 5 Mg 39 5.21 5 S 114 5.16 5 C 44537 2.51 5 N 14788 2.21 5 O 19170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "UB ARG 748": "NH1" <-> "NH2" Residue "UB ARG 756": "NH1" <-> "NH2" Residue "UB ASP 758": "OD1" <-> "OD2" Residue "UB GLU 762": "OE1" <-> "OE2" Residue "UC ARG 554": "NH1" <-> "NH2" Residue "UC ARG 566": "NH1" <-> "NH2" Residue "UX ASP 68": "OD1" <-> "OD2" Residue "UX ARG 163": "NH1" <-> "NH2" Residue "CK ARG 308": "NH1" <-> "NH2" Residue "CK GLU 344": "OE1" <-> "OE2" Residue "CK GLU 346": "OE1" <-> "OE2" Residue "CK PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CK ARG 349": "NH1" <-> "NH2" Residue "CL GLU 13": "OE1" <-> "OE2" Residue "CL ARG 45": "NH1" <-> "NH2" Residue "CL ARG 87": "NH1" <-> "NH2" Residue "CL ARG 91": "NH1" <-> "NH2" Residue "CL ARG 113": "NH1" <-> "NH2" Residue "CL PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CL PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CL ARG 193": "NH1" <-> "NH2" Residue "CL TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CL ARG 214": "NH1" <-> "NH2" Residue "CL ARG 218": "NH1" <-> "NH2" Residue "CL ARG 233": "NH1" <-> "NH2" Residue "CL PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CL ARG 568": "NH1" <-> "NH2" Residue "CL GLU 731": "OE1" <-> "OE2" Residue "CL TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CL GLU 768": "OE1" <-> "OE2" Residue "CL ARG 830": "NH1" <-> "NH2" Residue "CL ARG 831": "NH1" <-> "NH2" Residue "CL ARG 833": "NH1" <-> "NH2" Residue "CL ARG 853": "NH1" <-> "NH2" Residue "CL PHE 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CL ARG 866": "NH1" <-> "NH2" Residue "CL ARG 868": "NH1" <-> "NH2" Residue "CL TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CL PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CL ARG 912": "NH1" <-> "NH2" Residue "CL ARG 978": "NH1" <-> "NH2" Residue "CL ARG 1033": "NH1" <-> "NH2" Residue "CM PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM ARG 147": "NH1" <-> "NH2" Residue "CM ARG 231": "NH1" <-> "NH2" Residue "CM GLU 233": "OE1" <-> "OE2" Residue "CM ARG 321": "NH1" <-> "NH2" Residue "JL ARG 73": "NH1" <-> "NH2" Residue "JL GLU 85": "OE1" <-> "OE2" Residue "JL ARG 99": "NH1" <-> "NH2" Residue "JL ARG 146": "NH1" <-> "NH2" Residue "JL GLU 158": "OE1" <-> "OE2" Residue "JL ARG 166": "NH1" <-> "NH2" Residue "JL ARG 215": "NH1" <-> "NH2" Residue "JL PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JL ARG 236": "NH1" <-> "NH2" Residue "JL GLU 252": "OE1" <-> "OE2" Residue "JL ASP 267": "OD1" <-> "OD2" Residue "JL ARG 294": "NH1" <-> "NH2" Residue "JJ ARG 110": "NH1" <-> "NH2" Residue "JJ PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JJ ASP 148": "OD1" <-> "OD2" Residue "JJ ASP 157": "OD1" <-> "OD2" Residue "JJ ASP 178": "OD1" <-> "OD2" Residue "JJ TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JJ ASP 196": "OD1" <-> "OD2" Residue "JJ ARG 221": "NH1" <-> "NH2" Residue "JJ ASP 228": "OD1" <-> "OD2" Residue "JJ GLU 245": "OE1" <-> "OE2" Residue "JJ TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JJ ARG 264": "NH1" <-> "NH2" Residue "DS ARG 40": "NH1" <-> "NH2" Residue "DS GLU 60": "OE1" <-> "OE2" Residue "DA PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA ARG 87": "NH1" <-> "NH2" Residue "DA ARG 111": "NH1" <-> "NH2" Residue "DA ARG 115": "NH1" <-> "NH2" Residue "DA TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA ARG 144": "NH1" <-> "NH2" Residue "DA ARG 152": "NH1" <-> "NH2" Residue "DA GLU 170": "OE1" <-> "OE2" Residue "DA ARG 213": "NH1" <-> "NH2" Residue "DE ARG 11": "NH1" <-> "NH2" Residue "DE ARG 49": "NH1" <-> "NH2" Residue "DE ARG 59": "NH1" <-> "NH2" Residue "DE TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DE PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DE TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DE ARG 108": "NH1" <-> "NH2" Residue "DE GLU 118": "OE1" <-> "OE2" Residue "DE ARG 148": "NH1" <-> "NH2" Residue "DE PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DE ARG 187": "NH1" <-> "NH2" Residue "DE ARG 200": "NH1" <-> "NH2" Residue "DE ASP 202": "OD1" <-> "OD2" Residue "DE PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DE GLU 230": "OE1" <-> "OE2" Residue "DE TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DE ARG 252": "NH1" <-> "NH2" Residue "DG PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DG ASP 20": "OD1" <-> "OD2" Residue "DG GLU 21": "OE1" <-> "OE2" Residue "DG ARG 23": "NH1" <-> "NH2" Residue "DG TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DG ARG 92": "NH1" <-> "NH2" Residue "DG ARG 98": "NH1" <-> "NH2" Residue "DG ARG 137": "NH1" <-> "NH2" Residue "DG TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DG ARG 191": "NH1" <-> "NH2" Residue "DH GLU 33": "OE1" <-> "OE2" Residue "DH ARG 39": "NH1" <-> "NH2" Residue "DH PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DH GLU 95": "OE1" <-> "OE2" Residue "DH ARG 104": "NH1" <-> "NH2" Residue "DI ASP 6": "OD1" <-> "OD2" Residue "DI ARG 8": "NH1" <-> "NH2" Residue "DI ARG 22": "NH1" <-> "NH2" Residue "DI ARG 47": "NH1" <-> "NH2" Residue "DI ARG 59": "NH1" <-> "NH2" Residue "DI GLU 70": "OE1" <-> "OE2" Residue "DI TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DI ARG 110": "NH1" <-> "NH2" Residue "DI PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DI GLU 140": "OE1" <-> "OE2" Residue "DI ARG 164": "NH1" <-> "NH2" Residue "DI ARG 178": "NH1" <-> "NH2" Residue "DI TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DI ARG 194": "NH1" <-> "NH2" Residue "DJ ARG 3": "NH1" <-> "NH2" Residue "DJ TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DJ ARG 17": "NH1" <-> "NH2" Residue "DJ GLU 20": "OE1" <-> "OE2" Residue "DJ ARG 53": "NH1" <-> "NH2" Residue "DJ ARG 54": "NH1" <-> "NH2" Residue "DJ ARG 62": "NH1" <-> "NH2" Residue "DJ GLU 64": "OE1" <-> "OE2" Residue "DJ ASP 66": "OD1" <-> "OD2" Residue "DJ ARG 78": "NH1" <-> "NH2" Residue "DJ GLU 88": "OE1" <-> "OE2" Residue "DJ ASP 89": "OD1" <-> "OD2" Residue "DJ PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DJ ARG 168": "NH1" <-> "NH2" Residue "DJ ARG 174": "NH1" <-> "NH2" Residue "DL GLU 4": "OE1" <-> "OE2" Residue "DL GLU 10": "OE1" <-> "OE2" Residue "DL ARG 30": "NH1" <-> "NH2" Residue "DL ARG 33": "NH1" <-> "NH2" Residue "DL TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DL ASP 55": "OD1" <-> "OD2" Residue "DL ARG 116": "NH1" <-> "NH2" Residue "DN GLU 86": "OE1" <-> "OE2" Residue "DN GLU 103": "OE1" <-> "OE2" Residue "DN ARG 104": "NH1" <-> "NH2" Residue "DN ARG 106": "NH1" <-> "NH2" Residue "DN GLU 142": "OE1" <-> "OE2" Residue "DO ARG 90": "NH1" <-> "NH2" Residue "DO ARG 107": "NH1" <-> "NH2" Residue "DO ASP 117": "OD1" <-> "OD2" Residue "DW PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DW PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DW PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DW GLU 115": "OE1" <-> "OE2" Residue "DW TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DX ARG 16": "NH1" <-> "NH2" Residue "DX ARG 19": "NH1" <-> "NH2" Residue "DX PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DX ARG 69": "NH1" <-> "NH2" Residue "DX GLU 98": "OE1" <-> "OE2" Residue "DX ARG 121": "NH1" <-> "NH2" Residue "DX GLU 141": "OE1" <-> "OE2" Residue "DY ARG 20": "NH1" <-> "NH2" Residue "DY PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DY ARG 32": "NH1" <-> "NH2" Residue "DY GLU 39": "OE1" <-> "OE2" Residue "DY ASP 53": "OD1" <-> "OD2" Residue "DY TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DY GLU 81": "OE1" <-> "OE2" Residue "DY GLU 101": "OE1" <-> "OE2" Residue "DY ASP 115": "OD1" <-> "OD2" Residue "DY PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DY ARG 131": "NH1" <-> "NH2" Residue "UN GLU 371": "OE1" <-> "OE2" Residue "UN ARG 376": "NH1" <-> "NH2" Residue "UN ARG 396": "NH1" <-> "NH2" Residue "UN ARG 406": "NH1" <-> "NH2" Residue "UN ASP 462": "OD1" <-> "OD2" Residue "UN ARG 466": "NH1" <-> "NH2" Residue "UN GLU 470": "OE1" <-> "OE2" Residue "JD ARG 7": "NH1" <-> "NH2" Residue "JD ARG 33": "NH1" <-> "NH2" Residue "JD PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JD ARG 1209": "NH1" <-> "NH2" Residue "JD TYR 1212": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 80072 Number of models: 1 Model: "" Number of chains: 41 Chain: "UB" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2207 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 323} Link IDs: {'PTRANS': 15, 'TRANS': 387} Chain breaks: 5 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1175 Unresolved non-hydrogen angles: 1493 Unresolved non-hydrogen dihedrals: 974 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 16, 'TYR:plan': 13, 'ASN:plan1': 18, 'TRP:plan': 1, 'HIS:plan': 10, 'PHE:plan': 18, 'GLU:plan': 26, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 613 Chain: "UC" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 393 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "US" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 2411 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 447} Link IDs: {'PTRANS': 24, 'TRANS': 459} Chain breaks: 4 Unresolved chain link angles: 24 Unresolved non-hydrogen bonds: 1651 Unresolved non-hydrogen angles: 2117 Unresolved non-hydrogen dihedrals: 1404 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 15, 'TYR:plan': 19, 'ASN:plan1': 32, 'TRP:plan': 6, 'ASP:plan': 24, 'PHE:plan': 33, 'GLU:plan': 31, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 879 Chain: "UX" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1132 Classifications: {'peptide': 143} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 134} Chain: "CJ" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1083 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PTRANS': 10, 'TRANS': 208} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 710 Unresolved non-hydrogen angles: 909 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 9, 'TYR:plan': 4, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 12, 'GLU:plan': 12, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 399 Chain: "CK" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 645 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 3, 'TRANS': 88} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "CL" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5758 Classifications: {'peptide': 710} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 40, 'TRANS': 669} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "CM" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 342} Chain: "JF" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1071 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 658 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 17, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 304 Chain: "JG" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1096 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 199} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 669 Unresolved non-hydrogen angles: 847 Unresolved non-hydrogen dihedrals: 548 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 17, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 308 Chain: "JH" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1295 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 233} Link IDs: {'PTRANS': 14, 'TRANS': 246} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 886 Unresolved non-hydrogen angles: 1141 Unresolved non-hydrogen dihedrals: 753 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 12, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 15, 'GLU:plan': 14, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 472 Chain: "JL" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2262 Classifications: {'peptide': 283} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 265} Chain: "JJ" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1436 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain: "DF" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 970 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 5, 'TRANS': 190} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 583 Unresolved non-hydrogen angles: 738 Unresolved non-hydrogen dihedrals: 464 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 314 Chain: "DQ" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 616 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 6, 'TRANS': 118} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 375 Unresolved non-hydrogen angles: 475 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 177 Chain: "DS" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 630 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "DT" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 700 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 5, 'TRANS': 137} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 431 Unresolved non-hydrogen angles: 544 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 246 Chain: "Dc" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 310 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 96 Chain: "D3" Number of atoms: 29536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1387, 29536 Classifications: {'RNA': 1387} Modifications used: {'rna2p_pur': 134, 'rna2p_pyr': 133, 'rna3p_pur': 591, 'rna3p_pyr': 529} Link IDs: {'rna2p': 267, 'rna3p': 1119} Chain breaks: 6 Chain: "DA" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1709 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "DE" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "DG" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1799 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 216} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "DH" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1481 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain: "DI" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "DJ" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "DL" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1154 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "DN" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "DO" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 941 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "DZ" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 332 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 62} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 4, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 105 Chain: "DW" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "DX" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1115 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "DY" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1067 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "Db" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "UN" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 920 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain breaks: 1 Chain: "JD" Number of atoms: 4600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 4600 Classifications: {'peptide': 829} Incomplete info: {'truncation_to_alanine': 608} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 783} Chain breaks: 6 Unresolved chain link angles: 39 Unresolved non-hydrogen bonds: 2172 Unresolved non-hydrogen angles: 2740 Unresolved non-hydrogen dihedrals: 1817 Unresolved non-hydrogen chiralities: 190 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 31, 'TYR:plan': 21, 'ASN:plan1': 28, 'TRP:plan': 1, 'HIS:plan': 18, 'PHE:plan': 34, 'GLU:plan': 44, 'ARG:plan': 39} Unresolved non-hydrogen planarities: 1098 Chain: "D4" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 496 Unusual residues: {'M7G': 1} Classifications: {'RNA': 22, 'undetermined': 1} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 19, None: 1} Not linked: pdbres="M7GD4 0 " pdbres=" GD4 1 " Chain: "D5" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'RNA': 9} Modifications used: {'rna2p_pyr': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 4, 'rna3p': 4} Chain: "UX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "CL" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D3" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Unusual residues: {' MG': 37} Classifications: {'undetermined': 37} Link IDs: {None: 36} Chain: "DG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5448 SG CYSUX 101 188.266 126.794 170.230 1.00 54.61 S ATOM 5682 SG CYSUX 130 190.521 124.676 171.033 1.00 59.86 S ATOM 5757 SG CYSUX 140 187.150 123.790 170.089 1.00 49.29 S Time building chain proxies: 32.86, per 1000 atoms: 0.41 Number of scatterers: 80072 At special positions: 0 Unit cell: (238.275, 241.452, 325.113, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 114 16.00 P 1423 15.00 Mg 39 11.99 O 19170 8.00 N 14788 7.00 C 44537 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: 32.26 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNUX 201 " pdb="ZN ZNUX 201 " - pdb=" SG CYSUX 140 " pdb="ZN ZNUX 201 " - pdb=" SG CYSUX 101 " pdb="ZN ZNUX 201 " - pdb=" SG CYSUX 130 " pdb="ZN ZNUX 201 " - pdb=" ND1 HISUX 132 " Number of angles added : 3 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13956 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 268 helices and 54 sheets defined 37.5% alpha, 12.2% beta 426 base pairs and 718 stacking pairs defined. Time for finding SS restraints: 25.93 Creating SS restraints... Processing helix chain 'UB' and resid 292 through 315 Processing helix chain 'UB' and resid 385 through 392 Processing helix chain 'UB' and resid 400 through 412 Proline residue: UB 412 - end of helix Processing helix chain 'UB' and resid 421 through 439 Processing helix chain 'UB' and resid 445 through 461 removed outlier: 4.738A pdb=" N ARGUB 450 " --> pdb=" O GLNUB 446 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THRUB 451 " --> pdb=" O SERUB 447 " (cutoff:3.500A) Processing helix chain 'UB' and resid 468 through 487 Processing helix chain 'UB' and resid 496 through 507 Processing helix chain 'UB' and resid 518 through 531 Processing helix chain 'UB' and resid 537 through 553 Processing helix chain 'UB' and resid 562 through 575 Processing helix chain 'UB' and resid 617 through 622 Processing helix chain 'UB' and resid 629 through 649 Processing helix chain 'UB' and resid 651 through 653 No H-bonds generated for 'chain 'UB' and resid 651 through 653' Processing helix chain 'UB' and resid 655 through 672 removed outlier: 3.514A pdb=" N GLUUB 659 " --> pdb=" O PROUB 655 " (cutoff:3.500A) Proline residue: UB 663 - end of helix removed outlier: 3.554A pdb=" N GLNUB 666 " --> pdb=" O LEUUB 662 " (cutoff:3.500A) Processing helix chain 'UB' and resid 680 through 694 Processing helix chain 'UB' and resid 734 through 783 Processing helix chain 'UC' and resid 543 through 546 No H-bonds generated for 'chain 'UC' and resid 543 through 546' Processing helix chain 'UC' and resid 561 through 572 Processing helix chain 'UC' and resid 575 through 577 No H-bonds generated for 'chain 'UC' and resid 575 through 577' Processing helix chain 'US' and resid 2 through 12 Processing helix chain 'US' and resid 23 through 45 Proline residue: US 37 - end of helix removed outlier: 4.599A pdb=" N GLNUS 42 " --> pdb=" O GLUUS 38 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEUUS 43 " --> pdb=" O ASNUS 39 " (cutoff:3.500A) Processing helix chain 'US' and resid 55 through 73 Processing helix chain 'US' and resid 88 through 106 Processing helix chain 'US' and resid 114 through 132 Processing helix chain 'US' and resid 146 through 157 Processing helix chain 'US' and resid 177 through 183 Processing helix chain 'US' and resid 189 through 204 removed outlier: 3.621A pdb=" N GLUUS 204 " --> pdb=" O ASNUS 200 " (cutoff:3.500A) Processing helix chain 'US' and resid 206 through 214 Processing helix chain 'US' and resid 216 through 225 Processing helix chain 'US' and resid 250 through 264 Processing helix chain 'US' and resid 271 through 283 Processing helix chain 'US' and resid 292 through 303 Processing helix chain 'US' and resid 312 through 327 Proline residue: US 316 - end of helix Processing helix chain 'US' and resid 337 through 344 Processing helix chain 'US' and resid 347 through 350 No H-bonds generated for 'chain 'US' and resid 347 through 350' Processing helix chain 'US' and resid 355 through 367 removed outlier: 3.524A pdb=" N SERUS 367 " --> pdb=" O ASPUS 363 " (cutoff:3.500A) Processing helix chain 'US' and resid 373 through 388 Processing helix chain 'US' and resid 392 through 408 Proline residue: US 400 - end of helix Processing helix chain 'US' and resid 410 through 416 Processing helix chain 'US' and resid 419 through 421 No H-bonds generated for 'chain 'US' and resid 419 through 421' Processing helix chain 'US' and resid 429 through 440 Processing helix chain 'US' and resid 464 through 468 Processing helix chain 'US' and resid 475 through 485 Processing helix chain 'US' and resid 503 through 511 Processing helix chain 'UX' and resid 69 through 78 removed outlier: 3.833A pdb=" N ASNUX 73 " --> pdb=" O THRUX 69 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHEUX 74 " --> pdb=" O ASNUX 70 " (cutoff:3.500A) Processing helix chain 'UX' and resid 82 through 90 Processing helix chain 'UX' and resid 100 through 109 Processing helix chain 'UX' and resid 114 through 120 Processing helix chain 'UX' and resid 137 through 148 Processing helix chain 'UX' and resid 158 through 166 Processing helix chain 'CJ' and resid 98 through 110 Processing helix chain 'CJ' and resid 124 through 134 removed outlier: 3.631A pdb=" N SERCJ 134 " --> pdb=" O ALACJ 130 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 197 through 209 removed outlier: 3.801A pdb=" N LEUCJ 209 " --> pdb=" O ILECJ 205 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 282 through 285 Processing helix chain 'CK' and resid 299 through 319 Processing helix chain 'CK' and resid 324 through 326 No H-bonds generated for 'chain 'CK' and resid 324 through 326' Processing helix chain 'CK' and resid 359 through 374 Processing helix chain 'CL' and resid 20 through 22 No H-bonds generated for 'chain 'CL' and resid 20 through 22' Processing helix chain 'CL' and resid 36 through 50 Processing helix chain 'CL' and resid 83 through 94 Processing helix chain 'CL' and resid 125 through 134 Processing helix chain 'CL' and resid 150 through 162 removed outlier: 3.533A pdb=" N HISCL 162 " --> pdb=" O ILECL 158 " (cutoff:3.500A) Processing helix chain 'CL' and resid 180 through 197 Processing helix chain 'CL' and resid 218 through 227 Processing helix chain 'CL' and resid 237 through 239 No H-bonds generated for 'chain 'CL' and resid 237 through 239' Processing helix chain 'CL' and resid 255 through 261 Processing helix chain 'CL' and resid 311 through 318 Processing helix chain 'CL' and resid 549 through 554 removed outlier: 4.293A pdb=" N TYRCL 554 " --> pdb=" O GLYCL 550 " (cutoff:3.500A) Processing helix chain 'CL' and resid 560 through 568 Processing helix chain 'CL' and resid 618 through 624 Processing helix chain 'CL' and resid 629 through 634 removed outlier: 5.224A pdb=" N GLUCL 633 " --> pdb=" O ALACL 630 " (cutoff:3.500A) Processing helix chain 'CL' and resid 718 through 733 Processing helix chain 'CL' and resid 751 through 769 Processing helix chain 'CL' and resid 774 through 780 Processing helix chain 'CL' and resid 798 through 802 Processing helix chain 'CL' and resid 956 through 959 No H-bonds generated for 'chain 'CL' and resid 956 through 959' Processing helix chain 'CL' and resid 1020 through 1022 No H-bonds generated for 'chain 'CL' and resid 1020 through 1022' Processing helix chain 'CL' and resid 1035 through 1040 Processing helix chain 'CM' and resid 17 through 26 Processing helix chain 'CM' and resid 47 through 59 Processing helix chain 'CM' and resid 96 through 109 removed outlier: 4.322A pdb=" N GLUCM 101 " --> pdb=" O TYRCM 98 " (cutoff:3.500A) Proline residue: CM 102 - end of helix removed outlier: 3.744A pdb=" N ALACM 107 " --> pdb=" O LEUCM 104 " (cutoff:3.500A) Proline residue: CM 108 - end of helix Processing helix chain 'CM' and resid 131 through 143 removed outlier: 3.588A pdb=" N METCM 138 " --> pdb=" O LYSCM 134 " (cutoff:3.500A) Proline residue: CM 139 - end of helix Processing helix chain 'CM' and resid 203 through 215 Processing helix chain 'CM' and resid 268 through 285 Processing helix chain 'CM' and resid 294 through 302 Processing helix chain 'CM' and resid 315 through 317 No H-bonds generated for 'chain 'CM' and resid 315 through 317' Processing helix chain 'CM' and resid 320 through 332 Processing helix chain 'JF' and resid 75 through 80 Processing helix chain 'JF' and resid 90 through 98 Processing helix chain 'JF' and resid 103 through 106 No H-bonds generated for 'chain 'JF' and resid 103 through 106' Processing helix chain 'JF' and resid 134 through 146 removed outlier: 3.878A pdb=" N GLYJF 139 " --> pdb=" O LYSJF 135 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEUJF 140 " --> pdb=" O ARGJF 136 " (cutoff:3.500A) Processing helix chain 'JF' and resid 189 through 194 Processing helix chain 'JF' and resid 234 through 249 Processing helix chain 'JG' and resid 75 through 80 Processing helix chain 'JG' and resid 90 through 99 Processing helix chain 'JG' and resid 103 through 106 No H-bonds generated for 'chain 'JG' and resid 103 through 106' Processing helix chain 'JG' and resid 134 through 145 Processing helix chain 'JG' and resid 167 through 169 No H-bonds generated for 'chain 'JG' and resid 167 through 169' Processing helix chain 'JG' and resid 189 through 195 Processing helix chain 'JG' and resid 234 through 246 Processing helix chain 'JH' and resid 208 through 222 Processing helix chain 'JH' and resid 231 through 238 Proline residue: JH 237 - end of helix Processing helix chain 'JH' and resid 243 through 248 Processing helix chain 'JH' and resid 251 through 253 No H-bonds generated for 'chain 'JH' and resid 251 through 253' Processing helix chain 'JH' and resid 256 through 267 Processing helix chain 'JH' and resid 272 through 281 Processing helix chain 'JH' and resid 283 through 292 Processing helix chain 'JH' and resid 301 through 312 Processing helix chain 'JH' and resid 317 through 320 No H-bonds generated for 'chain 'JH' and resid 317 through 320' Processing helix chain 'JH' and resid 323 through 328 Processing helix chain 'JH' and resid 332 through 344 Processing helix chain 'JH' and resid 349 through 361 Processing helix chain 'JH' and resid 366 through 377 Processing helix chain 'JH' and resid 384 through 397 removed outlier: 3.786A pdb=" N PHEJH 397 " --> pdb=" O TYRJH 393 " (cutoff:3.500A) Processing helix chain 'JH' and resid 415 through 427 Processing helix chain 'JH' and resid 434 through 447 Processing helix chain 'JH' and resid 452 through 460 Processing helix chain 'JL' and resid 44 through 52 removed outlier: 3.713A pdb=" N ALAJL 52 " --> pdb=" O ILEJL 48 " (cutoff:3.500A) Processing helix chain 'JL' and resid 71 through 77 Processing helix chain 'JL' and resid 88 through 97 Processing helix chain 'JL' and resid 114 through 116 No H-bonds generated for 'chain 'JL' and resid 114 through 116' Processing helix chain 'JL' and resid 131 through 142 removed outlier: 5.044A pdb=" N SERJL 135 " --> pdb=" O GLNJL 132 " (cutoff:3.500A) Proline residue: JL 136 - end of helix Processing helix chain 'JL' and resid 157 through 163 Processing helix chain 'JL' and resid 174 through 182 Processing helix chain 'JL' and resid 221 through 230 Processing helix chain 'JL' and resid 238 through 241 No H-bonds generated for 'chain 'JL' and resid 238 through 241' Processing helix chain 'JL' and resid 245 through 262 Processing helix chain 'JL' and resid 273 through 287 Processing helix chain 'JL' and resid 300 through 312 Processing helix chain 'JJ' and resid 103 through 105 No H-bonds generated for 'chain 'JJ' and resid 103 through 105' Processing helix chain 'JJ' and resid 107 through 111 Processing helix chain 'JJ' and resid 113 through 115 No H-bonds generated for 'chain 'JJ' and resid 113 through 115' Processing helix chain 'JJ' and resid 117 through 121 Processing helix chain 'JJ' and resid 149 through 164 removed outlier: 4.042A pdb=" N LEUJJ 152 " --> pdb=" O PROJJ 149 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLNJJ 153 " --> pdb=" O GLYJJ 150 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILEJJ 159 " --> pdb=" O ALAJJ 156 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEUJJ 164 " --> pdb=" O ALAJJ 161 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 168 through 176 Processing helix chain 'JJ' and resid 196 through 206 Processing helix chain 'JJ' and resid 208 through 218 removed outlier: 6.079A pdb=" N THRJJ 212 " --> pdb=" O ASPJJ 209 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 237 through 251 Processing helix chain 'JJ' and resid 256 through 271 Processing helix chain 'DF' and resid 31 through 38 removed outlier: 3.951A pdb=" N THRDF 38 " --> pdb=" O GLNDF 34 " (cutoff:3.500A) Processing helix chain 'DF' and resid 82 through 84 No H-bonds generated for 'chain 'DF' and resid 82 through 84' Processing helix chain 'DF' and resid 89 through 97 Processing helix chain 'DF' and resid 108 through 124 Processing helix chain 'DF' and resid 129 through 139 Processing helix chain 'DF' and resid 164 through 182 Processing helix chain 'DF' and resid 190 through 203 Processing helix chain 'DF' and resid 209 through 223 Processing helix chain 'DQ' and resid 46 through 51 Proline residue: DQ 51 - end of helix Processing helix chain 'DQ' and resid 74 through 92 removed outlier: 3.519A pdb=" N VALDQ 78 " --> pdb=" O HISDQ 74 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYRDQ 79 " --> pdb=" O VALDQ 75 " (cutoff:3.500A) Processing helix chain 'DQ' and resid 99 through 117 removed outlier: 8.397A pdb=" N THRDQ 115 " --> pdb=" O SERDQ 111 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEUDQ 116 " --> pdb=" O TYRDQ 112 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEUDQ 117 " --> pdb=" O ASPDQ 113 " (cutoff:3.500A) Processing helix chain 'DS' and resid 40 through 49 Processing helix chain 'DS' and resid 63 through 74 Processing helix chain 'DS' and resid 77 through 79 No H-bonds generated for 'chain 'DS' and resid 77 through 79' Processing helix chain 'DS' and resid 83 through 85 No H-bonds generated for 'chain 'DS' and resid 83 through 85' Processing helix chain 'DT' and resid 12 through 25 Processing helix chain 'DT' and resid 32 through 35 Processing helix chain 'DT' and resid 50 through 67 removed outlier: 4.071A pdb=" N PHEDT 54 " --> pdb=" O ALADT 50 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYRDT 55 " --> pdb=" O GLUDT 51 " (cutoff:3.500A) Processing helix chain 'DT' and resid 73 through 79 Processing helix chain 'DT' and resid 98 through 110 removed outlier: 3.742A pdb=" N GLUDT 109 " --> pdb=" O LEUDT 105 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYSDT 110 " --> pdb=" O GLNDT 106 " (cutoff:3.500A) Processing helix chain 'DT' and resid 126 through 140 Processing helix chain 'DA' and resid 23 through 25 No H-bonds generated for 'chain 'DA' and resid 23 through 25' Processing helix chain 'DA' and resid 58 through 60 No H-bonds generated for 'chain 'DA' and resid 58 through 60' Processing helix chain 'DA' and resid 70 through 74 Processing helix chain 'DA' and resid 107 through 113 Processing helix chain 'DA' and resid 161 through 176 Processing helix chain 'DA' and resid 182 through 188 Processing helix chain 'DA' and resid 192 through 201 Processing helix chain 'DA' and resid 225 through 231 Processing helix chain 'DE' and resid 16 through 18 No H-bonds generated for 'chain 'DE' and resid 16 through 18' Processing helix chain 'DE' and resid 44 through 48 Processing helix chain 'DE' and resid 60 through 67 removed outlier: 4.169A pdb=" N GLNDE 67 " --> pdb=" O ALADE 63 " (cutoff:3.500A) Processing helix chain 'DE' and resid 94 through 96 No H-bonds generated for 'chain 'DE' and resid 94 through 96' Processing helix chain 'DE' and resid 222 through 224 No H-bonds generated for 'chain 'DE' and resid 222 through 224' Processing helix chain 'DE' and resid 248 through 257 Processing helix chain 'DG' and resid 21 through 27 removed outlier: 4.568A pdb=" N PHEDG 27 " --> pdb=" O ARGDG 23 " (cutoff:3.500A) Processing helix chain 'DG' and resid 43 through 45 No H-bonds generated for 'chain 'DG' and resid 43 through 45' Processing helix chain 'DG' and resid 58 through 60 No H-bonds generated for 'chain 'DG' and resid 58 through 60' Processing helix chain 'DG' and resid 138 through 144 Processing helix chain 'DG' and resid 153 through 155 No H-bonds generated for 'chain 'DG' and resid 153 through 155' Processing helix chain 'DG' and resid 181 through 222 Processing helix chain 'DH' and resid 15 through 28 Processing helix chain 'DH' and resid 65 through 71 Processing helix chain 'DH' and resid 76 through 83 Processing helix chain 'DH' and resid 114 through 116 No H-bonds generated for 'chain 'DH' and resid 114 through 116' Processing helix chain 'DH' and resid 118 through 129 Processing helix chain 'DH' and resid 131 through 133 No H-bonds generated for 'chain 'DH' and resid 131 through 133' Processing helix chain 'DH' and resid 159 through 161 No H-bonds generated for 'chain 'DH' and resid 159 through 161' Processing helix chain 'DH' and resid 166 through 177 Processing helix chain 'DI' and resid 26 through 28 No H-bonds generated for 'chain 'DI' and resid 26 through 28' Processing helix chain 'DI' and resid 88 through 93 removed outlier: 3.815A pdb=" N ARGDI 92 " --> pdb=" O ASNDI 88 " (cutoff:3.500A) Processing helix chain 'DI' and resid 107 through 116 Processing helix chain 'DI' and resid 138 through 145 Processing helix chain 'DI' and resid 154 through 162 Processing helix chain 'DI' and resid 187 through 198 Processing helix chain 'DJ' and resid 21 through 33 Processing helix chain 'DJ' and resid 39 through 60 Processing helix chain 'DJ' and resid 67 through 83 Processing helix chain 'DJ' and resid 93 through 97 removed outlier: 3.512A pdb=" N VALDJ 96 " --> pdb=" O LEUDJ 93 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 101 through 107 removed outlier: 3.770A pdb=" N ARGDJ 107 " --> pdb=" O ASPDJ 103 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 109 through 115 Processing helix chain 'DJ' and resid 123 through 131 Processing helix chain 'DJ' and resid 172 through 183 Processing helix chain 'DL' and resid 46 through 50 Processing helix chain 'DN' and resid 30 through 43 Processing helix chain 'DN' and resid 47 through 56 Processing helix chain 'DN' and resid 63 through 67 Processing helix chain 'DN' and resid 71 through 77 Processing helix chain 'DN' and resid 86 through 104 Processing helix chain 'DN' and resid 111 through 131 Processing helix chain 'DN' and resid 143 through 150 Processing helix chain 'DO' and resid 45 through 47 No H-bonds generated for 'chain 'DO' and resid 45 through 47' Processing helix chain 'DO' and resid 57 through 72 Processing helix chain 'DO' and resid 96 through 106 Processing helix chain 'DZ' and resid 45 through 53 Processing helix chain 'DZ' and resid 63 through 65 No H-bonds generated for 'chain 'DZ' and resid 63 through 65' Processing helix chain 'DW' and resid 6 through 19 Processing helix chain 'DW' and resid 32 through 43 Processing helix chain 'DW' and resid 85 through 92 Processing helix chain 'DW' and resid 113 through 116 No H-bonds generated for 'chain 'DW' and resid 113 through 116' Processing helix chain 'DX' and resid 12 through 21 Processing helix chain 'DX' and resid 27 through 34 Processing helix chain 'DX' and resid 67 through 69 No H-bonds generated for 'chain 'DX' and resid 67 through 69' Processing helix chain 'DX' and resid 90 through 93 Processing helix chain 'DX' and resid 132 through 136 Processing helix chain 'DY' and resid 37 through 47 Processing helix chain 'DY' and resid 52 through 54 No H-bonds generated for 'chain 'DY' and resid 52 through 54' Processing helix chain 'DY' and resid 79 through 85 Processing helix chain 'DY' and resid 88 through 94 Processing helix chain 'DY' and resid 105 through 117 Processing helix chain 'DY' and resid 124 through 131 Processing helix chain 'Db' and resid 12 through 17 Processing helix chain 'UN' and resid 372 through 398 Processing helix chain 'UN' and resid 403 through 420 Processing helix chain 'UN' and resid 428 through 441 Processing helix chain 'UN' and resid 449 through 456 Processing helix chain 'UN' and resid 463 through 480 Processing helix chain 'JD' and resid 11 through 27 removed outlier: 3.870A pdb=" N SERJD 14 " --> pdb=" O LYSJD 11 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLYJD 15 " --> pdb=" O ALAJD 12 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARGJD 27 " --> pdb=" O LYSJD 24 " (cutoff:3.500A) Processing helix chain 'JD' and resid 29 through 32 No H-bonds generated for 'chain 'JD' and resid 29 through 32' Processing helix chain 'JD' and resid 89 through 120 removed outlier: 3.921A pdb=" N TYRJD 120 " --> pdb=" O LYSJD 116 " (cutoff:3.500A) Processing helix chain 'JD' and resid 382 through 389 Processing helix chain 'JD' and resid 397 through 405 Processing helix chain 'JD' and resid 421 through 428 Proline residue: JD 425 - end of helix Processing helix chain 'JD' and resid 452 through 462 Processing helix chain 'JD' and resid 494 through 502 Processing helix chain 'JD' and resid 523 through 539 Processing helix chain 'JD' and resid 565 through 568 No H-bonds generated for 'chain 'JD' and resid 565 through 568' Processing helix chain 'JD' and resid 602 through 615 Processing helix chain 'JD' and resid 630 through 639 Processing helix chain 'JD' and resid 740 through 747 removed outlier: 3.583A pdb=" N PHEJD 747 " --> pdb=" O GLNJD 743 " (cutoff:3.500A) Processing helix chain 'JD' and resid 762 through 765 removed outlier: 3.809A pdb=" N GLUJD 765 " --> pdb=" O ASNJD 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'JD' and resid 762 through 765' Processing helix chain 'JD' and resid 803 through 813 Processing helix chain 'JD' and resid 827 through 831 Processing helix chain 'JD' and resid 842 through 844 No H-bonds generated for 'chain 'JD' and resid 842 through 844' Processing helix chain 'JD' and resid 848 through 856 Processing helix chain 'JD' and resid 862 through 864 No H-bonds generated for 'chain 'JD' and resid 862 through 864' Processing helix chain 'JD' and resid 873 through 885 Processing helix chain 'JD' and resid 897 through 903 Processing helix chain 'JD' and resid 909 through 916 Processing helix chain 'JD' and resid 924 through 933 Processing helix chain 'JD' and resid 976 through 994 Processing helix chain 'JD' and resid 1003 through 1013 Processing helix chain 'JD' and resid 1021 through 1027 Processing helix chain 'JD' and resid 1034 through 1052 Processing helix chain 'JD' and resid 1060 through 1065 Processing helix chain 'JD' and resid 1076 through 1085 Processing helix chain 'JD' and resid 1161 through 1163 No H-bonds generated for 'chain 'JD' and resid 1161 through 1163' Processing helix chain 'JD' and resid 1176 through 1180 Processing helix chain 'JD' and resid 1253 through 1261 Processing sheet with id= A, first strand: chain 'UX' and resid 65 through 67 removed outlier: 6.824A pdb=" N ILEUX 152 " --> pdb=" O LEUUX 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'UX' and resid 97 through 99 removed outlier: 6.895A pdb=" N LYSUX 126 " --> pdb=" O ILEUX 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'UX' and resid 173 through 176 Processing sheet with id= D, first strand: chain 'CJ' and resid 88 through 90 removed outlier: 3.836A pdb=" N VALCJ 115 " --> pdb=" O ILECJ 88 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VALCJ 90 " --> pdb=" O VALCJ 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'CJ' and resid 138 through 142 removed outlier: 5.455A pdb=" N SERCJ 166 " --> pdb=" O LEUCJ 258 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEUCJ 258 " --> pdb=" O SERCJ 166 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'CJ' and resid 220 through 225 Processing sheet with id= G, first strand: chain 'CL' and resid 204 through 206 removed outlier: 9.337A pdb=" N PHECL 205 " --> pdb=" O VALCL 167 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLYCL 169 " --> pdb=" O PHECL 205 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'CL' and resid 294 through 297 removed outlier: 7.045A pdb=" N TYRCL 272 " --> pdb=" O ASPCL 247 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHECL 249 " --> pdb=" O ALACL 270 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ALACL 270 " --> pdb=" O PHECL 249 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'CL' and resid 859 through 861 removed outlier: 6.521A pdb=" N ARGCL 828 " --> pdb=" O VALCL 919 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VALCL 919 " --> pdb=" O ARGCL 828 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ARGCL 830 " --> pdb=" O GLYCL 917 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLYCL 917 " --> pdb=" O ARGCL 830 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLYCL 898 " --> pdb=" O ALACL 914 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N THRCL 916 " --> pdb=" O PHECL 896 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHECL 896 " --> pdb=" O THRCL 916 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILECL 918 " --> pdb=" O THRCL 894 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THRCL 894 " --> pdb=" O ILECL 918 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'CL' and resid 966 through 968 removed outlier: 6.665A pdb=" N PHECL 947 " --> pdb=" O TYRCL 939 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILECL 941 " --> pdb=" O THRCL 945 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THRCL 945 " --> pdb=" O ILECL 941 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ALACL 990 " --> pdb=" O ILECL 976 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILECL 976 " --> pdb=" O ALACL 990 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'CM' and resid 9 through 12 Processing sheet with id= L, first strand: chain 'CM' and resid 84 through 89 removed outlier: 6.736A pdb=" N HISCM 167 " --> pdb=" O THRCM 153 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N THRCM 153 " --> pdb=" O HISCM 167 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VALCM 169 " --> pdb=" O LEUCM 151 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEUCM 151 " --> pdb=" O VALCM 169 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'CM' and resid 226 through 230 Processing sheet with id= N, first strand: chain 'CM' and resid 308 through 313 Processing sheet with id= O, first strand: chain 'JF' and resid 223 through 225 removed outlier: 6.364A pdb=" N SERJF 201 " --> pdb=" O ARGJF 176 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VALJF 178 " --> pdb=" O SERJF 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYSJF 203 " --> pdb=" O VALJF 178 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEUJF 180 " --> pdb=" O CYSJF 203 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHEJF 205 " --> pdb=" O LEUJF 180 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILEJF 42 " --> pdb=" O VALJF 204 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VALJF 206 " --> pdb=" O ILEJF 42 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VALJF 44 " --> pdb=" O VALJF 206 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILEJF 150 " --> pdb=" O LEUJF 159 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'JF' and resid 52 through 54 Processing sheet with id= Q, first strand: chain 'JG' and resid 176 through 179 removed outlier: 3.789A pdb=" N PHEJG 205 " --> pdb=" O VALJG 178 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILEJG 42 " --> pdb=" O VALJG 204 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N VALJG 206 " --> pdb=" O ILEJG 42 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VALJG 44 " --> pdb=" O VALJG 206 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'JL' and resid 183 through 191 removed outlier: 6.881A pdb=" N VALJL 206 " --> pdb=" O ILEJL 188 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LYSJL 190 " --> pdb=" O SERJL 204 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N SERJL 204 " --> pdb=" O LYSJL 190 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYSJL 125 " --> pdb=" O ILEJL 152 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N METJL 154 " --> pdb=" O CYSJL 125 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SERJL 127 " --> pdb=" O METJL 154 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N GLNJL 156 " --> pdb=" O SERJL 127 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASNJL 80 " --> pdb=" O VALJL 60 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLUJL 62 " --> pdb=" O ASNJL 80 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VALJL 82 " --> pdb=" O GLUJL 62 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'JJ' and resid 95 through 100 Processing sheet with id= T, first strand: chain 'JJ' and resid 181 through 185 Processing sheet with id= U, first strand: chain 'DF' and resid 145 through 149 Processing sheet with id= V, first strand: chain 'DQ' and resid 6 through 12 removed outlier: 6.340A pdb=" N LEUDQ 28 " --> pdb=" O ILEDQ 65 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VALDQ 67 " --> pdb=" O LEUDQ 28 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYSDQ 30 " --> pdb=" O VALDQ 67 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VALDQ 69 " --> pdb=" O LYSDQ 30 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'DS' and resid 15 through 17 Processing sheet with id= X, first strand: chain 'Dc' and resid 53 through 56 removed outlier: 7.249A pdb=" N ARGDc 29 " --> pdb=" O ILEDc 13 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'DA' and resid 65 through 69 removed outlier: 4.831A pdb=" N LYSDA 214 " --> pdb=" O PHEDA 138 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VALDA 134 " --> pdb=" O LEUDA 218 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'DA' and resid 29 through 33 Processing sheet with id= AA, first strand: chain 'DA' and resid 88 through 92 removed outlier: 6.741A pdb=" N LEUDA 97 " --> pdb=" O ASPDA 89 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VALDA 91 " --> pdb=" O ASNDA 95 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASNDA 95 " --> pdb=" O VALDA 91 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'DE' and resid 70 through 72 removed outlier: 4.433A pdb=" N ASNDE 98 " --> pdb=" O ILEDE 114 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HISDE 112 " --> pdb=" O ARGDE 100 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'DE' and resid 121 through 125 removed outlier: 6.005A pdb=" N ASPDE 163 " --> pdb=" O ILEDE 169 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILEDE 169 " --> pdb=" O ASPDE 163 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'DE' and resid 128 through 131 Processing sheet with id= AE, first strand: chain 'DE' and resid 225 through 229 removed outlier: 6.191A pdb=" N LEUDE 180 " --> pdb=" O ILEDE 228 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HISDE 209 " --> pdb=" O VALDE 196 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYSDE 198 " --> pdb=" O LEUDE 207 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEUDE 207 " --> pdb=" O LYSDE 198 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'DG' and resid 12 through 17 removed outlier: 6.677A pdb=" N VALDG 49 " --> pdb=" O VALDG 114 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'DG' and resid 72 through 77 Processing sheet with id= AH, first strand: chain 'DG' and resid 160 through 164 Processing sheet with id= AI, first strand: chain 'DG' and resid 54 through 57 Processing sheet with id= AJ, first strand: chain 'DH' and resid 45 through 51 removed outlier: 6.629A pdb=" N HISDH 89 " --> pdb=" O LEUDH 58 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILEDH 60 " --> pdb=" O HISDH 89 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILEDH 91 " --> pdb=" O ILEDH 60 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'DH' and resid 137 through 142 Processing sheet with id= AL, first strand: chain 'DI' and resid 62 through 67 Processing sheet with id= AM, first strand: chain 'DI' and resid 181 through 183 removed outlier: 4.633A pdb=" N ALADI 100 " --> pdb=" O ILEDI 169 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLNDI 103 " --> pdb=" O VALDI 81 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VALDI 81 " --> pdb=" O GLNDI 103 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'DI' and resid 42 through 48 removed outlier: 4.998A pdb=" N ASNDI 52 " --> pdb=" O THRDI 48 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'DL' and resid 99 through 110 removed outlier: 6.066A pdb=" N ARGDL 87 " --> pdb=" O VALDL 75 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VALDL 75 " --> pdb=" O ARGDL 87 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ALADL 89 " --> pdb=" O GLYDL 73 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N GLYDL 73 " --> pdb=" O ALADL 89 " (cutoff:3.500A) removed outlier: 15.960A pdb=" N LEUDL 91 " --> pdb=" O LEUDL 71 " (cutoff:3.500A) removed outlier: 17.263A pdb=" N LEUDL 71 " --> pdb=" O LEUDL 91 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLYDL 126 " --> pdb=" O VALDL 139 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N VALDL 139 " --> pdb=" O GLYDL 126 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'DO' and resid 38 through 43 removed outlier: 6.604A pdb=" N VALDO 30 " --> pdb=" O ILEDO 39 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARGDO 41 " --> pdb=" O VALDO 28 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VALDO 28 " --> pdb=" O ARGDO 41 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THRDO 43 " --> pdb=" O THRDO 26 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THRDO 26 " --> pdb=" O THRDO 43 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALADO 78 " --> pdb=" O GLYDO 15 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALADO 17 " --> pdb=" O ALADO 78 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N HISDO 80 " --> pdb=" O ALADO 17 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILEDO 19 " --> pdb=" O HISDO 80 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYSDO 82 " --> pdb=" O ILEDO 19 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALADO 21 " --> pdb=" O LYSDO 82 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARGDO 84 " --> pdb=" O ALADO 21 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARGDO 111 " --> pdb=" O VALDO 79 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VALDO 81 " --> pdb=" O ARGDO 111 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLYDO 113 " --> pdb=" O VALDO 81 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ILEDO 83 " --> pdb=" O GLYDO 113 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'DW' and resid 24 through 27 Processing sheet with id= AR, first strand: chain 'DW' and resid 71 through 74 removed outlier: 6.921A pdb=" N ILEDW 103 " --> pdb=" O LEUDW 126 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHEDW 128 " --> pdb=" O TYRDW 101 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYRDW 101 " --> pdb=" O PHEDW 128 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'DX' and resid 82 through 85 removed outlier: 6.176A pdb=" N GLNDX 75 " --> pdb=" O VALDX 53 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VALDX 53 " --> pdb=" O GLNDX 75 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALADX 105 " --> pdb=" O VALDX 124 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VALDX 124 " --> pdb=" O ALADX 105 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'DY' and resid 5 through 10 Processing sheet with id= AU, first strand: chain 'DY' and resid 13 through 15 Processing sheet with id= AV, first strand: chain 'Db' and resid 43 through 47 Processing sheet with id= AW, first strand: chain 'JD' and resid 579 through 582 removed outlier: 6.503A pdb=" N LEUJD 555 " --> pdb=" O VALJD 410 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILEJD 412 " --> pdb=" O LEUJD 555 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILEJD 557 " --> pdb=" O ILEJD 412 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'JD' and resid 590 through 594 removed outlier: 6.377A pdb=" N GLYJD 819 " --> pdb=" O SERJD 591 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N HISJD 593 " --> pdb=" O GLYJD 819 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N CYSJD 821 " --> pdb=" O HISJD 593 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'JD' and resid 775 through 777 removed outlier: 6.925A pdb=" N LEUJD 756 " --> pdb=" O ILEJD 622 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N VALJD 624 " --> pdb=" O LEUJD 756 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILEJD 758 " --> pdb=" O VALJD 624 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'JD' and resid 781 through 785 Processing sheet with id= BA, first strand: chain 'JD' and resid 1157 through 1160 Processing sheet with id= BB, first strand: chain 'JD' and resid 1202 through 1205 removed outlier: 6.573A pdb=" N GLUJD1208 " --> pdb=" O LEUJD1204 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LYSJD1239 " --> pdb=" O VALJD1247 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N VALJD1247 " --> pdb=" O LYSJD1239 " (cutoff:3.500A) 2229 hydrogen bonds defined for protein. 6243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1033 hydrogen bonds 1658 hydrogen bond angles 0 basepair planarities 426 basepair parallelities 718 stacking parallelities Total time for adding SS restraints: 60.18 Time building geometry restraints manager: 34.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 10480 1.29 - 1.43: 29820 1.43 - 1.57: 41042 1.57 - 1.71: 2643 1.71 - 1.84: 191 Bond restraints: 84176 Sorted by residual: bond pdb=" C2' M7GD4 0 " pdb=" C3' M7GD4 0 " ideal model delta sigma weight residual 1.544 1.222 0.322 2.00e-02 2.50e+03 2.59e+02 bond pdb=" C3' M7GD4 0 " pdb=" C4' M7GD4 0 " ideal model delta sigma weight residual 1.304 1.582 -0.278 2.00e-02 2.50e+03 1.94e+02 bond pdb=" CA ARGJJ 105 " pdb=" C ARGJJ 105 " ideal model delta sigma weight residual 1.526 1.410 0.115 1.23e-02 6.61e+03 8.81e+01 bond pdb=" C4' M7GD4 0 " pdb=" C5' M7GD4 0 " ideal model delta sigma weight residual 1.515 1.392 0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C GLYDY 59 " pdb=" O GLYDY 59 " ideal model delta sigma weight residual 1.235 1.155 0.080 1.35e-02 5.49e+03 3.53e+01 ... (remaining 84171 not shown) Histogram of bond angle deviations from ideal: 89.44 - 100.58: 270 100.58 - 111.73: 48694 111.73 - 122.88: 60964 122.88 - 134.02: 11064 134.02 - 145.17: 44 Bond angle restraints: 121036 Sorted by residual: angle pdb=" C CYSCL 897 " pdb=" N GLYCL 898 " pdb=" CA GLYCL 898 " ideal model delta sigma weight residual 121.61 115.44 6.17 7.70e-01 1.69e+00 6.41e+01 angle pdb=" C ALAJD1174 " pdb=" N SERJD1175 " pdb=" CA SERJD1175 " ideal model delta sigma weight residual 121.90 112.29 9.61 1.26e+00 6.30e-01 5.82e+01 angle pdb=" C ARGDW 28 " pdb=" N PRODW 29 " pdb=" CA PRODW 29 " ideal model delta sigma weight residual 127.00 145.17 -18.17 2.40e+00 1.74e-01 5.73e+01 angle pdb=" N PROUB 412 " pdb=" CA PROUB 412 " pdb=" CB PROUB 412 " ideal model delta sigma weight residual 103.20 110.22 -7.02 9.50e-01 1.11e+00 5.46e+01 angle pdb=" O3' GD3 503 " pdb=" C3' GD3 503 " pdb=" C2' GD3 503 " ideal model delta sigma weight residual 113.70 124.36 -10.66 1.50e+00 4.44e-01 5.05e+01 ... (remaining 121031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 45855 35.91 - 71.82: 1669 71.82 - 107.74: 159 107.74 - 143.65: 17 143.65 - 179.56: 32 Dihedral angle restraints: 47732 sinusoidal: 26330 harmonic: 21402 Sorted by residual: dihedral pdb=" CA LEUDL 5 " pdb=" C LEUDL 5 " pdb=" N THRDL 6 " pdb=" CA THRDL 6 " ideal model delta harmonic sigma weight residual 180.00 -121.94 -58.06 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA SERDO 123 " pdb=" C SERDO 123 " pdb=" N ASPDO 124 " pdb=" CA ASPDO 124 " ideal model delta harmonic sigma weight residual -180.00 -125.43 -54.57 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" O4' UD3 45 " pdb=" C1' UD3 45 " pdb=" N1 UD3 45 " pdb=" C2 UD3 45 " ideal model delta sinusoidal sigma weight residual -160.00 19.56 -179.56 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 47729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 13810 0.120 - 0.240: 1342 0.240 - 0.360: 112 0.360 - 0.479: 20 0.479 - 0.599: 5 Chirality restraints: 15289 Sorted by residual: chirality pdb=" C1' GD3 834 " pdb=" O4' GD3 834 " pdb=" C2' GD3 834 " pdb=" N9 GD3 834 " both_signs ideal model delta sigma weight residual False 2.44 1.84 0.60 2.00e-01 2.50e+01 8.98e+00 chirality pdb=" CB ILECL 105 " pdb=" CA ILECL 105 " pdb=" CG1 ILECL 105 " pdb=" CG2 ILECL 105 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.59 2.00e-01 2.50e+01 8.83e+00 chirality pdb=" CB THRDI 36 " pdb=" CA THRDI 36 " pdb=" OG1 THRDI 36 " pdb=" CG2 THRDI 36 " both_signs ideal model delta sigma weight residual False 2.55 2.02 0.53 2.00e-01 2.50e+01 6.97e+00 ... (remaining 15286 not shown) Planarity restraints: 10479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' M7GD4 0 " 0.509 2.00e-02 2.50e+03 6.63e-01 9.88e+03 pdb=" C2' M7GD4 0 " -0.613 2.00e-02 2.50e+03 pdb=" C3' M7GD4 0 " -0.210 2.00e-02 2.50e+03 pdb=" C4' M7GD4 0 " 0.189 2.00e-02 2.50e+03 pdb=" C5' M7GD4 0 " -0.979 2.00e-02 2.50e+03 pdb=" N9 M7GD4 0 " -0.144 2.00e-02 2.50e+03 pdb=" O2' M7GD4 0 " -0.657 2.00e-02 2.50e+03 pdb=" O3' M7GD4 0 " 1.030 2.00e-02 2.50e+03 pdb=" O4' M7GD4 0 " 0.874 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HISUX 132 " 0.043 2.00e-02 2.50e+03 5.21e-02 4.07e+01 pdb=" CG HISUX 132 " -0.111 2.00e-02 2.50e+03 pdb=" ND1 HISUX 132 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 HISUX 132 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 HISUX 132 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HISUX 132 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CD31501 " -0.019 2.00e-02 2.50e+03 3.35e-02 2.52e+01 pdb=" N1 CD31501 " 0.020 2.00e-02 2.50e+03 pdb=" C2 CD31501 " -0.075 2.00e-02 2.50e+03 pdb=" O2 CD31501 " 0.056 2.00e-02 2.50e+03 pdb=" N3 CD31501 " -0.002 2.00e-02 2.50e+03 pdb=" C4 CD31501 " -0.014 2.00e-02 2.50e+03 pdb=" N4 CD31501 " 0.004 2.00e-02 2.50e+03 pdb=" C5 CD31501 " 0.015 2.00e-02 2.50e+03 pdb=" C6 CD31501 " 0.014 2.00e-02 2.50e+03 ... (remaining 10476 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 42 2.22 - 2.89: 32020 2.89 - 3.56: 114544 3.56 - 4.23: 199620 4.23 - 4.90: 306768 Nonbonded interactions: 652994 Sorted by model distance: nonbonded pdb=" O3B M7GD4 0 " pdb=" O5' GD4 1 " model vdw 1.552 3.040 nonbonded pdb=" O3B M7GD4 0 " pdb=" P GD4 1 " model vdw 1.557 3.400 nonbonded pdb=" OP2 CD3 361 " pdb="MG MGD32005 " model vdw 1.909 2.170 nonbonded pdb=" OP2 AD3 863 " pdb="MG MGD32028 " model vdw 1.928 2.170 nonbonded pdb=" OP2 AD3 401 " pdb="MG MGD32016 " model vdw 1.979 2.170 ... (remaining 652989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'JF' selection = (chain 'JG' and (resid 29 through 55 or resid 63 through 251)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 26.860 Check model and map are aligned: 0.940 Set scattering table: 0.560 Process input model: 227.000 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 269.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 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 : 0.019 0.322 84176 Z= 1.171 Angle : 1.399 20.421 121036 Z= 0.730 Chirality : 0.074 0.599 15289 Planarity : 0.011 0.663 10479 Dihedral : 17.418 179.562 33776 Min Nonbonded Distance : 1.552 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.32 % Favored : 91.49 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.04 % Twisted Proline : 0.92 % Twisted General : 0.31 % 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: -2.91 (0.09), residues: 7273 helix: -1.09 (0.08), residues: 2931 sheet: -1.88 (0.15), residues: 993 loop : -2.73 (0.10), residues: 3349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 553 time to evaluate : 5.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 560 average time/residue: 0.7748 time to fit residues: 733.6187 Evaluate side-chains 440 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 437 time to evaluate : 5.384 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5490 time to fit residues: 9.9585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 865 random chunks: chunk 730 optimal weight: 1.9990 chunk 655 optimal weight: 0.9990 chunk 363 optimal weight: 20.0000 chunk 223 optimal weight: 0.9980 chunk 442 optimal weight: 0.7980 chunk 350 optimal weight: 1.9990 chunk 677 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 412 optimal weight: 50.0000 chunk 504 optimal weight: 0.9990 chunk 785 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** UX 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** UX 143 HIS CL 737 ASN ** CM 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JL 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JJ 123 HIS JJ 262 ASN DA 95 ASN ** DA 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DE 36 HIS ** DE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DE 258 GLN DG 80 ASN DG 139 ASN DG 182 GLN DN 5 HIS ** DW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 80 ASN DX 89 ASN UN 444 HIS UN 447 ASN JD1237 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 84176 Z= 0.210 Angle : 0.711 23.002 121036 Z= 0.361 Chirality : 0.042 0.415 15289 Planarity : 0.005 0.091 10479 Dihedral : 16.487 179.543 24818 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.75 % Favored : 94.18 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.04 % Twisted Proline : 0.31 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.09), residues: 7273 helix: 0.32 (0.09), residues: 2968 sheet: -1.52 (0.16), residues: 984 loop : -2.32 (0.10), residues: 3321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 554 time to evaluate : 5.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 23 residues processed: 566 average time/residue: 0.7636 time to fit residues: 739.7388 Evaluate side-chains 507 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 484 time to evaluate : 5.353 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5643 time to fit residues: 31.7182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 865 random chunks: chunk 436 optimal weight: 5.9990 chunk 243 optimal weight: 50.0000 chunk 653 optimal weight: 4.9990 chunk 534 optimal weight: 20.0000 chunk 216 optimal weight: 2.9990 chunk 786 optimal weight: 3.9990 chunk 850 optimal weight: 30.0000 chunk 700 optimal weight: 0.8980 chunk 780 optimal weight: 0.3980 chunk 268 optimal weight: 20.0000 chunk 631 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** UX 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** UX 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 316 ASN ** CL 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CM 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DE 258 GLN DG 182 GLN DW 24 GLN ** UN 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.091 84176 Z= 0.389 Angle : 0.731 20.494 121036 Z= 0.371 Chirality : 0.044 0.424 15289 Planarity : 0.005 0.074 10479 Dihedral : 16.306 179.296 24818 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.40 % Favored : 92.55 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.04 % Twisted Proline : 0.31 % Twisted General : 0.06 % 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: -1.19 (0.10), residues: 7273 helix: 0.86 (0.10), residues: 2951 sheet: -1.43 (0.15), residues: 1045 loop : -2.16 (0.10), residues: 3277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 514 time to evaluate : 5.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 42 residues processed: 560 average time/residue: 0.7655 time to fit residues: 738.4849 Evaluate side-chains 528 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 486 time to evaluate : 5.392 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.5714 time to fit residues: 53.0197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 865 random chunks: chunk 777 optimal weight: 0.6980 chunk 591 optimal weight: 0.0070 chunk 408 optimal weight: 20.0000 chunk 87 optimal weight: 50.0000 chunk 375 optimal weight: 9.9990 chunk 528 optimal weight: 20.0000 chunk 789 optimal weight: 30.0000 chunk 836 optimal weight: 10.0000 chunk 412 optimal weight: 40.0000 chunk 748 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 overall best weight: 3.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: UC 573 GLN UX 132 HIS UX 147 GLN CL 24 GLN ** CL 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 293 GLN ** CM 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 232 HIS ** DE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DE 258 GLN DG 22 HIS ** DW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 10 ASN ** UN 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** UN 447 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.126 84176 Z= 0.527 Angle : 0.799 18.833 121036 Z= 0.405 Chirality : 0.047 0.391 15289 Planarity : 0.006 0.072 10479 Dihedral : 16.438 178.877 24818 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.30 % Favored : 91.63 % Rotamer Outliers : 3.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.26 (0.10), residues: 7273 helix: 0.88 (0.10), residues: 2930 sheet: -1.55 (0.15), residues: 1051 loop : -2.24 (0.10), residues: 3292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 481 time to evaluate : 5.508 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 81 residues processed: 581 average time/residue: 0.8057 time to fit residues: 821.2440 Evaluate side-chains 554 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 473 time to evaluate : 5.359 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 0 residues processed: 81 average time/residue: 0.6330 time to fit residues: 104.4164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 865 random chunks: chunk 696 optimal weight: 1.9990 chunk 474 optimal weight: 9.9990 chunk 12 optimal weight: 50.0000 chunk 622 optimal weight: 0.8980 chunk 344 optimal weight: 0.0970 chunk 713 optimal weight: 3.9990 chunk 577 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 chunk 426 optimal weight: 2.9990 chunk 750 optimal weight: 2.9990 chunk 210 optimal weight: 0.0040 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: UC 573 GLN UX 143 HIS UX 147 GLN CL 803 ASN ** CM 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JL 132 GLN DE 258 GLN DG 182 GLN DH 161 GLN ** DW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UN 416 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 84176 Z= 0.171 Angle : 0.608 18.076 121036 Z= 0.309 Chirality : 0.039 0.362 15289 Planarity : 0.004 0.067 10479 Dihedral : 15.974 179.763 24818 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.79 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.63 (0.10), residues: 7273 helix: 1.47 (0.10), residues: 2939 sheet: -1.27 (0.16), residues: 1029 loop : -1.96 (0.10), residues: 3305 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 552 time to evaluate : 5.417 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 31 residues processed: 592 average time/residue: 0.7766 time to fit residues: 791.1459 Evaluate side-chains 521 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 490 time to evaluate : 5.521 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.5705 time to fit residues: 40.8809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 865 random chunks: chunk 281 optimal weight: 9.9990 chunk 752 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 490 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 836 optimal weight: 8.9990 chunk 694 optimal weight: 0.5980 chunk 387 optimal weight: 50.0000 chunk 69 optimal weight: 20.0000 chunk 276 optimal weight: 40.0000 chunk 439 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: UC 573 GLN UX 143 HIS CK 303 GLN ** CL 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 57 ASN ** DE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DE 258 GLN DG 182 GLN ** DW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 65 ASN UN 416 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.098 84176 Z= 0.371 Angle : 0.677 18.043 121036 Z= 0.342 Chirality : 0.042 0.369 15289 Planarity : 0.004 0.064 10479 Dihedral : 15.988 179.729 24818 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.25 % Favored : 92.70 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.67 (0.10), residues: 7273 helix: 1.46 (0.10), residues: 2945 sheet: -1.26 (0.16), residues: 1036 loop : -2.02 (0.10), residues: 3292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 493 time to evaluate : 7.013 Fit side-chains outliers start: 76 outliers final: 48 residues processed: 547 average time/residue: 0.7649 time to fit residues: 722.1590 Evaluate side-chains 530 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 482 time to evaluate : 5.343 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.6073 time to fit residues: 62.6874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 865 random chunks: chunk 806 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 476 optimal weight: 3.9990 chunk 611 optimal weight: 0.7980 chunk 473 optimal weight: 9.9990 chunk 704 optimal weight: 0.9990 chunk 467 optimal weight: 4.9990 chunk 833 optimal weight: 5.9990 chunk 521 optimal weight: 3.9990 chunk 508 optimal weight: 3.9990 chunk 384 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: UC 573 GLN UX 147 GLN ** CL 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 15 GLN ** DA 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 57 ASN ** DE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DE 258 GLN ** DW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 65 ASN UN 416 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.093 84176 Z= 0.302 Angle : 0.642 17.734 121036 Z= 0.326 Chirality : 0.041 0.361 15289 Planarity : 0.004 0.068 10479 Dihedral : 15.878 179.218 24818 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.48 % Favored : 93.47 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.56 (0.10), residues: 7273 helix: 1.55 (0.10), residues: 2953 sheet: -1.21 (0.16), residues: 1044 loop : -1.96 (0.11), residues: 3276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 492 time to evaluate : 5.445 Fit side-chains outliers start: 41 outliers final: 25 residues processed: 518 average time/residue: 0.7706 time to fit residues: 688.0189 Evaluate side-chains 496 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 471 time to evaluate : 5.435 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.5930 time to fit residues: 35.0730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 865 random chunks: chunk 515 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 497 optimal weight: 20.0000 chunk 251 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 530 optimal weight: 10.0000 chunk 568 optimal weight: 0.7980 chunk 412 optimal weight: 20.0000 chunk 77 optimal weight: 40.0000 chunk 655 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: UC 573 GLN UX 147 GLN ** CL 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DE 258 GLN DG 189 HIS ** DW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UN 416 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 84176 Z= 0.275 Angle : 0.625 17.579 121036 Z= 0.317 Chirality : 0.040 0.358 15289 Planarity : 0.004 0.065 10479 Dihedral : 15.786 178.809 24818 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.68 % Favored : 93.26 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.48 (0.10), residues: 7273 helix: 1.61 (0.10), residues: 2955 sheet: -1.16 (0.16), residues: 1051 loop : -1.92 (0.11), residues: 3267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 492 time to evaluate : 5.522 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 21 residues processed: 517 average time/residue: 0.7835 time to fit residues: 699.0688 Evaluate side-chains 500 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 479 time to evaluate : 5.443 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.6253 time to fit residues: 31.1809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 865 random chunks: chunk 758 optimal weight: 0.8980 chunk 798 optimal weight: 30.0000 chunk 728 optimal weight: 2.9990 chunk 776 optimal weight: 6.9990 chunk 467 optimal weight: 4.9990 chunk 338 optimal weight: 0.7980 chunk 610 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 702 optimal weight: 0.6980 chunk 734 optimal weight: 0.9990 chunk 774 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: UC 573 GLN ** CL 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 149 GLN ** DA 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 69 HIS ** DE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DE 258 GLN ** DW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UN 416 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 84176 Z= 0.168 Angle : 0.576 17.467 121036 Z= 0.293 Chirality : 0.038 0.352 15289 Planarity : 0.004 0.067 10479 Dihedral : 15.598 179.575 24818 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.27 % Favored : 94.69 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.21 (0.10), residues: 7273 helix: 1.85 (0.10), residues: 2945 sheet: -0.99 (0.16), residues: 1039 loop : -1.78 (0.11), residues: 3289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 516 time to evaluate : 5.372 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 525 average time/residue: 0.8289 time to fit residues: 753.1143 Evaluate side-chains 493 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 484 time to evaluate : 5.613 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.7035 time to fit residues: 18.5105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 865 random chunks: chunk 510 optimal weight: 4.9990 chunk 821 optimal weight: 30.0000 chunk 501 optimal weight: 4.9990 chunk 389 optimal weight: 0.9990 chunk 571 optimal weight: 0.9990 chunk 861 optimal weight: 0.0040 chunk 793 optimal weight: 40.0000 chunk 686 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 530 optimal weight: 10.0000 chunk 420 optimal weight: 4.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CK 303 GLN ** CL 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JJ 262 ASN ** DA 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 57 ASN ** DE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UN 416 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 84176 Z= 0.240 Angle : 0.597 17.523 121036 Z= 0.302 Chirality : 0.039 0.359 15289 Planarity : 0.004 0.067 10479 Dihedral : 15.573 179.426 24818 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.84 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.19 (0.10), residues: 7273 helix: 1.86 (0.10), residues: 2954 sheet: -0.96 (0.16), residues: 1041 loop : -1.78 (0.11), residues: 3278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14546 Ramachandran restraints generated. 7273 Oldfield, 0 Emsley, 7273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 483 time to evaluate : 5.367 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 491 average time/residue: 0.7884 time to fit residues: 667.0375 Evaluate side-chains 480 residues out of total 6487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 470 time to evaluate : 5.405 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5980 time to fit residues: 18.1653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 865 random chunks: chunk 545 optimal weight: 10.0000 chunk 730 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 632 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 687 optimal weight: 0.6980 chunk 287 optimal weight: 30.0000 chunk 705 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: UC 558 ASN CK 303 GLN ** CL 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 149 GLN ** DW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UN 416 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.145922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.110270 restraints weight = 163435.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105963 restraints weight = 184976.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106330 restraints weight = 156241.314| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 84176 Z= 0.298 Angle : 0.631 17.646 121036 Z= 0.320 Chirality : 0.040 0.372 15289 Planarity : 0.004 0.066 10479 Dihedral : 15.630 179.763 24818 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.70 % Favored : 93.26 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.28 (0.10), residues: 7273 helix: 1.77 (0.10), residues: 2951 sheet: -0.99 (0.16), residues: 1059 loop : -1.81 (0.11), residues: 3263 =============================================================================== Job complete usr+sys time: 13838.21 seconds wall clock time: 246 minutes 27.42 seconds (14787.42 seconds total)