Starting phenix.real_space_refine (version: dev) on Fri Dec 16 13:46:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qco_13898/12_2022/7qco_13898_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qco_13898/12_2022/7qco_13898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qco_13898/12_2022/7qco_13898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qco_13898/12_2022/7qco_13898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qco_13898/12_2022/7qco_13898_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qco_13898/12_2022/7qco_13898_updated.pdb" } resolution = 3.7 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 460": "OD1" <-> "OD2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "A ASP 617": "OD1" <-> "OD2" Residue "A PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 486": "OD1" <-> "OD2" Residue "B ARG 671": "NH1" <-> "NH2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 28": "OD1" <-> "OD2" Residue "V ASP 41": "OD1" <-> "OD2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F ASP 115": "OD1" <-> "OD2" Residue "I PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "L TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 85": "NH1" <-> "NH2" Residue "L PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 65": "OD1" <-> "OD2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 460": "OD1" <-> "OD2" Residue "E PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 572": "NH1" <-> "NH2" Residue "E ASP 617": "OD1" <-> "OD2" Residue "E PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 699": "OE1" <-> "OE2" Residue "E TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 400": "NH1" <-> "NH2" Residue "G PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 486": "OD1" <-> "OD2" Residue "G ARG 671": "NH1" <-> "NH2" Residue "G GLU 676": "OE1" <-> "OE2" Residue "G GLU 686": "OE1" <-> "OE2" Residue "G PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "N PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 28": "OD1" <-> "OD2" Residue "W ASP 41": "OD1" <-> "OD2" Residue "W PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 50": "OD1" <-> "OD2" Residue "O PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 110": "OE1" <-> "OE2" Residue "O ASP 115": "OD1" <-> "OD2" Residue "P PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 85": "NH1" <-> "NH2" Residue "S PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 65": "OD1" <-> "OD2" Residue "e ARG 97": "NH1" <-> "NH2" Residue "e GLU 189": "OE1" <-> "OE2" Residue "e PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 460": "OD1" <-> "OD2" Residue "e PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 572": "NH1" <-> "NH2" Residue "e ASP 617": "OD1" <-> "OD2" Residue "e PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 699": "OE1" <-> "OE2" Residue "e TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 15": "OD1" <-> "OD2" Residue "g TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 172": "OE1" <-> "OE2" Residue "g PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 400": "NH1" <-> "NH2" Residue "g PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 486": "OD1" <-> "OD2" Residue "g ARG 671": "NH1" <-> "NH2" Residue "g GLU 676": "OE1" <-> "OE2" Residue "g GLU 686": "OE1" <-> "OE2" Residue "g PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 110": "OE1" <-> "OE2" Residue "n TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 28": "OD1" <-> "OD2" Residue "v ASP 41": "OD1" <-> "OD2" Residue "v PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 50": "OD1" <-> "OD2" Residue "o PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 110": "OE1" <-> "OE2" Residue "o ASP 115": "OD1" <-> "OD2" Residue "p PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 65": "OE1" <-> "OE2" Residue "s TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "s PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 65": "OD1" <-> "OD2" Residue "a ARG 97": "NH1" <-> "NH2" Residue "a GLU 189": "OE1" <-> "OE2" Residue "a PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 460": "OD1" <-> "OD2" Residue "a PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 572": "NH1" <-> "NH2" Residue "a ASP 617": "OD1" <-> "OD2" Residue "a PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 699": "OE1" <-> "OE2" Residue "a TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 15": "OD1" <-> "OD2" Residue "b TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 172": "OE1" <-> "OE2" Residue "b PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 400": "NH1" <-> "NH2" Residue "b PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 486": "OD1" <-> "OD2" Residue "b ARG 671": "NH1" <-> "NH2" Residue "b GLU 676": "OE1" <-> "OE2" Residue "b GLU 686": "OE1" <-> "OE2" Residue "b PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 26": "OE1" <-> "OE2" Residue "d TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 28": "OD1" <-> "OD2" Residue "w ASP 41": "OD1" <-> "OD2" Residue "w PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 50": "OD1" <-> "OD2" Residue "f PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 110": "OE1" <-> "OE2" Residue "f ASP 115": "OD1" <-> "OD2" Residue "i PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 65": "OE1" <-> "OE2" Residue "l TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 85": "NH1" <-> "NH2" Residue "l PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 90396 Number of models: 1 Model: "" Number of chains: 78 Chain: "A" Number of atoms: 5713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5713 Classifications: {'peptide': 728} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 697} Chain: "B" Number of atoms: 5857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5857 Classifications: {'peptide': 734} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 704} Chain: "C" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 605 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 76} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1080 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 127} Chain: "V" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 494 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "F" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1093 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 129} Chain: "I" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 295 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 34} Chain: "J" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 311 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "K" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 474 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 6, 'TRANS': 58} Chain: "L" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1134 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 136} Chain: "M" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 238 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "E" Number of atoms: 5713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5713 Classifications: {'peptide': 728} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 697} Chain: "G" Number of atoms: 5857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5857 Classifications: {'peptide': 734} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 704} Chain: "H" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 605 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 76} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 125} Chain: "W" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 494 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "O" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1093 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 129} Chain: "P" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 295 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 34} Chain: "Q" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 311 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "R" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 474 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 6, 'TRANS': 58} Chain: "S" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1134 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 136} Chain: "T" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 238 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "e" Number of atoms: 5713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5713 Classifications: {'peptide': 728} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 697} Chain: "g" Number of atoms: 5857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5857 Classifications: {'peptide': 734} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 704} Chain: "h" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 605 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 76} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "n" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1080 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 127} Chain: "v" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 494 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "o" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1093 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 129} Chain: "p" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 295 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 34} Chain: "q" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 311 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "r" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 474 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 6, 'TRANS': 58} Chain: "s" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1134 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 136} Chain: "t" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 238 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "a" Number of atoms: 5713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5713 Classifications: {'peptide': 728} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 697} Chain: "b" Number of atoms: 5857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5857 Classifications: {'peptide': 734} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 704} Chain: "c" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 605 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 76} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 125} Chain: "w" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 494 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "f" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1093 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 129} Chain: "i" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 295 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 34} Chain: "j" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 311 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "k" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 474 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 6, 'TRANS': 58} Chain: "l" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1134 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 136} Chain: "m" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 238 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "A" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 2535 Unusual residues: {'BCR': 6, 'CLA': 44, 'LHG': 2, 'PQN': 1} Classifications: {'undetermined': 53} Link IDs: {None: 52} Unresolved non-hydrogen bonds: 696 Unresolved non-hydrogen angles: 835 Unresolved non-hydrogen dihedrals: 377 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 2235 Unusual residues: {'BCR': 6, 'CLA': 40, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 48} Link IDs: {None: 47} Unresolved non-hydrogen bonds: 646 Unresolved non-hydrogen angles: 777 Unresolved non-hydrogen dihedrals: 348 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'CLA:plan-5': 10} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'BCR': 1, 'CLA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'BCR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CLA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CLA:plan-3': 1, 'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 225 Unusual residues: {'BCR': 2, 'CLA': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 2447 Unusual residues: {'BCR': 6, 'CLA': 44, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 52} Link IDs: {None: 51} Unresolved non-hydrogen bonds: 694 Unresolved non-hydrogen angles: 836 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'CLA:plan-3': 1, 'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 33 Chain: "G" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 2272 Unusual residues: {'BCR': 6, 'CLA': 41, 'PQN': 1} Classifications: {'undetermined': 48} Link IDs: {None: 47} Unresolved non-hydrogen bonds: 666 Unresolved non-hydrogen angles: 801 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'CLA:plan-5': 11} Unresolved non-hydrogen planarities: 51 Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 125 Unusual residues: {'BCR': 2, 'CLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'BCR': 1, 'CLA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 255 Unusual residues: {'BCR': 3, 'CLA': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'CLA:plan-5': 3} Unresolved non-hydrogen planarities: 15 Chain: "T" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 2485 Unusual residues: {'BCR': 6, 'CLA': 43, 'LHG': 2, 'PQN': 1} Classifications: {'undetermined': 52} Link IDs: {None: 51} Unresolved non-hydrogen bonds: 681 Unresolved non-hydrogen angles: 817 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 25 Chain: "g" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 2285 Unusual residues: {'BCR': 6, 'CLA': 41, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 49} Link IDs: {None: 48} Unresolved non-hydrogen bonds: 661 Unresolved non-hydrogen angles: 795 Unresolved non-hydrogen dihedrals: 356 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'CLA:plan-5': 10} Unresolved non-hydrogen planarities: 46 Chain: "h" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'BCR': 1, 'CLA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "p" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'BCR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CLA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CLA:plan-3': 1, 'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 13 Chain: "s" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 225 Unusual residues: {'BCR': 2, 'CLA': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "a" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 2495 Unusual residues: {'BCR': 7, 'CLA': 43, 'LHG': 1, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 53} Link IDs: {None: 52} Unresolved non-hydrogen bonds: 670 Unresolved non-hydrogen angles: 806 Unresolved non-hydrogen dihedrals: 358 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 25 Chain: "b" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 2213 Unusual residues: {'BCR': 6, 'CLA': 40, 'PQN': 1} Classifications: {'undetermined': 47} Link IDs: {None: 46} Unresolved non-hydrogen bonds: 660 Unresolved non-hydrogen angles: 795 Unresolved non-hydrogen dihedrals: 354 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'CLA:plan-3': 1, 'CLA:plan-5': 12} Unresolved non-hydrogen planarities: 59 Chain: "c" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 125 Unusual residues: {'BCR': 2, 'CLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "i" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'BCR': 1, 'CLA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "l" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 270 Unusual residues: {'BCR': 2, 'CLA': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 10 Chain: "m" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11934 SG CYS C 50 162.300 178.203 39.319 1.00122.53 S ATOM 11960 SG CYS C 53 157.915 181.350 35.982 1.00140.06 S ATOM 11689 SG CYS C 16 158.884 183.812 30.112 1.00153.91 S ATOM 11649 SG CYS C 10 153.222 186.351 28.022 1.00173.06 S ATOM 29228 SG CYS H 50 216.284 101.596 35.254 1.00123.31 S ATOM 29254 SG CYS H 53 220.538 104.139 31.292 1.00129.19 S ATOM 28983 SG CYS H 16 221.552 102.124 25.262 1.00132.00 S ATOM 28943 SG CYS H 10 225.974 106.098 22.516 1.00144.73 S ATOM 46508 SG CYS h 50 121.262 60.898 39.029 1.00122.64 S ATOM 46534 SG CYS h 53 125.686 57.787 35.710 1.00136.37 S ATOM 46263 SG CYS h 16 124.764 55.324 29.834 1.00149.92 S ATOM 46223 SG CYS h 10 130.454 52.828 27.769 1.00172.19 S ATOM 63802 SG CYS c 50 67.059 137.587 35.534 1.00132.06 S ATOM 63828 SG CYS c 53 62.874 134.969 31.548 1.00137.47 S ATOM 63557 SG CYS c 16 61.754 137.057 25.562 1.00141.73 S ATOM 63517 SG CYS c 10 57.457 132.982 22.767 1.00148.94 S Time building chain proxies: 36.48, per 1000 atoms: 0.40 Number of scatterers: 90396 At special positions: 0 Unit cell: (284.756, 240.436, 120.772, 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) Fe 48 26.01 S 308 16.00 P 5 15.00 Mg 359 11.99 O 13851 8.00 N 13108 7.00 C 62717 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS F 31 " - pdb=" SG CYS F 66 " distance=2.03 Simple disulfide: pdb=" SG CYS O 31 " - pdb=" SG CYS O 66 " distance=2.03 Simple disulfide: pdb=" SG CYS o 31 " - pdb=" SG CYS o 66 " distance=2.03 Simple disulfide: pdb=" SG CYS f 31 " - pdb=" SG CYS f 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM85398 O2A CLA a 807 .*. O " rejected from bonding due to valence issues. Atom "HETATM80054 O2A CLA e 806 .*. O " rejected from bonding due to valence issues. Atom "HETATM74777 O2A CLA E 807 .*. O " rejected from bonding due to valence issues. Atom "HETATM69482 O2A CLA A 807 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=156, symmetry=0 Number of additional bonds: simple=156, symmetry=0 Coordination: Other bonds: Time building additional restraints: 31.12 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 803 " pdb=" FE1 SF4 B 803 " - pdb=" SG CYS A 575 " pdb=" SF4 C 101 " pdb=" FE1 SF4 C 101 " - pdb=" SG CYS C 50 " pdb=" FE3 SF4 C 101 " - pdb=" SG CYS C 53 " pdb=" FE4 SF4 C 101 " - pdb=" SG CYS C 47 " pdb=" FE2 SF4 C 101 " - pdb=" SG CYS C 20 " pdb=" SF4 C 102 " pdb=" FE1 SF4 C 102 " - pdb=" SG CYS C 16 " pdb=" FE4 SF4 C 102 " - pdb=" SG CYS C 10 " pdb=" FE2 SF4 C 102 " - pdb=" SG CYS C 13 " pdb=" FE3 SF4 C 102 " - pdb=" SG CYS C 57 " pdb=" SF4 E 847 " pdb=" FE2 SF4 E 847 " - pdb=" SG CYS E 575 " pdb=" SF4 H 101 " pdb=" FE1 SF4 H 101 " - pdb=" SG CYS H 50 " pdb=" FE3 SF4 H 101 " - pdb=" SG CYS H 53 " pdb=" FE4 SF4 H 101 " - pdb=" SG CYS H 47 " pdb=" FE2 SF4 H 101 " - pdb=" SG CYS H 20 " pdb=" SF4 H 102 " pdb=" FE1 SF4 H 102 " - pdb=" SG CYS H 16 " pdb=" FE4 SF4 H 102 " - pdb=" SG CYS H 10 " pdb=" FE2 SF4 H 102 " - pdb=" SG CYS H 13 " pdb=" FE3 SF4 H 102 " - pdb=" SG CYS H 57 " pdb=" SF4 a 846 " pdb=" FE2 SF4 a 846 " - pdb=" SG CYS a 575 " pdb=" SF4 c 101 " pdb=" FE1 SF4 c 101 " - pdb=" SG CYS c 50 " pdb=" FE3 SF4 c 101 " - pdb=" SG CYS c 53 " pdb=" FE4 SF4 c 101 " - pdb=" SG CYS c 47 " pdb=" FE2 SF4 c 101 " - pdb=" SG CYS c 20 " pdb=" SF4 c 102 " pdb=" FE1 SF4 c 102 " - pdb=" SG CYS c 16 " pdb=" FE4 SF4 c 102 " - pdb=" SG CYS c 10 " pdb=" FE2 SF4 c 102 " - pdb=" SG CYS c 13 " pdb=" FE3 SF4 c 102 " - pdb=" SG CYS c 57 " pdb=" SF4 g 804 " pdb=" FE1 SF4 g 804 " - pdb=" SG CYS e 575 " pdb=" SF4 h 101 " pdb=" FE1 SF4 h 101 " - pdb=" SG CYS h 50 " pdb=" FE3 SF4 h 101 " - pdb=" SG CYS h 53 " pdb=" FE4 SF4 h 101 " - pdb=" SG CYS h 47 " pdb=" FE2 SF4 h 101 " - pdb=" SG CYS h 20 " pdb=" SF4 h 102 " pdb=" FE1 SF4 h 102 " - pdb=" SG CYS h 16 " pdb=" FE4 SF4 h 102 " - pdb=" SG CYS h 10 " pdb=" FE2 SF4 h 102 " - pdb=" SG CYS h 13 " pdb=" FE3 SF4 h 102 " - pdb=" SG CYS h 57 " Number of angles added : 108 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15984 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 348 helices and 32 sheets defined 49.4% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.43 Creating SS restraints... Processing helix chain 'A' and resid 46 through 53 removed outlier: 4.114A pdb=" N ASN A 51 " --> pdb=" O TRP A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 67 through 97 Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 144 through 150 Processing helix chain 'A' and resid 156 through 182 Processing helix chain 'A' and resid 194 through 228 removed outlier: 3.879A pdb=" N LEU A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.518A pdb=" N ILE A 244 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 291 through 309 Processing helix chain 'A' and resid 322 through 328 removed outlier: 3.866A pdb=" N LEU A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'A' and resid 350 through 368 Processing helix chain 'A' and resid 386 through 415 removed outlier: 4.369A pdb=" N GLY A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 431 No H-bonds generated for 'chain 'A' and resid 428 through 431' Processing helix chain 'A' and resid 434 through 465 removed outlier: 4.222A pdb=" N LEU A 455 " --> pdb=" O HIS A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 531 through 557 removed outlier: 3.649A pdb=" N ILE A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 616 Processing helix chain 'A' and resid 636 through 639 No H-bonds generated for 'chain 'A' and resid 636 through 639' Processing helix chain 'A' and resid 643 through 655 removed outlier: 3.525A pdb=" N TYR A 650 " --> pdb=" O TRP A 646 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ALA A 653 " --> pdb=" O ASP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 673 through 688 removed outlier: 3.593A pdb=" N HIS A 677 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 679 " --> pdb=" O GLY A 675 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 688 " --> pdb=" O LEU A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 707 Processing helix chain 'A' and resid 721 through 749 Processing helix chain 'B' and resid 18 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 39 through 71 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 132 through 157 removed outlier: 3.617A pdb=" N ILE B 144 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 172 through 179 Processing helix chain 'B' and resid 184 through 196 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 270 through 286 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 301 through 304 No H-bonds generated for 'chain 'B' and resid 301 through 304' Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.861A pdb=" N ASN B 331 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 354 Processing helix chain 'B' and resid 369 through 400 removed outlier: 4.102A pdb=" N PHE B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 386 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 411 through 450 removed outlier: 3.954A pdb=" N HIS B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 422 " --> pdb=" O HIS B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 Processing helix chain 'B' and resid 497 through 505 Processing helix chain 'B' and resid 517 through 542 Processing helix chain 'B' and resid 551 through 556 removed outlier: 4.038A pdb=" N LYS B 554 " --> pdb=" O PRO B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 605 removed outlier: 3.709A pdb=" N THR B 589 " --> pdb=" O TRP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 615 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.916A pdb=" N ASN B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLY B 637 " --> pdb=" O GLN B 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 632 through 637' Processing helix chain 'B' and resid 647 through 668 Processing helix chain 'B' and resid 676 through 685 removed outlier: 3.580A pdb=" N THR B 680 " --> pdb=" O GLU B 676 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 735 removed outlier: 3.940A pdb=" N THR B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR B 724 " --> pdb=" O TYR B 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 46 No H-bonds generated for 'chain 'C' and resid 44 through 46' Processing helix chain 'C' and resid 52 through 56 removed outlier: 3.518A pdb=" N ALA C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 52 through 56' Processing helix chain 'C' and resid 74 through 77 No H-bonds generated for 'chain 'C' and resid 74 through 77' Processing helix chain 'D' and resid 23 through 26 No H-bonds generated for 'chain 'D' and resid 23 through 26' Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 74 through 77 No H-bonds generated for 'chain 'D' and resid 74 through 77' Processing helix chain 'V' and resid 55 through 57 No H-bonds generated for 'chain 'V' and resid 55 through 57' Processing helix chain 'F' and resid 35 through 42 Processing helix chain 'F' and resid 53 through 62 removed outlier: 3.801A pdb=" N ALA F 62 " --> pdb=" O PHE F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 111 Processing helix chain 'F' and resid 126 through 134 Proline residue: F 131 - end of helix Processing helix chain 'F' and resid 139 through 148 Processing helix chain 'I' and resid 6 through 8 No H-bonds generated for 'chain 'I' and resid 6 through 8' Processing helix chain 'I' and resid 12 through 16 Processing helix chain 'I' and resid 18 through 32 removed outlier: 3.594A pdb=" N GLU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 15 removed outlier: 3.596A pdb=" N LEU J 12 " --> pdb=" O ASN J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 39 removed outlier: 3.645A pdb=" N PHE J 36 " --> pdb=" O LEU J 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 41 Processing helix chain 'K' and resid 68 through 88 removed outlier: 5.694A pdb=" N ASN K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 48 Processing helix chain 'L' and resid 59 through 73 Processing helix chain 'L' and resid 76 through 79 No H-bonds generated for 'chain 'L' and resid 76 through 79' Processing helix chain 'L' and resid 90 through 114 Processing helix chain 'L' and resid 136 through 160 Processing helix chain 'L' and resid 164 through 166 No H-bonds generated for 'chain 'L' and resid 164 through 166' Processing helix chain 'M' and resid 23 through 31 removed outlier: 3.627A pdb=" N VAL M 31 " --> pdb=" O VAL M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 47 removed outlier: 5.252A pdb=" N LEU M 47 " --> pdb=" O LEU M 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 53 removed outlier: 4.115A pdb=" N ASN E 51 " --> pdb=" O TRP E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 67 through 97 Processing helix chain 'E' and resid 101 through 104 No H-bonds generated for 'chain 'E' and resid 101 through 104' Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 156 through 182 Processing helix chain 'E' and resid 194 through 228 removed outlier: 3.879A pdb=" N LEU E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU E 222 " --> pdb=" O ILE E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 240 through 244 removed outlier: 3.518A pdb=" N ILE E 244 " --> pdb=" O HIS E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'E' and resid 291 through 309 Processing helix chain 'E' and resid 322 through 328 removed outlier: 3.865A pdb=" N LEU E 326 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU E 327 " --> pdb=" O LYS E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 347 Processing helix chain 'E' and resid 350 through 368 Processing helix chain 'E' and resid 386 through 415 removed outlier: 4.368A pdb=" N GLY E 404 " --> pdb=" O PHE E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 431 No H-bonds generated for 'chain 'E' and resid 428 through 431' Processing helix chain 'E' and resid 434 through 465 removed outlier: 4.221A pdb=" N LEU E 455 " --> pdb=" O HIS E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 470 No H-bonds generated for 'chain 'E' and resid 468 through 470' Processing helix chain 'E' and resid 482 through 492 Processing helix chain 'E' and resid 531 through 557 removed outlier: 3.648A pdb=" N ILE E 535 " --> pdb=" O ALA E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 616 Processing helix chain 'E' and resid 636 through 639 No H-bonds generated for 'chain 'E' and resid 636 through 639' Processing helix chain 'E' and resid 643 through 655 removed outlier: 3.525A pdb=" N TYR E 650 " --> pdb=" O TRP E 646 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ALA E 653 " --> pdb=" O ASP E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 665 through 667 No H-bonds generated for 'chain 'E' and resid 665 through 667' Processing helix chain 'E' and resid 673 through 688 removed outlier: 3.593A pdb=" N HIS E 677 " --> pdb=" O PHE E 673 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE E 678 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL E 679 " --> pdb=" O GLY E 675 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE E 686 " --> pdb=" O PHE E 682 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE E 688 " --> pdb=" O LEU E 684 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 707 Processing helix chain 'E' and resid 721 through 749 Processing helix chain 'G' and resid 18 through 24 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 39 through 71 Processing helix chain 'G' and resid 74 through 79 Processing helix chain 'G' and resid 99 through 103 Processing helix chain 'G' and resid 120 through 127 Processing helix chain 'G' and resid 132 through 157 removed outlier: 3.617A pdb=" N ILE G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS G 156 " --> pdb=" O ALA G 152 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU G 157 " --> pdb=" O GLY G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 161 No H-bonds generated for 'chain 'G' and resid 159 through 161' Processing helix chain 'G' and resid 165 through 169 Processing helix chain 'G' and resid 172 through 179 Processing helix chain 'G' and resid 184 through 196 Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 224 through 226 No H-bonds generated for 'chain 'G' and resid 224 through 226' Processing helix chain 'G' and resid 270 through 286 Processing helix chain 'G' and resid 288 through 290 No H-bonds generated for 'chain 'G' and resid 288 through 290' Processing helix chain 'G' and resid 301 through 304 No H-bonds generated for 'chain 'G' and resid 301 through 304' Processing helix chain 'G' and resid 318 through 320 No H-bonds generated for 'chain 'G' and resid 318 through 320' Processing helix chain 'G' and resid 327 through 332 removed outlier: 3.861A pdb=" N ASN G 331 " --> pdb=" O TYR G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 354 Processing helix chain 'G' and resid 369 through 400 removed outlier: 4.102A pdb=" N PHE G 385 " --> pdb=" O TYR G 381 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU G 386 " --> pdb=" O ILE G 382 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 388 " --> pdb=" O VAL G 384 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL G 399 " --> pdb=" O GLY G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 407 No H-bonds generated for 'chain 'G' and resid 405 through 407' Processing helix chain 'G' and resid 411 through 450 removed outlier: 3.954A pdb=" N HIS G 418 " --> pdb=" O ARG G 414 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU G 420 " --> pdb=" O LEU G 416 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA G 421 " --> pdb=" O GLN G 417 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE G 422 " --> pdb=" O HIS G 418 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 471 Processing helix chain 'G' and resid 497 through 505 Processing helix chain 'G' and resid 517 through 542 Processing helix chain 'G' and resid 551 through 556 removed outlier: 4.038A pdb=" N LYS G 554 " --> pdb=" O PRO G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 577 through 605 removed outlier: 3.709A pdb=" N THR G 589 " --> pdb=" O TRP G 585 " (cutoff:3.500A) Processing helix chain 'G' and resid 610 through 615 Processing helix chain 'G' and resid 619 through 625 Processing helix chain 'G' and resid 632 through 637 removed outlier: 3.916A pdb=" N ASN G 636 " --> pdb=" O ALA G 632 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLY G 637 " --> pdb=" O GLN G 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 632 through 637' Processing helix chain 'G' and resid 647 through 668 Processing helix chain 'G' and resid 676 through 685 removed outlier: 3.580A pdb=" N THR G 680 " --> pdb=" O GLU G 676 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS G 685 " --> pdb=" O LEU G 681 " (cutoff:3.500A) Processing helix chain 'G' and resid 705 through 735 removed outlier: 3.940A pdb=" N THR G 723 " --> pdb=" O GLY G 719 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR G 724 " --> pdb=" O TYR G 720 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 46 No H-bonds generated for 'chain 'H' and resid 44 through 46' Processing helix chain 'H' and resid 52 through 56 removed outlier: 3.518A pdb=" N ALA H 56 " --> pdb=" O ARG H 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 52 through 56' Processing helix chain 'H' and resid 74 through 77 No H-bonds generated for 'chain 'H' and resid 74 through 77' Processing helix chain 'N' and resid 65 through 72 Processing helix chain 'W' and resid 55 through 57 No H-bonds generated for 'chain 'W' and resid 55 through 57' Processing helix chain 'O' and resid 35 through 42 Processing helix chain 'O' and resid 53 through 61 Processing helix chain 'O' and resid 87 through 111 Processing helix chain 'O' and resid 126 through 134 Proline residue: O 131 - end of helix Processing helix chain 'O' and resid 139 through 148 Processing helix chain 'P' and resid 6 through 8 No H-bonds generated for 'chain 'P' and resid 6 through 8' Processing helix chain 'P' and resid 12 through 16 Processing helix chain 'P' and resid 18 through 32 removed outlier: 3.593A pdb=" N GLU P 32 " --> pdb=" O LEU P 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 15 removed outlier: 3.596A pdb=" N LEU Q 12 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 39 removed outlier: 3.644A pdb=" N PHE Q 36 " --> pdb=" O LEU Q 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 68 through 88 removed outlier: 5.693A pdb=" N ASN R 88 " --> pdb=" O LEU R 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 48 Processing helix chain 'S' and resid 59 through 73 Processing helix chain 'S' and resid 76 through 79 No H-bonds generated for 'chain 'S' and resid 76 through 79' Processing helix chain 'S' and resid 90 through 114 Processing helix chain 'S' and resid 136 through 160 Processing helix chain 'S' and resid 164 through 166 No H-bonds generated for 'chain 'S' and resid 164 through 166' Processing helix chain 'T' and resid 23 through 31 removed outlier: 3.628A pdb=" N VAL T 31 " --> pdb=" O VAL T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 47 removed outlier: 5.251A pdb=" N LEU T 47 " --> pdb=" O LEU T 43 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 53 removed outlier: 4.114A pdb=" N ASN e 51 " --> pdb=" O TRP e 48 " (cutoff:3.500A) Processing helix chain 'e' and resid 59 through 61 No H-bonds generated for 'chain 'e' and resid 59 through 61' Processing helix chain 'e' and resid 67 through 97 Processing helix chain 'e' and resid 101 through 104 No H-bonds generated for 'chain 'e' and resid 101 through 104' Processing helix chain 'e' and resid 144 through 150 Processing helix chain 'e' and resid 156 through 182 Processing helix chain 'e' and resid 194 through 228 removed outlier: 3.880A pdb=" N LEU e 206 " --> pdb=" O LEU e 202 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU e 222 " --> pdb=" O ILE e 218 " (cutoff:3.500A) Proline residue: e 223 - end of helix Processing helix chain 'e' and resid 240 through 244 removed outlier: 3.517A pdb=" N ILE e 244 " --> pdb=" O HIS e 241 " (cutoff:3.500A) Processing helix chain 'e' and resid 248 through 252 Processing helix chain 'e' and resid 270 through 272 No H-bonds generated for 'chain 'e' and resid 270 through 272' Processing helix chain 'e' and resid 291 through 309 Processing helix chain 'e' and resid 322 through 328 removed outlier: 3.866A pdb=" N LEU e 326 " --> pdb=" O ILE e 322 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU e 327 " --> pdb=" O LYS e 323 " (cutoff:3.500A) Processing helix chain 'e' and resid 342 through 347 Processing helix chain 'e' and resid 350 through 368 Processing helix chain 'e' and resid 386 through 415 removed outlier: 4.368A pdb=" N GLY e 404 " --> pdb=" O PHE e 400 " (cutoff:3.500A) Processing helix chain 'e' and resid 428 through 431 No H-bonds generated for 'chain 'e' and resid 428 through 431' Processing helix chain 'e' and resid 434 through 465 removed outlier: 4.222A pdb=" N LEU e 455 " --> pdb=" O HIS e 451 " (cutoff:3.500A) Processing helix chain 'e' and resid 468 through 470 No H-bonds generated for 'chain 'e' and resid 468 through 470' Processing helix chain 'e' and resid 482 through 492 Processing helix chain 'e' and resid 531 through 557 removed outlier: 3.649A pdb=" N ILE e 535 " --> pdb=" O ALA e 531 " (cutoff:3.500A) Processing helix chain 'e' and resid 589 through 616 Processing helix chain 'e' and resid 636 through 639 No H-bonds generated for 'chain 'e' and resid 636 through 639' Processing helix chain 'e' and resid 643 through 655 removed outlier: 3.525A pdb=" N TYR e 650 " --> pdb=" O TRP e 646 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ALA e 653 " --> pdb=" O ASP e 649 " (cutoff:3.500A) Processing helix chain 'e' and resid 665 through 667 No H-bonds generated for 'chain 'e' and resid 665 through 667' Processing helix chain 'e' and resid 673 through 688 removed outlier: 3.593A pdb=" N HIS e 677 " --> pdb=" O PHE e 673 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE e 678 " --> pdb=" O LEU e 674 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL e 679 " --> pdb=" O GLY e 675 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE e 686 " --> pdb=" O PHE e 682 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU e 687 " --> pdb=" O SER e 683 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE e 688 " --> pdb=" O LEU e 684 " (cutoff:3.500A) Processing helix chain 'e' and resid 692 through 707 Processing helix chain 'e' and resid 721 through 749 Processing helix chain 'g' and resid 18 through 24 Processing helix chain 'g' and resid 31 through 33 No H-bonds generated for 'chain 'g' and resid 31 through 33' Processing helix chain 'g' and resid 39 through 71 Processing helix chain 'g' and resid 74 through 79 Processing helix chain 'g' and resid 99 through 103 Processing helix chain 'g' and resid 120 through 127 Processing helix chain 'g' and resid 132 through 157 removed outlier: 3.617A pdb=" N ILE g 144 " --> pdb=" O VAL g 140 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS g 156 " --> pdb=" O ALA g 152 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU g 157 " --> pdb=" O GLY g 153 " (cutoff:3.500A) Processing helix chain 'g' and resid 159 through 161 No H-bonds generated for 'chain 'g' and resid 159 through 161' Processing helix chain 'g' and resid 165 through 169 Processing helix chain 'g' and resid 172 through 179 Processing helix chain 'g' and resid 184 through 196 Processing helix chain 'g' and resid 198 through 203 Processing helix chain 'g' and resid 211 through 213 No H-bonds generated for 'chain 'g' and resid 211 through 213' Processing helix chain 'g' and resid 224 through 226 No H-bonds generated for 'chain 'g' and resid 224 through 226' Processing helix chain 'g' and resid 270 through 286 Processing helix chain 'g' and resid 288 through 290 No H-bonds generated for 'chain 'g' and resid 288 through 290' Processing helix chain 'g' and resid 301 through 304 No H-bonds generated for 'chain 'g' and resid 301 through 304' Processing helix chain 'g' and resid 318 through 320 No H-bonds generated for 'chain 'g' and resid 318 through 320' Processing helix chain 'g' and resid 327 through 332 removed outlier: 3.861A pdb=" N ASN g 331 " --> pdb=" O TYR g 327 " (cutoff:3.500A) Processing helix chain 'g' and resid 335 through 354 Processing helix chain 'g' and resid 369 through 400 removed outlier: 4.102A pdb=" N PHE g 385 " --> pdb=" O TYR g 381 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU g 386 " --> pdb=" O ILE g 382 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL g 388 " --> pdb=" O VAL g 384 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL g 399 " --> pdb=" O GLY g 395 " (cutoff:3.500A) Processing helix chain 'g' and resid 405 through 407 No H-bonds generated for 'chain 'g' and resid 405 through 407' Processing helix chain 'g' and resid 411 through 450 removed outlier: 3.954A pdb=" N HIS g 418 " --> pdb=" O ARG g 414 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU g 420 " --> pdb=" O LEU g 416 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA g 421 " --> pdb=" O GLN g 417 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE g 422 " --> pdb=" O HIS g 418 " (cutoff:3.500A) Processing helix chain 'g' and resid 463 through 471 Processing helix chain 'g' and resid 497 through 505 Processing helix chain 'g' and resid 517 through 542 Processing helix chain 'g' and resid 551 through 556 removed outlier: 4.037A pdb=" N LYS g 554 " --> pdb=" O PRO g 551 " (cutoff:3.500A) Processing helix chain 'g' and resid 577 through 605 removed outlier: 3.710A pdb=" N THR g 589 " --> pdb=" O TRP g 585 " (cutoff:3.500A) Processing helix chain 'g' and resid 610 through 615 Processing helix chain 'g' and resid 619 through 625 Processing helix chain 'g' and resid 632 through 637 removed outlier: 3.916A pdb=" N ASN g 636 " --> pdb=" O ALA g 632 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLY g 637 " --> pdb=" O GLN g 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 632 through 637' Processing helix chain 'g' and resid 647 through 668 Processing helix chain 'g' and resid 676 through 685 removed outlier: 3.580A pdb=" N THR g 680 " --> pdb=" O GLU g 676 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS g 685 " --> pdb=" O LEU g 681 " (cutoff:3.500A) Processing helix chain 'g' and resid 705 through 735 removed outlier: 3.940A pdb=" N THR g 723 " --> pdb=" O GLY g 719 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR g 724 " --> pdb=" O TYR g 720 " (cutoff:3.500A) Processing helix chain 'h' and resid 44 through 46 No H-bonds generated for 'chain 'h' and resid 44 through 46' Processing helix chain 'h' and resid 52 through 56 removed outlier: 3.518A pdb=" N ALA h 56 " --> pdb=" O ARG h 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 52 through 56' Processing helix chain 'h' and resid 74 through 77 No H-bonds generated for 'chain 'h' and resid 74 through 77' Processing helix chain 'n' and resid 23 through 26 No H-bonds generated for 'chain 'n' and resid 23 through 26' Processing helix chain 'n' and resid 64 through 72 Processing helix chain 'n' and resid 74 through 77 No H-bonds generated for 'chain 'n' and resid 74 through 77' Processing helix chain 'v' and resid 55 through 57 No H-bonds generated for 'chain 'v' and resid 55 through 57' Processing helix chain 'o' and resid 35 through 42 Processing helix chain 'o' and resid 53 through 62 removed outlier: 3.802A pdb=" N ALA o 62 " --> pdb=" O PHE o 58 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 111 Processing helix chain 'o' and resid 126 through 134 Proline residue: o 131 - end of helix Processing helix chain 'o' and resid 139 through 148 Processing helix chain 'p' and resid 6 through 8 No H-bonds generated for 'chain 'p' and resid 6 through 8' Processing helix chain 'p' and resid 12 through 16 Processing helix chain 'p' and resid 18 through 32 removed outlier: 3.593A pdb=" N GLU p 32 " --> pdb=" O LEU p 28 " (cutoff:3.500A) Processing helix chain 'q' and resid 9 through 15 removed outlier: 3.596A pdb=" N LEU q 12 " --> pdb=" O ASN q 9 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 39 removed outlier: 3.644A pdb=" N PHE q 36 " --> pdb=" O LEU q 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 41 Processing helix chain 'r' and resid 68 through 88 removed outlier: 5.693A pdb=" N ASN r 88 " --> pdb=" O LEU r 84 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 48 Processing helix chain 's' and resid 59 through 73 Processing helix chain 's' and resid 76 through 79 No H-bonds generated for 'chain 's' and resid 76 through 79' Processing helix chain 's' and resid 90 through 114 Processing helix chain 's' and resid 136 through 160 Processing helix chain 's' and resid 164 through 166 No H-bonds generated for 'chain 's' and resid 164 through 166' Processing helix chain 't' and resid 23 through 31 removed outlier: 3.627A pdb=" N VAL t 31 " --> pdb=" O VAL t 28 " (cutoff:3.500A) Processing helix chain 't' and resid 35 through 47 removed outlier: 5.252A pdb=" N LEU t 47 " --> pdb=" O LEU t 43 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 53 removed outlier: 4.114A pdb=" N ASN a 51 " --> pdb=" O TRP a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 59 through 61 No H-bonds generated for 'chain 'a' and resid 59 through 61' Processing helix chain 'a' and resid 67 through 97 Processing helix chain 'a' and resid 101 through 104 No H-bonds generated for 'chain 'a' and resid 101 through 104' Processing helix chain 'a' and resid 144 through 150 Processing helix chain 'a' and resid 156 through 182 Processing helix chain 'a' and resid 194 through 228 removed outlier: 3.879A pdb=" N LEU a 206 " --> pdb=" O LEU a 202 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU a 222 " --> pdb=" O ILE a 218 " (cutoff:3.500A) Proline residue: a 223 - end of helix Processing helix chain 'a' and resid 240 through 244 removed outlier: 3.518A pdb=" N ILE a 244 " --> pdb=" O HIS a 241 " (cutoff:3.500A) Processing helix chain 'a' and resid 248 through 252 Processing helix chain 'a' and resid 270 through 272 No H-bonds generated for 'chain 'a' and resid 270 through 272' Processing helix chain 'a' and resid 291 through 309 Processing helix chain 'a' and resid 322 through 328 removed outlier: 3.865A pdb=" N LEU a 326 " --> pdb=" O ILE a 322 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU a 327 " --> pdb=" O LYS a 323 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 347 Processing helix chain 'a' and resid 350 through 368 Processing helix chain 'a' and resid 386 through 415 removed outlier: 4.368A pdb=" N GLY a 404 " --> pdb=" O PHE a 400 " (cutoff:3.500A) Processing helix chain 'a' and resid 428 through 431 No H-bonds generated for 'chain 'a' and resid 428 through 431' Processing helix chain 'a' and resid 434 through 465 removed outlier: 4.223A pdb=" N LEU a 455 " --> pdb=" O HIS a 451 " (cutoff:3.500A) Processing helix chain 'a' and resid 468 through 470 No H-bonds generated for 'chain 'a' and resid 468 through 470' Processing helix chain 'a' and resid 482 through 492 Processing helix chain 'a' and resid 531 through 557 removed outlier: 3.649A pdb=" N ILE a 535 " --> pdb=" O ALA a 531 " (cutoff:3.500A) Processing helix chain 'a' and resid 589 through 616 Processing helix chain 'a' and resid 636 through 639 No H-bonds generated for 'chain 'a' and resid 636 through 639' Processing helix chain 'a' and resid 643 through 655 removed outlier: 3.525A pdb=" N TYR a 650 " --> pdb=" O TRP a 646 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ALA a 653 " --> pdb=" O ASP a 649 " (cutoff:3.500A) Processing helix chain 'a' and resid 665 through 667 No H-bonds generated for 'chain 'a' and resid 665 through 667' Processing helix chain 'a' and resid 673 through 688 removed outlier: 3.593A pdb=" N HIS a 677 " --> pdb=" O PHE a 673 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE a 678 " --> pdb=" O LEU a 674 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL a 679 " --> pdb=" O GLY a 675 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE a 686 " --> pdb=" O PHE a 682 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU a 687 " --> pdb=" O SER a 683 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE a 688 " --> pdb=" O LEU a 684 " (cutoff:3.500A) Processing helix chain 'a' and resid 692 through 707 Processing helix chain 'a' and resid 721 through 749 Processing helix chain 'b' and resid 18 through 24 Processing helix chain 'b' and resid 31 through 33 No H-bonds generated for 'chain 'b' and resid 31 through 33' Processing helix chain 'b' and resid 39 through 71 Processing helix chain 'b' and resid 74 through 79 Processing helix chain 'b' and resid 99 through 103 Processing helix chain 'b' and resid 120 through 127 Processing helix chain 'b' and resid 132 through 157 removed outlier: 3.617A pdb=" N ILE b 144 " --> pdb=" O VAL b 140 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS b 156 " --> pdb=" O ALA b 152 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU b 157 " --> pdb=" O GLY b 153 " (cutoff:3.500A) Processing helix chain 'b' and resid 159 through 161 No H-bonds generated for 'chain 'b' and resid 159 through 161' Processing helix chain 'b' and resid 165 through 169 Processing helix chain 'b' and resid 172 through 179 Processing helix chain 'b' and resid 184 through 196 Processing helix chain 'b' and resid 198 through 203 Processing helix chain 'b' and resid 211 through 213 No H-bonds generated for 'chain 'b' and resid 211 through 213' Processing helix chain 'b' and resid 224 through 226 No H-bonds generated for 'chain 'b' and resid 224 through 226' Processing helix chain 'b' and resid 270 through 286 Processing helix chain 'b' and resid 288 through 290 No H-bonds generated for 'chain 'b' and resid 288 through 290' Processing helix chain 'b' and resid 301 through 304 No H-bonds generated for 'chain 'b' and resid 301 through 304' Processing helix chain 'b' and resid 318 through 320 No H-bonds generated for 'chain 'b' and resid 318 through 320' Processing helix chain 'b' and resid 327 through 332 removed outlier: 3.862A pdb=" N ASN b 331 " --> pdb=" O TYR b 327 " (cutoff:3.500A) Processing helix chain 'b' and resid 335 through 354 Processing helix chain 'b' and resid 369 through 400 removed outlier: 4.102A pdb=" N PHE b 385 " --> pdb=" O TYR b 381 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU b 386 " --> pdb=" O ILE b 382 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL b 388 " --> pdb=" O VAL b 384 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL b 399 " --> pdb=" O GLY b 395 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 407 No H-bonds generated for 'chain 'b' and resid 405 through 407' Processing helix chain 'b' and resid 411 through 450 removed outlier: 3.954A pdb=" N HIS b 418 " --> pdb=" O ARG b 414 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU b 420 " --> pdb=" O LEU b 416 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA b 421 " --> pdb=" O GLN b 417 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE b 422 " --> pdb=" O HIS b 418 " (cutoff:3.500A) Processing helix chain 'b' and resid 463 through 471 Processing helix chain 'b' and resid 497 through 505 Processing helix chain 'b' and resid 517 through 542 Processing helix chain 'b' and resid 551 through 556 removed outlier: 4.038A pdb=" N LYS b 554 " --> pdb=" O PRO b 551 " (cutoff:3.500A) Processing helix chain 'b' and resid 577 through 605 removed outlier: 3.710A pdb=" N THR b 589 " --> pdb=" O TRP b 585 " (cutoff:3.500A) Processing helix chain 'b' and resid 610 through 615 Processing helix chain 'b' and resid 619 through 625 Processing helix chain 'b' and resid 632 through 637 removed outlier: 3.916A pdb=" N ASN b 636 " --> pdb=" O ALA b 632 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLY b 637 " --> pdb=" O GLN b 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 632 through 637' Processing helix chain 'b' and resid 647 through 668 Processing helix chain 'b' and resid 676 through 685 removed outlier: 3.580A pdb=" N THR b 680 " --> pdb=" O GLU b 676 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS b 685 " --> pdb=" O LEU b 681 " (cutoff:3.500A) Processing helix chain 'b' and resid 705 through 735 removed outlier: 3.940A pdb=" N THR b 723 " --> pdb=" O GLY b 719 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR b 724 " --> pdb=" O TYR b 720 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 46 No H-bonds generated for 'chain 'c' and resid 44 through 46' Processing helix chain 'c' and resid 52 through 56 removed outlier: 3.518A pdb=" N ALA c 56 " --> pdb=" O ARG c 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 52 through 56' Processing helix chain 'c' and resid 74 through 77 No H-bonds generated for 'chain 'c' and resid 74 through 77' Processing helix chain 'd' and resid 64 through 72 Processing helix chain 'w' and resid 55 through 57 No H-bonds generated for 'chain 'w' and resid 55 through 57' Processing helix chain 'f' and resid 35 through 42 Processing helix chain 'f' and resid 53 through 62 removed outlier: 3.802A pdb=" N ALA f 62 " --> pdb=" O PHE f 58 " (cutoff:3.500A) Processing helix chain 'f' and resid 87 through 111 Processing helix chain 'f' and resid 126 through 134 Proline residue: f 131 - end of helix Processing helix chain 'f' and resid 139 through 148 Processing helix chain 'i' and resid 6 through 8 No H-bonds generated for 'chain 'i' and resid 6 through 8' Processing helix chain 'i' and resid 12 through 16 Processing helix chain 'i' and resid 18 through 32 removed outlier: 3.594A pdb=" N GLU i 32 " --> pdb=" O LEU i 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 15 removed outlier: 3.597A pdb=" N LEU j 12 " --> pdb=" O ASN j 9 " (cutoff:3.500A) Processing helix chain 'j' and resid 19 through 39 removed outlier: 3.644A pdb=" N PHE j 36 " --> pdb=" O LEU j 32 " (cutoff:3.500A) Processing helix chain 'k' and resid 30 through 41 Processing helix chain 'k' and resid 68 through 88 removed outlier: 5.695A pdb=" N ASN k 88 " --> pdb=" O LEU k 84 " (cutoff:3.500A) Processing helix chain 'l' and resid 41 through 48 Processing helix chain 'l' and resid 59 through 73 Processing helix chain 'l' and resid 76 through 79 No H-bonds generated for 'chain 'l' and resid 76 through 79' Processing helix chain 'l' and resid 90 through 114 Processing helix chain 'l' and resid 136 through 160 Processing helix chain 'l' and resid 164 through 166 No H-bonds generated for 'chain 'l' and resid 164 through 166' Processing helix chain 'm' and resid 23 through 31 removed outlier: 3.627A pdb=" N VAL m 31 " --> pdb=" O VAL m 28 " (cutoff:3.500A) Processing helix chain 'm' and resid 35 through 47 removed outlier: 5.252A pdb=" N LEU m 47 " --> pdb=" O LEU m 43 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 620 through 622 Processing sheet with id= B, first strand: chain 'A' and resid 515 through 517 removed outlier: 5.932A pdb=" N VAL A 517 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE A 521 " --> pdb=" O VAL A 517 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= D, first strand: chain 'C' and resid 26 through 29 Processing sheet with id= E, first strand: chain 'D' and resid 84 through 89 removed outlier: 3.712A pdb=" N TRP D 33 " --> pdb=" O ASN D 56 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 40 through 42 Processing sheet with id= G, first strand: chain 'V' and resid 8 through 10 Processing sheet with id= H, first strand: chain 'V' and resid 50 through 53 removed outlier: 3.538A pdb=" N SER V 26 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG V 39 " --> pdb=" O VAL V 24 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL V 24 " --> pdb=" O ARG V 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 620 through 622 Processing sheet with id= J, first strand: chain 'E' and resid 515 through 517 removed outlier: 5.933A pdb=" N VAL E 517 " --> pdb=" O ILE E 521 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ILE E 521 " --> pdb=" O VAL E 517 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 3 through 5 Processing sheet with id= L, first strand: chain 'H' and resid 26 through 29 Processing sheet with id= M, first strand: chain 'N' and resid 84 through 88 removed outlier: 3.523A pdb=" N TRP N 33 " --> pdb=" O ASN N 56 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'N' and resid 40 through 42 Processing sheet with id= O, first strand: chain 'W' and resid 8 through 10 Processing sheet with id= P, first strand: chain 'W' and resid 50 through 53 removed outlier: 3.537A pdb=" N SER W 26 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG W 39 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL W 24 " --> pdb=" O ARG W 39 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'e' and resid 620 through 622 Processing sheet with id= R, first strand: chain 'e' and resid 515 through 517 removed outlier: 5.931A pdb=" N VAL e 517 " --> pdb=" O ILE e 521 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE e 521 " --> pdb=" O VAL e 517 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'h' and resid 3 through 5 Processing sheet with id= T, first strand: chain 'h' and resid 26 through 29 Processing sheet with id= U, first strand: chain 'n' and resid 84 through 89 Processing sheet with id= V, first strand: chain 'n' and resid 40 through 42 Processing sheet with id= W, first strand: chain 'v' and resid 8 through 10 Processing sheet with id= X, first strand: chain 'v' and resid 50 through 53 removed outlier: 3.537A pdb=" N SER v 26 " --> pdb=" O ILE v 37 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG v 39 " --> pdb=" O VAL v 24 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL v 24 " --> pdb=" O ARG v 39 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'a' and resid 620 through 622 Processing sheet with id= Z, first strand: chain 'a' and resid 515 through 517 removed outlier: 5.932A pdb=" N VAL a 517 " --> pdb=" O ILE a 521 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE a 521 " --> pdb=" O VAL a 517 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'c' and resid 3 through 5 Processing sheet with id= AB, first strand: chain 'c' and resid 26 through 29 Processing sheet with id= AC, first strand: chain 'd' and resid 84 through 88 Processing sheet with id= AD, first strand: chain 'd' and resid 40 through 42 Processing sheet with id= AE, first strand: chain 'w' and resid 8 through 10 Processing sheet with id= AF, first strand: chain 'w' and resid 50 through 53 removed outlier: 3.538A pdb=" N SER w 26 " --> pdb=" O ILE w 37 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG w 39 " --> pdb=" O VAL w 24 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL w 24 " --> pdb=" O ARG w 39 " (cutoff:3.500A) 2971 hydrogen bonds defined for protein. 8598 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 30.42 Time building geometry restraints manager: 34.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 41104 1.43 - 1.64: 52420 1.64 - 1.85: 453 1.85 - 2.07: 714 2.07 - 2.28: 866 Bond restraints: 95557 Sorted by residual: bond pdb=" C1A CLA L 204 " pdb=" CHA CLA L 204 " ideal model delta sigma weight residual 1.367 1.611 -0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C1A CLA S 204 " pdb=" CHA CLA S 204 " ideal model delta sigma weight residual 1.367 1.610 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C1A CLA s 203 " pdb=" CHA CLA s 203 " ideal model delta sigma weight residual 1.367 1.610 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C1A CLA l 205 " pdb=" CHA CLA l 205 " ideal model delta sigma weight residual 1.367 1.610 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" ND CLA S 204 " pdb="MG CLA S 204 " ideal model delta sigma weight residual 2.022 2.241 -0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 95552 not shown) Histogram of bond angle deviations from ideal: 73.63 - 94.47: 1580 94.47 - 115.30: 60167 115.30 - 136.13: 73285 136.13 - 156.97: 375 156.97 - 177.80: 718 Bond angle restraints: 136125 Sorted by residual: angle pdb=" CA GLU e 699 " pdb=" CB GLU e 699 " pdb=" CG GLU e 699 " ideal model delta sigma weight residual 114.10 126.85 -12.75 2.00e+00 2.50e-01 4.06e+01 angle pdb=" CA GLU a 699 " pdb=" CB GLU a 699 " pdb=" CG GLU a 699 " ideal model delta sigma weight residual 114.10 126.84 -12.74 2.00e+00 2.50e-01 4.05e+01 angle pdb=" CA GLU A 699 " pdb=" CB GLU A 699 " pdb=" CG GLU A 699 " ideal model delta sigma weight residual 114.10 126.83 -12.73 2.00e+00 2.50e-01 4.05e+01 angle pdb=" CA GLU E 699 " pdb=" CB GLU E 699 " pdb=" CG GLU E 699 " ideal model delta sigma weight residual 114.10 126.83 -12.73 2.00e+00 2.50e-01 4.05e+01 angle pdb=" C3A CLA l 205 " pdb=" C2A CLA l 205 " pdb=" CAA CLA l 205 " ideal model delta sigma weight residual 112.02 96.43 15.59 3.00e+00 1.11e-01 2.70e+01 ... (remaining 136120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.15: 39604 25.15 - 50.30: 3462 50.30 - 75.45: 1029 75.45 - 100.60: 233 100.60 - 125.75: 84 Dihedral angle restraints: 44412 sinusoidal: 19360 harmonic: 25052 Sorted by residual: dihedral pdb=" CA PHE G 560 " pdb=" C PHE G 560 " pdb=" N PRO G 561 " pdb=" CA PRO G 561 " ideal model delta harmonic sigma weight residual -180.00 -144.04 -35.96 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA PHE B 560 " pdb=" C PHE B 560 " pdb=" N PRO B 561 " pdb=" CA PRO B 561 " ideal model delta harmonic sigma weight residual 180.00 -144.06 -35.94 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA PHE b 560 " pdb=" C PHE b 560 " pdb=" N PRO b 561 " pdb=" CA PRO b 561 " ideal model delta harmonic sigma weight residual -180.00 -144.10 -35.90 0 5.00e+00 4.00e-02 5.15e+01 ... (remaining 44409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 11020 0.091 - 0.182: 712 0.182 - 0.273: 41 0.273 - 0.364: 8 0.364 - 0.456: 4 Chirality restraints: 11785 Sorted by residual: chirality pdb=" CG LEU R 74 " pdb=" CB LEU R 74 " pdb=" CD1 LEU R 74 " pdb=" CD2 LEU R 74 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" CG LEU K 74 " pdb=" CB LEU K 74 " pdb=" CD1 LEU K 74 " pdb=" CD2 LEU K 74 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" CG LEU k 74 " pdb=" CB LEU k 74 " pdb=" CD1 LEU k 74 " pdb=" CD2 LEU k 74 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.16e+00 ... (remaining 11782 not shown) Planarity restraints: 18332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 BCR a 848 " 0.343 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C21 BCR a 848 " -0.505 2.00e-02 2.50e+03 pdb=" C22 BCR a 848 " -0.115 2.00e-02 2.50e+03 pdb=" C23 BCR a 848 " 0.138 2.00e-02 2.50e+03 pdb=" C37 BCR a 848 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR B 845 " 0.496 2.00e-02 2.50e+03 2.73e-01 9.31e+02 pdb=" C11 BCR B 845 " -0.319 2.00e-02 2.50e+03 pdb=" C34 BCR B 845 " -0.086 2.00e-02 2.50e+03 pdb=" C8 BCR B 845 " -0.126 2.00e-02 2.50e+03 pdb=" C9 BCR B 845 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR G 845 " 0.496 2.00e-02 2.50e+03 2.73e-01 9.30e+02 pdb=" C11 BCR G 845 " -0.319 2.00e-02 2.50e+03 pdb=" C34 BCR G 845 " -0.086 2.00e-02 2.50e+03 pdb=" C8 BCR G 845 " -0.126 2.00e-02 2.50e+03 pdb=" C9 BCR G 845 " 0.034 2.00e-02 2.50e+03 ... (remaining 18329 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 1021 2.53 - 3.12: 69521 3.12 - 3.71: 148756 3.71 - 4.31: 197339 4.31 - 4.90: 315026 Nonbonded interactions: 731663 Sorted by model distance: nonbonded pdb=" OD2 ASP h 8 " pdb=" OH TYR v 34 " model vdw 1.932 2.440 nonbonded pdb=" O PHE B 612 " pdb=" OG SER B 616 " model vdw 2.002 2.440 nonbonded pdb=" O PHE b 612 " pdb=" OG SER b 616 " model vdw 2.002 2.440 nonbonded pdb=" O PHE g 612 " pdb=" OG SER g 616 " model vdw 2.002 2.440 nonbonded pdb=" O PHE G 612 " pdb=" OG SER G 616 " model vdw 2.003 2.440 ... (remaining 731658 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 'A' and (resid 25 through 752 or resid 804 through 811 or (resid 812 thro \ ugh 814 and (name NB or name ND or name C1A or name C1B or name C1C or name C1D \ or name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name \ C3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or n \ ame CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD \ or name CED or name CGA or name CGD or name CHA or name CHB or name CHC or name \ CHD or name CMA or name CMB or name CMC or name CMD or name NA or name NC or nam \ e O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or resid 815 \ or (resid 816 through 818 and (name NB or name ND or name C1A or name C1B or na \ me C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name C3A o \ r name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or name C \ 4D or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or na \ me CBC or name CBD or name CED or name CGA or name CGD or name CHA or name CHB o \ r name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name N \ A or name NC or name O1A or name O1D or name O2A or name O2D or name OBD or name \ MG )) or resid 819 through 823 or (resid 824 through 825 and (name NB or name N \ D or name C1 or name C1A or name C1B or name C1C or name C1D or name C2 or name \ C2A or name C2B or name C2C or name C2D or name C3 or name C3A or name C3B or na \ me C3C or name C3D or name C4 or name C4A or name C4B or name C4C or name C4D or \ name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or name CB \ C or name CBD or name CED or name CGA or name CGD or name CHA or name CHB or nam \ e CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA or \ name NC or name O1A or name O1D or name O2A or name O2D or name OBD or name MG ) \ ) or resid 826 through 836 or (resid 837 through 839 and (name NB or name ND or \ name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C \ or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name \ C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or \ name CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD \ or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name \ CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or na \ me O2D or name OBD or name MG )) or (resid 840 through 842 and (name NB or name \ ND or name C1 or name C1A or name C1B or name C1C or name C1D or name C2 or name \ C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or \ name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB \ or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name \ CED or name CGA or name CGD or name CHA or name CHB or name CHC or name CHD or \ name CMA or name CMB or name CMC or name CMD or name NA or name NC or name O1A o \ r name O1D or name O2A or name O2D or name OBD or name MG )) or resid 843 throug \ h 844 or resid 849 through 851)) selection = (chain 'E' and (resid 25 through 752 or resid 804 through 811 or (resid 812 thro \ ugh 814 and (name NB or name ND or name C1A or name C1B or name C1C or name C1D \ or name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name \ C3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or n \ ame CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD \ or name CED or name CGA or name CGD or name CHA or name CHB or name CHC or name \ CHD or name CMA or name CMB or name CMC or name CMD or name NA or name NC or nam \ e O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or resid 815 \ or (resid 816 through 818 and (name NB or name ND or name C1A or name C1B or na \ me C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name C3A o \ r name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or name C \ 4D or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or na \ me CBC or name CBD or name CED or name CGA or name CGD or name CHA or name CHB o \ r name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name N \ A or name NC or name O1A or name O1D or name O2A or name O2D or name OBD or name \ MG )) or resid 819 through 823 or (resid 824 through 825 and (name NB or name N \ D or name C1 or name C1A or name C1B or name C1C or name C1D or name C2 or name \ C2A or name C2B or name C2C or name C2D or name C3 or name C3A or name C3B or na \ me C3C or name C3D or name C4 or name C4A or name C4B or name C4C or name C4D or \ name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or name CB \ C or name CBD or name CED or name CGA or name CGD or name CHA or name CHB or nam \ e CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA or \ name NC or name O1A or name O1D or name O2A or name O2D or name OBD or name MG ) \ ) or resid 826 through 836 or (resid 837 through 839 and (name NB or name ND or \ name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C \ or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name \ C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or \ name CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD \ or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name \ CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or na \ me O2D or name OBD or name MG )) or (resid 840 through 842 and (name NB or name \ ND or name C1 or name C1A or name C1B or name C1C or name C1D or name C2 or name \ C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or \ name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB \ or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name \ CED or name CGA or name CGD or name CHA or name CHB or name CHC or name CHD or \ name CMA or name CMB or name CMC or name CMD or name NA or name NC or name O1A o \ r name O1D or name O2A or name O2D or name OBD or name MG )) or resid 843 throug \ h 844 or resid 849 through 851)) selection = (chain 'a' and (resid 25 through 752 or resid 804 through 811 or (resid 812 thro \ ugh 814 and (name NB or name ND or name C1A or name C1B or name C1C or name C1D \ or name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name \ C3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or n \ ame CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD \ or name CED or name CGA or name CGD or name CHA or name CHB or name CHC or name \ CHD or name CMA or name CMB or name CMC or name CMD or name NA or name NC or nam \ e O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or resid 815 \ or (resid 816 through 818 and (name NB or name ND or name C1A or name C1B or na \ me C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name C3A o \ r name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or name C \ 4D or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or na \ me CBC or name CBD or name CED or name CGA or name CGD or name CHA or name CHB o \ r name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name N \ A or name NC or name O1A or name O1D or name O2A or name O2D or name OBD or name \ MG )) or resid 819 through 823 or (resid 824 through 825 and (name NB or name N \ D or name C1 or name C1A or name C1B or name C1C or name C1D or name C2 or name \ C2A or name C2B or name C2C or name C2D or name C3 or name C3A or name C3B or na \ me C3C or name C3D or name C4 or name C4A or name C4B or name C4C or name C4D or \ name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or name CB \ C or name CBD or name CED or name CGA or name CGD or name CHA or name CHB or nam \ e CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA or \ name NC or name O1A or name O1D or name O2A or name O2D or name OBD or name MG ) \ ) or resid 826 through 836 or (resid 837 through 839 and (name NB or name ND or \ name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C \ or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name \ C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or \ name CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD \ or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name \ CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or na \ me O2D or name OBD or name MG )) or (resid 840 through 842 and (name NB or name \ ND or name C1 or name C1A or name C1B or name C1C or name C1D or name C2 or name \ C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or \ name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB \ or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name \ CED or name CGA or name CGD or name CHA or name CHB or name CHC or name CHD or \ name CMA or name CMB or name CMC or name CMD or name NA or name NC or name O1A o \ r name O1D or name O2A or name O2D or name OBD or name MG )) or resid 843 throug \ h 844 or resid 849 through 851)) selection = (chain 'e' and (resid 25 through 752 or resid 804 through 812 or (resid 813 thro \ ugh 814 and (name NB or name ND or name C1A or name C1B or name C1C or name C1D \ or name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name \ C3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or n \ ame CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD \ or name CED or name CGA or name CGD or name CHA or name CHB or name CHC or name \ CHD or name CMA or name CMB or name CMC or name CMD or name NA or name NC or nam \ e O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or resid 815 \ through 817 or (resid 818 and (name NB or name ND or name C1A or name C1B or na \ me C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name C3A o \ r name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or name C \ 4D or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or na \ me CBC or name CBD or name CED or name CGA or name CGD or name CHA or name CHB o \ r name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name N \ A or name NC or name O1A or name O1D or name O2A or name O2D or name OBD or name \ MG )) or (resid 819 and (name NB or name ND or name C1 or name C1A or name C1B \ or name C1C or name C1D or name C2 or name C2A or name C2B or name C2C or name C \ 2D or name C3 or name C3A or name C3B or name C3C or name C3D or name C4 or name \ C4A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or \ name CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA \ or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name \ CMB or name CMC or name CMD or name NA or name NC or name O1A or name O1D or na \ me O2A or name O2D or name OBD or name MG )) or resid 820 through 824 or (resid \ 825 and (name NB or name ND or name C1 or name C1A or name C1B or name C1C or na \ me C1D or name C2 or name C2A or name C2B or name C2C or name C2D or name C3 or \ name C3A or name C3B or name C3C or name C3D or name C4 or name C4A or name C4B \ or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or name \ CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or n \ ame CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CMC \ or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name O2 \ D or name OBD or name MG )) or resid 826 through 837 or (resid 838 through 839 a \ nd (name NB or name ND or name C1A or name C1B or name C1C or name C1D or name C \ 2A or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or na \ me C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB o \ r name CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name C \ ED or name CGA or name CGD or name CHA or name CHB or name CHC or name CHD or na \ me CMA or name CMB or name CMC or name CMD or name NA or name NC or name O1A or \ name O1D or name O2A or name O2D or name OBD or name MG )) or (resid 840 through \ 842 and (name NB or name ND or name C1 or name C1A or name C1B or name C1C or n \ ame C1D or name C2 or name C2A or name C2B or name C2C or name C2D or name C3A o \ r name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or name C \ 4D or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or na \ me CBC or name CBD or name CED or name CGA or name CGD or name CHA or name CHB o \ r name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name N \ A or name NC or name O1A or name O1D or name O2A or name O2D or name OBD or name \ MG )) or resid 843 through 844 or resid 849 through 851)) } ncs_group { reference = (chain 'B' and (resid 3 through 736 or (resid 801 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CGA or name CHA or name CHB or \ name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA \ or name NC or name O1A or name O2A or name OBD or name MG )) or resid 802 or re \ sid 805 through 810 or (resid 811 through 817 and (name NB or name ND or name C1 \ A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or nam \ e C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4B or \ name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or name CB \ A or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or nam \ e CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CMC or \ name CMD or name NA or name NC or name O1A or name O1D or name O2A or name O2D \ or name OBD or name MG )) or resid 818 through 819 or (resid 820 and (name NB or \ name ND or name C1 or name C1A or name C1B or name C1C or name C1D or name C2 o \ r name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name C \ 3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or na \ me CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD o \ r name CED or name CGA or name CGD or name CHA or name CHB or name CHC or name C \ HD or name CMA or name CMB or name CMC or name CMD or name NA or name NC or name \ O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or (resid 821 \ through 825 and (name NB or name ND or name C1A or name C1B or name C1C or name \ C1D or name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or \ name C3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA \ or name CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name \ CBD or name CED or name CGA or name CGD or name CHA or name CHB or name CHC or \ name CHD or name CMA or name CMB or name CMC or name CMD or name NA or name NC o \ r name O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or (res \ id 826 through 827 and (name NB or name ND or name C1 or name C1A or name C1B or \ name C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name C3 \ A or name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or nam \ e C4D or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or \ name CBC or name CBD or name CED or name CGA or name CGD or name CHA or name CH \ B or name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or nam \ e NA or name NC or name O1A or name O1D or name O2A or name O2D or name OBD or n \ ame MG )) or resid 828 through 829 or (resid 830 through 832 and (name NB or nam \ e ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A \ or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name \ CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB \ or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name O \ 2A or name O2D or name OBD or name MG )) or (resid 833 and (name NB or name ND o \ r name C1 or name C1A or name C1B or name C1C or name C1D or name C2 or name C2A \ or name C2B or name C2C or name C2D or name C3 or name C3A or name C3B or name \ C3C or name C3D or name C4 or name C4A or name C4B or name C4C or name C4D or na \ me CAA or name CAB or name CAC or name CAD or name CBA or name CBB or name CBC o \ r name CBD or name CED or name CGA or name CGD or name CHA or name CHB or name C \ HC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA or nam \ e NC or name O1A or name O1D or name O2A or name O2D or name OBD or name MG )) o \ r (resid 834 through 837 and (name NB or name ND or name C1A or name C1B or name \ C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name C3A or \ name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or name C4D \ or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or name \ CBC or name CBD or name CED or name CGA or name CGD or name CHA or name CHB or \ name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA \ or name NC or name O1A or name O1D or name O2A or name O2D or name OBD or name M \ G )) or (resid 838 through 840 and (name NB or name ND or name C1 or name C1A or \ name C1B or name C1C or name C1D or name C2 or name C2A or name C2B or name C2C \ or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name \ C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or \ name CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD \ or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name \ CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or na \ me O2D or name OBD or name MG )) or resid 844 through 847)) selection = (chain 'G' and (resid 3 through 736 or (resid 801 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CGA or name CHA or name CHB or \ name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA \ or name NC or name O1A or name O2A or name OBD or name MG )) or resid 802 or re \ sid 805 through 810 or (resid 811 through 817 and (name NB or name ND or name C1 \ A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or nam \ e C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4B or \ name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or name CB \ A or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or nam \ e CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CMC or \ name CMD or name NA or name NC or name O1A or name O1D or name O2A or name O2D \ or name OBD or name MG )) or resid 818 through 819 or (resid 820 and (name NB or \ name ND or name C1 or name C1A or name C1B or name C1C or name C1D or name C2 o \ r name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name C \ 3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or na \ me CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD o \ r name CED or name CGA or name CGD or name CHA or name CHB or name CHC or name C \ HD or name CMA or name CMB or name CMC or name CMD or name NA or name NC or name \ O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or (resid 821 \ through 825 and (name NB or name ND or name C1A or name C1B or name C1C or name \ C1D or name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or \ name C3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA \ or name CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name \ CBD or name CED or name CGA or name CGD or name CHA or name CHB or name CHC or \ name CHD or name CMA or name CMB or name CMC or name CMD or name NA or name NC o \ r name O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or (res \ id 826 through 827 and (name NB or name ND or name C1 or name C1A or name C1B or \ name C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name C3 \ A or name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or nam \ e C4D or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or \ name CBC or name CBD or name CED or name CGA or name CGD or name CHA or name CH \ B or name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or nam \ e NA or name NC or name O1A or name O1D or name O2A or name O2D or name OBD or n \ ame MG )) or resid 828 through 829 or (resid 830 through 832 and (name NB or nam \ e ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A \ or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name \ CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB \ or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name O \ 2A or name O2D or name OBD or name MG )) or (resid 833 and (name NB or name ND o \ r name C1 or name C1A or name C1B or name C1C or name C1D or name C2 or name C2A \ or name C2B or name C2C or name C2D or name C3 or name C3A or name C3B or name \ C3C or name C3D or name C4 or name C4A or name C4B or name C4C or name C4D or na \ me CAA or name CAB or name CAC or name CAD or name CBA or name CBB or name CBC o \ r name CBD or name CED or name CGA or name CGD or name CHA or name CHB or name C \ HC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA or nam \ e NC or name O1A or name O1D or name O2A or name O2D or name OBD or name MG )) o \ r (resid 834 through 837 and (name NB or name ND or name C1A or name C1B or name \ C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name C3A or \ name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or name C4D \ or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or name \ CBC or name CBD or name CED or name CGA or name CGD or name CHA or name CHB or \ name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA \ or name NC or name O1A or name O1D or name O2A or name O2D or name OBD or name M \ G )) or (resid 838 through 840 and (name NB or name ND or name C1 or name C1A or \ name C1B or name C1C or name C1D or name C2 or name C2A or name C2B or name C2C \ or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name \ C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or \ name CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD \ or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name \ CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or na \ me O2D or name OBD or name MG )) or resid 844 through 847)) selection = (chain 'b' and (resid 3 through 736 or resid 801 through 802 or resid 805 throug \ h 812 or (resid 813 through 817 and (name NB or name ND or name C1A or name C1B \ or name C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name \ C3A or name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or n \ ame C4D or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB \ or name CBC or name CBD or name CED or name CGA or name CGD or name CHA or name \ CHB or name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or n \ ame NA or name NC or name O1A or name O1D or name O2A or name O2D or name OBD or \ name MG )) or resid 818 through 821 or (resid 822 through 825 and (name NB or n \ ame ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B o \ r name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C \ 4A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or na \ me CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA o \ r name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name C \ MB or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or (resid 826 through 827 and (name N \ B or name ND or name C1 or name C1A or name C1B or name C1C or name C1D or name \ C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or n \ ame C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB \ or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name \ CED or name CGA or name CGD or name CHA or name CHB or name CHC or name CHD or n \ ame CMA or name CMB or name CMC or name CMD or name NA or name NC or name O1A or \ name O1D or name O2A or name O2D or name OBD or name MG )) or resid 828 through \ 830 or (resid 831 through 832 and (name NB or name ND or name C1A or name C1B o \ r name C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name C \ 3A or name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or na \ me C4D or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB o \ r name CBC or name CBD or name CED or name CGA or name CGD or name CHA or name C \ HB or name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or na \ me NA or name NC or name O1A or name O1D or name O2A or name O2D or name OBD or \ name MG )) or (resid 833 and (name NB or name ND or name C1 or name C1A or name \ C1B or name C1C or name C1D or name C2 or name C2A or name C2B or name C2C or na \ me C2D or name C3 or name C3A or name C3B or name C3C or name C3D or name C4 or \ name C4A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC \ or name CAD or name CBA or name CBB or name CBC or name CBD or name CED or name \ CGA or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or \ name CMB or name CMC or name CMD or name NA or name NC or name O1A or name O1D o \ r name O2A or name O2D or name OBD or name MG )) or (resid 834 through 837 and ( \ name NB or name ND or name C1A or name C1B or name C1C or name C1D or name C2A o \ r name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or name C \ 3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB or na \ me CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name CED o \ r name CGA or name CGD or name CHA or name CHB or name CHC or name CHD or name C \ MA or name CMB or name CMC or name CMD or name NA or name NC or name O1A or name \ O1D or name O2A or name O2D or name OBD or name MG )) or (resid 838 through 840 \ and (name NB or name ND or name C1 or name C1A or name C1B or name C1C or name \ C1D or name C2 or name C2A or name C2B or name C2C or name C2D or name C3A or na \ me C3B or name C3C or name C3D or name C4A or name C4B or name C4C or name C4D o \ r name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or name C \ BC or name CBD or name CED or name CGA or name CGD or name CHA or name CHB or na \ me CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA or \ name NC or name O1A or name O1D or name O2A or name O2D or name OBD or name MG \ )) or resid 844 through 847)) selection = (chain 'g' and (resid 3 through 736 or (resid 801 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CGA or name CHA or name CHB or \ name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA \ or name NC or name O1A or name O2A or name OBD or name MG )) or resid 802 or re \ sid 805 through 810 or (resid 811 through 817 and (name NB or name ND or name C1 \ A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or nam \ e C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4B or \ name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or name CB \ A or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or nam \ e CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CMC or \ name CMD or name NA or name NC or name O1A or name O1D or name O2A or name O2D \ or name OBD or name MG )) or resid 818 through 819 or (resid 820 and (name NB or \ name ND or name C1 or name C1A or name C1B or name C1C or name C1D or name C2 o \ r name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name C \ 3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or na \ me CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD o \ r name CED or name CGA or name CGD or name CHA or name CHB or name CHC or name C \ HD or name CMA or name CMB or name CMC or name CMD or name NA or name NC or name \ O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or (resid 821 \ through 825 and (name NB or name ND or name C1A or name C1B or name C1C or name \ C1D or name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or \ name C3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA \ or name CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name \ CBD or name CED or name CGA or name CGD or name CHA or name CHB or name CHC or \ name CHD or name CMA or name CMB or name CMC or name CMD or name NA or name NC o \ r name O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or (res \ id 826 through 827 and (name NB or name ND or name C1 or name C1A or name C1B or \ name C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name C3 \ A or name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or nam \ e C4D or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or \ name CBC or name CBD or name CED or name CGA or name CGD or name CHA or name CH \ B or name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or nam \ e NA or name NC or name O1A or name O1D or name O2A or name O2D or name OBD or n \ ame MG )) or resid 828 through 829 or (resid 830 through 832 and (name NB or nam \ e ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or \ name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A \ or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name \ CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB \ or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name O \ 2A or name O2D or name OBD or name MG )) or resid 833 or (resid 834 through 837 \ and (name NB or name ND or name C1A or name C1B or name C1C or name C1D or name \ C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or n \ ame C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB \ or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name \ CED or name CGA or name CGD or name CHA or name CHB or name CHC or name CHD or n \ ame CMA or name CMB or name CMC or name CMD or name NA or name NC or name O1A or \ name O1D or name O2A or name O2D or name OBD or name MG )) or (resid 838 throug \ h 840 and (name NB or name ND or name C1 or name C1A or name C1B or name C1C or \ name C1D or name C2 or name C2A or name C2B or name C2C or name C2D or name C3A \ or name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or name \ C4D or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or n \ ame CBC or name CBD or name CED or name CGA or name CGD or name CHA or name CHB \ or name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name \ NA or name NC or name O1A or name O1D or name O2A or name O2D or name OBD or nam \ e MG )) or resid 844 through 847)) } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'c' selection = chain 'h' } ncs_group { reference = (chain 'D' and resid 7 through 141) selection = chain 'N' selection = chain 'd' selection = (chain 'n' and resid 7 through 141) } ncs_group { reference = (chain 'F' and (resid 24 through 164 or resid 201)) selection = (chain 'O' and (resid 24 through 164 or resid 201)) selection = (chain 'f' and (resid 24 through 164 or resid 201)) selection = (chain 'o' and (resid 24 through 164 or resid 201)) } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'i' selection = chain 'p' } ncs_group { reference = (chain 'J' and (resid 8 through 44 or resid 101)) selection = chain 'Q' selection = chain 'j' selection = (chain 'q' and (resid 8 through 44 or resid 101)) } ncs_group { reference = (chain 'K' and (resid 29 through 93 or resid 102)) selection = (chain 'R' and (resid 29 through 93 or resid 102)) selection = (chain 'k' and (resid 29 through 93 or resid 4002)) selection = (chain 'r' and (resid 29 through 93 or resid 102)) } ncs_group { reference = (chain 'L' and (resid 23 through 172 or resid 203)) selection = (chain 'S' and (resid 23 through 172 or resid 203)) selection = (chain 'l' and (resid 23 through 172 or (resid 203 and (name NB or name ND or na \ me C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C o \ r name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C \ 4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or na \ me CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD o \ r name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name C \ MC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBD or name MG )))) selection = (chain 's' and (resid 23 through 172 or (resid 203 and (name NB or name ND or na \ me C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C o \ r name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C \ 4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or na \ me CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD o \ r name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name C \ MC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBD or name MG )))) } ncs_group { reference = chain 'M' selection = (chain 'T' and resid 19 through 49) selection = (chain 'm' and resid 19 through 49) selection = chain 't' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'v' selection = chain 'w' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 48 7.16 5 P 5 5.49 5 Mg 359 5.21 5 S 308 5.16 5 C 62717 2.51 5 N 13108 2.21 5 O 13851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 17.320 Check model and map are aligned: 1.050 Convert atoms to be neutral: 0.590 Process input model: 188.560 Find NCS groups from input model: 6.910 Set up NCS constraints: 1.170 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 221.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 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 : 0.006 0.244 95557 Z= 0.365 Angle : 0.929 15.589 136125 Z= 0.425 Chirality : 0.050 0.456 11785 Planarity : 0.023 0.292 18332 Dihedral : 21.593 125.745 28416 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.86 % Favored : 85.96 % Rotamer Outliers : 9.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.73 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.08), residues: 8724 helix: -1.76 (0.07), residues: 4110 sheet: -1.93 (0.42), residues: 128 loop : -3.92 (0.08), residues: 4486 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2341 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 688 poor density : 1653 time to evaluate : 6.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 688 outliers final: 134 residues processed: 2063 average time/residue: 0.8490 time to fit residues: 3063.4112 Evaluate side-chains 1055 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 921 time to evaluate : 6.442 Switching outliers to nearest non-outliers outliers start: 134 outliers final: 0 residues processed: 134 average time/residue: 0.6886 time to fit residues: 182.0655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 729 optimal weight: 10.0000 chunk 654 optimal weight: 10.0000 chunk 363 optimal weight: 30.0000 chunk 223 optimal weight: 20.0000 chunk 441 optimal weight: 8.9990 chunk 349 optimal weight: 10.0000 chunk 677 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 chunk 411 optimal weight: 0.8980 chunk 504 optimal weight: 6.9990 chunk 784 optimal weight: 6.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 53 HIS A 80 GLN A 116 GLN A 199 ASN ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN A 539 HIS A 615 GLN A 651 GLN A 657 GLN B 10 GLN B 34 HIS B 41 ASN B 242 HIS B 275 HIS ** B 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN B 332 ASN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS B 367 GLN ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS ** B 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 GLN D 73 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN K 76 HIS ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN E 116 GLN ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 HIS ** E 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 HIS ** E 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 HIS E 615 GLN E 723 GLN G 10 GLN ** G 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS G 41 ASN G 242 HIS G 266 GLN ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 ASN G 332 ASN G 367 GLN G 380 GLN G 531 HIS ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 ASN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS N 140 ASN O 39 GLN O 46 ASN O 55 GLN R 76 HIS T 25 GLN e 51 ASN e 80 GLN e 116 GLN e 199 ASN ** e 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 356 ASN ** e 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 440 HIS ** e 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 539 HIS e 615 GLN ** e 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 657 GLN g 10 GLN g 34 HIS g 41 ASN g 242 HIS g 275 HIS ** g 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 309 ASN g 332 ASN ** g 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 367 GLN g 471 HIS ** g 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 685 HIS g 707 GLN n 73 GLN n 113 GLN n 121 ASN ** n 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 55 GLN q 37 ASN r 76 HIS a 51 ASN a 80 GLN a 116 GLN ** a 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 296 HIS ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 422 ASN a 440 HIS ** a 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 539 HIS a 615 GLN b 10 GLN ** b 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 34 HIS b 242 HIS b 266 GLN ** b 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 309 ASN b 332 ASN b 367 GLN b 531 HIS b 657 HIS ** c 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 56 ASN ** d 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 HIS d 140 ASN f 73 HIS l 48 ASN m 25 GLN Total number of N/Q/H flips: 102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 95557 Z= 0.271 Angle : 0.929 18.212 136125 Z= 0.404 Chirality : 0.051 0.558 11785 Planarity : 0.006 0.106 18332 Dihedral : 20.918 122.291 13334 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.18 % Favored : 87.73 % Rotamer Outliers : 4.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.73 % 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: -3.09 (0.08), residues: 8724 helix: -0.77 (0.08), residues: 4210 sheet: -2.02 (0.41), residues: 146 loop : -3.51 (0.08), residues: 4368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1318 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1003 time to evaluate : 6.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 315 outliers final: 178 residues processed: 1225 average time/residue: 0.8176 time to fit residues: 1775.6922 Evaluate side-chains 990 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 812 time to evaluate : 6.493 Switching outliers to nearest non-outliers outliers start: 178 outliers final: 0 residues processed: 178 average time/residue: 0.6545 time to fit residues: 227.6754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 436 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 653 optimal weight: 5.9990 chunk 534 optimal weight: 5.9990 chunk 216 optimal weight: 40.0000 chunk 786 optimal weight: 5.9990 chunk 849 optimal weight: 4.9990 chunk 700 optimal weight: 0.8980 chunk 779 optimal weight: 5.9990 chunk 267 optimal weight: 0.8980 chunk 630 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN A 657 GLN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 ASN K 88 ASN L 49 ASN M 25 GLN ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 HIS ** E 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 601 HIS G 636 ASN H 15 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN ** N 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 GLN e 53 HIS ** e 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 422 ASN ** e 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 34 HIS ** g 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 355 HIS ** g 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 636 ASN ** n 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 88 ASN a 199 ASN ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 601 ASN ** a 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 715 GLN ** b 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 41 ASN ** b 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 636 ASN c 37 GLN ** d 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 95 GLN d 140 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 95557 Z= 0.250 Angle : 0.840 13.435 136125 Z= 0.373 Chirality : 0.048 0.467 11785 Planarity : 0.006 0.111 18332 Dihedral : 19.635 117.694 13334 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.52 % Favored : 88.47 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.73 % 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: -2.55 (0.09), residues: 8724 helix: -0.33 (0.08), residues: 4214 sheet: -1.77 (0.39), residues: 170 loop : -3.23 (0.09), residues: 4340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 945 time to evaluate : 6.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 207 outliers final: 80 residues processed: 1094 average time/residue: 0.7652 time to fit residues: 1475.1707 Evaluate side-chains 900 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 820 time to evaluate : 6.494 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 0.6722 time to fit residues: 108.0186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 776 optimal weight: 6.9990 chunk 590 optimal weight: 5.9990 chunk 407 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 375 optimal weight: 5.9990 chunk 527 optimal weight: 30.0000 chunk 788 optimal weight: 0.9990 chunk 835 optimal weight: 10.0000 chunk 412 optimal weight: 1.9990 chunk 747 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 HIS A 601 ASN ** B 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN ** B 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 HIS E 370 HIS ** E 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 601 ASN ** E 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 GLN H 37 GLN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 591 HIS g 34 HIS g 156 HIS ** g 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 367 GLN ** g 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 369 HIS a 408 HIS a 459 ASN ** a 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 641 ASN b 158 GLN ** b 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 37 ASN m 25 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 95557 Z= 0.260 Angle : 0.825 12.841 136125 Z= 0.368 Chirality : 0.048 0.440 11785 Planarity : 0.006 0.111 18332 Dihedral : 18.980 117.138 13334 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.82 % Favored : 88.17 % Rotamer Outliers : 3.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.73 % Twisted General : 0.02 % 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: -2.27 (0.09), residues: 8724 helix: -0.14 (0.08), residues: 4230 sheet: -1.61 (0.39), residues: 170 loop : -3.06 (0.09), residues: 4324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 894 time to evaluate : 6.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 260 outliers final: 138 residues processed: 1063 average time/residue: 0.7821 time to fit residues: 1481.9213 Evaluate side-chains 946 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 808 time to evaluate : 6.493 Switching outliers to nearest non-outliers outliers start: 138 outliers final: 0 residues processed: 138 average time/residue: 0.6577 time to fit residues: 179.5973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 695 optimal weight: 6.9990 chunk 474 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 621 optimal weight: 7.9990 chunk 344 optimal weight: 0.0050 chunk 712 optimal weight: 9.9990 chunk 577 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 426 optimal weight: 10.0000 chunk 749 optimal weight: 9.9990 chunk 210 optimal weight: 0.9980 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** L 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 459 ASN E 641 ASN ** G 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 ASN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 369 HIS ** e 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 ASN o 55 GLN ** s 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 352 GLN a 370 HIS a 591 HIS ** b 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 601 HIS ** b 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 25 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 95557 Z= 0.228 Angle : 0.790 13.235 136125 Z= 0.353 Chirality : 0.047 0.439 11785 Planarity : 0.006 0.113 18332 Dihedral : 18.466 115.433 13334 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.15 % Favored : 88.84 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.09), residues: 8724 helix: 0.01 (0.08), residues: 4258 sheet: -1.61 (0.37), residues: 194 loop : -2.96 (0.09), residues: 4272 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 902 time to evaluate : 6.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 76 residues processed: 1026 average time/residue: 0.7638 time to fit residues: 1386.0630 Evaluate side-chains 895 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 819 time to evaluate : 7.826 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 0.6580 time to fit residues: 102.2199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 280 optimal weight: 20.0000 chunk 752 optimal weight: 9.9990 chunk 165 optimal weight: 0.0030 chunk 490 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 835 optimal weight: 0.2980 chunk 693 optimal weight: 3.9990 chunk 387 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 276 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 overall best weight: 2.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 380 GLN G 456 GLN ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 95557 Z= 0.187 Angle : 0.759 13.438 136125 Z= 0.337 Chirality : 0.046 0.392 11785 Planarity : 0.005 0.110 18332 Dihedral : 18.033 114.408 13334 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.02 % 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: -1.85 (0.09), residues: 8724 helix: 0.11 (0.08), residues: 4316 sheet: -0.80 (0.45), residues: 150 loop : -2.80 (0.09), residues: 4258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 917 time to evaluate : 6.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 147 outliers final: 78 residues processed: 1007 average time/residue: 0.7555 time to fit residues: 1349.6735 Evaluate side-chains 899 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 821 time to evaluate : 6.544 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 78 outliers final: 1 residues processed: 78 average time/residue: 0.6525 time to fit residues: 103.4899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 805 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 476 optimal weight: 8.9990 chunk 610 optimal weight: 9.9990 chunk 472 optimal weight: 6.9990 chunk 703 optimal weight: 3.9990 chunk 466 optimal weight: 7.9990 chunk 832 optimal weight: 7.9990 chunk 521 optimal weight: 5.9990 chunk 507 optimal weight: 7.9990 chunk 384 optimal weight: 0.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 HIS ** B 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 HIS ** E 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 GLN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 ASN O 55 GLN e 247 ASN ** e 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 601 ASN e 657 GLN ** g 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 95 GLN ** n 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 352 GLN ** a 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 95557 Z= 0.301 Angle : 0.855 13.172 136125 Z= 0.385 Chirality : 0.050 0.531 11785 Planarity : 0.006 0.117 18332 Dihedral : 18.122 115.119 13334 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.23 % Favored : 87.77 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.73 % 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: -2.05 (0.09), residues: 8724 helix: -0.07 (0.08), residues: 4274 sheet: -1.31 (0.37), residues: 198 loop : -2.84 (0.09), residues: 4252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 845 time to evaluate : 6.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 152 outliers final: 92 residues processed: 950 average time/residue: 0.7684 time to fit residues: 1291.6009 Evaluate side-chains 886 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 794 time to evaluate : 7.423 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 0 residues processed: 92 average time/residue: 0.6815 time to fit residues: 124.5270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 515 optimal weight: 6.9990 chunk 332 optimal weight: 5.9990 chunk 497 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 529 optimal weight: 8.9990 chunk 567 optimal weight: 10.0000 chunk 411 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 654 optimal weight: 1.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 GLN ** G 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 95557 Z= 0.208 Angle : 0.786 18.680 136125 Z= 0.352 Chirality : 0.047 0.438 11785 Planarity : 0.005 0.110 18332 Dihedral : 17.733 111.725 13334 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.09), residues: 8724 helix: 0.11 (0.08), residues: 4294 sheet: -1.17 (0.37), residues: 198 loop : -2.75 (0.09), residues: 4232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 871 time to evaluate : 6.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 54 residues processed: 931 average time/residue: 0.7630 time to fit residues: 1262.6810 Evaluate side-chains 864 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 810 time to evaluate : 6.681 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.6752 time to fit residues: 76.0523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 757 optimal weight: 0.9980 chunk 797 optimal weight: 9.9990 chunk 727 optimal weight: 5.9990 chunk 776 optimal weight: 6.9990 chunk 467 optimal weight: 8.9990 chunk 338 optimal weight: 0.3980 chunk 609 optimal weight: 6.9990 chunk 238 optimal weight: 20.0000 chunk 701 optimal weight: 0.4980 chunk 733 optimal weight: 8.9990 chunk 773 optimal weight: 4.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 140 ASN ** a 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 95557 Z= 0.203 Angle : 0.769 15.772 136125 Z= 0.346 Chirality : 0.046 0.394 11785 Planarity : 0.005 0.112 18332 Dihedral : 17.492 111.124 13334 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.05 % 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: -1.68 (0.09), residues: 8724 helix: 0.23 (0.08), residues: 4282 sheet: -0.89 (0.41), residues: 174 loop : -2.65 (0.09), residues: 4268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 865 time to evaluate : 6.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 38 residues processed: 903 average time/residue: 0.7990 time to fit residues: 1276.3227 Evaluate side-chains 853 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 815 time to evaluate : 6.535 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.7346 time to fit residues: 59.3267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 509 optimal weight: 0.8980 chunk 820 optimal weight: 1.9990 chunk 500 optimal weight: 20.0000 chunk 389 optimal weight: 8.9990 chunk 570 optimal weight: 9.9990 chunk 860 optimal weight: 7.9990 chunk 792 optimal weight: 1.9990 chunk 685 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 529 optimal weight: 0.0270 chunk 420 optimal weight: 0.9980 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 HIS ** B 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** E 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 355 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 685 HIS ** a 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 199 ASN ** a 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 355 HIS ** b 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 95557 Z= 0.176 Angle : 0.749 15.028 136125 Z= 0.336 Chirality : 0.045 0.349 11785 Planarity : 0.005 0.107 18332 Dihedral : 17.190 109.791 13334 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.09), residues: 8724 helix: 0.30 (0.08), residues: 4296 sheet: -1.05 (0.35), residues: 222 loop : -2.56 (0.09), residues: 4206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17448 Ramachandran restraints generated. 8724 Oldfield, 0 Emsley, 8724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 908 time to evaluate : 6.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 920 average time/residue: 0.7900 time to fit residues: 1288.5337 Evaluate side-chains 848 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 838 time to evaluate : 6.516 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.7142 time to fit residues: 21.0703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 544 optimal weight: 5.9990 chunk 730 optimal weight: 0.4980 chunk 209 optimal weight: 2.9990 chunk 632 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 686 optimal weight: 9.9990 chunk 287 optimal weight: 1.9990 chunk 704 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 HIS ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN ** E 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 219 HIS ** a 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.118975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.104066 restraints weight = 335486.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.105507 restraints weight = 223100.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.105761 restraints weight = 177897.985| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 95557 Z= 0.197 Angle : 0.753 15.487 136125 Z= 0.341 Chirality : 0.045 0.334 11785 Planarity : 0.005 0.113 18332 Dihedral : 17.109 111.253 13334 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.09), residues: 8724 helix: 0.35 (0.08), residues: 4300 sheet: -1.30 (0.33), residues: 242 loop : -2.51 (0.09), residues: 4182 =============================================================================== Job complete usr+sys time: 22285.05 seconds wall clock time: 390 minutes 21.64 seconds (23421.64 seconds total)