Starting phenix.real_space_refine on Tue Feb 20 23:04:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qco_13898/02_2024/7qco_13898_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qco_13898/02_2024/7qco_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_13898/02_2024/7qco_13898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qco_13898/02_2024/7qco_13898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qco_13898/02_2024/7qco_13898_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qco_13898/02_2024/7qco_13898_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 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. 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-5238/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: 33.48, per 1000 atoms: 0.37 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: 28.89 Conformation dependent library (CDL) restraints added in 9.3 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: 16.84 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: 31.34 Time building geometry restraints manager: 31.73 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: 39670 25.15 - 50.30: 3518 50.30 - 75.45: 1036 75.45 - 100.60: 233 100.60 - 125.75: 84 Dihedral angle restraints: 44541 sinusoidal: 19489 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 44538 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 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: 3.250 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: 0.080 Extract box with map and model: 15.720 Check model and map are aligned: 1.050 Set scattering table: 0.640 Process input model: 197.700 Find NCS groups from input model: 6.420 Set up NCS constraints: 1.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 228.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 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 : 21.642 125.745 28545 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.86 % Favored : 85.96 % Rotamer: Outliers : 9.61 % Allowed : 7.46 % Favored : 82.92 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a 29 HIS 0.012 0.001 HIS G 471 PHE 0.022 0.002 PHE d 104 TYR 0.024 0.002 TYR E 669 ARG 0.006 0.000 ARG b 695 *********************** 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 : 7.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.7322 (p0) cc_final: 0.6822 (p0) REVERT: A 88 LEU cc_start: 0.8147 (pp) cc_final: 0.7853 (tp) REVERT: A 248 SER cc_start: 0.6562 (OUTLIER) cc_final: 0.6339 (t) REVERT: A 298 HIS cc_start: 0.7100 (m90) cc_final: 0.6686 (m-70) REVERT: A 545 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8163 (t) REVERT: A 745 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7942 (mm-30) REVERT: B 135 LEU cc_start: 0.5444 (pt) cc_final: 0.5234 (mp) REVERT: B 157 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7226 (tp) REVERT: B 425 HIS cc_start: 0.7248 (m90) cc_final: 0.6463 (m-70) REVERT: B 458 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.5696 (tt) REVERT: B 570 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8241 (p) REVERT: B 704 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7786 (t) REVERT: C 9 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7996 (p) REVERT: C 44 THR cc_start: 0.7682 (p) cc_final: 0.7401 (t) REVERT: C 76 SER cc_start: 0.6148 (OUTLIER) cc_final: 0.5718 (p) REVERT: D 52 ARG cc_start: 0.4026 (mmt90) cc_final: 0.3764 (tpp-160) REVERT: D 79 ARG cc_start: 0.8523 (mtt-85) cc_final: 0.8309 (mtt180) REVERT: D 89 TYR cc_start: 0.6949 (m-10) cc_final: 0.6662 (m-80) REVERT: V 6 SER cc_start: 0.3732 (OUTLIER) cc_final: 0.3494 (m) REVERT: F 156 ASP cc_start: 0.5983 (OUTLIER) cc_final: 0.5743 (m-30) REVERT: F 162 SER cc_start: 0.7063 (OUTLIER) cc_final: 0.6692 (t) REVERT: I 10 ILE cc_start: 0.6730 (pt) cc_final: 0.6243 (mt) REVERT: K 52 MET cc_start: 0.4275 (tpp) cc_final: 0.3886 (ttp) REVERT: K 92 LEU cc_start: 0.3214 (OUTLIER) cc_final: 0.2837 (pt) REVERT: L 74 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7877 (tt) REVERT: E 59 PHE cc_start: 0.7225 (m-80) cc_final: 0.6875 (m-80) REVERT: E 249 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6293 (mt) REVERT: E 252 GLU cc_start: 0.5959 (mt-10) cc_final: 0.5486 (tp30) REVERT: E 437 ILE cc_start: 0.7020 (mt) cc_final: 0.6737 (mm) REVERT: E 462 MET cc_start: 0.7073 (mmm) cc_final: 0.6615 (mmm) REVERT: E 599 MET cc_start: 0.8027 (ppp) cc_final: 0.7398 (ppp) REVERT: E 680 TRP cc_start: 0.7623 (t60) cc_final: 0.7400 (t60) REVERT: E 713 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.6743 (p) REVERT: G 96 PHE cc_start: 0.5027 (p90) cc_final: 0.4789 (p90) REVERT: G 129 MET cc_start: 0.5781 (mmp) cc_final: 0.5511 (mmp) REVERT: G 135 LEU cc_start: 0.7019 (pt) cc_final: 0.6524 (mp) REVERT: G 157 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7807 (mt) REVERT: G 162 ARG cc_start: 0.7267 (tpp-160) cc_final: 0.6647 (tpt170) REVERT: G 352 VAL cc_start: 0.8742 (t) cc_final: 0.8411 (t) REVERT: G 384 VAL cc_start: 0.7636 (OUTLIER) cc_final: 0.7392 (m) REVERT: G 450 PHE cc_start: 0.5953 (t80) cc_final: 0.5132 (t80) REVERT: G 695 ARG cc_start: 0.6336 (ptt-90) cc_final: 0.4810 (tpt-90) REVERT: N 43 MET cc_start: 0.6771 (ptp) cc_final: 0.6464 (ptm) REVERT: O 164 ARG cc_start: 0.4036 (mpt90) cc_final: 0.3365 (ttp80) REVERT: e 58 ASP cc_start: 0.7286 (p0) cc_final: 0.6909 (p0) REVERT: e 88 LEU cc_start: 0.8147 (pp) cc_final: 0.7106 (tp) REVERT: e 298 HIS cc_start: 0.7112 (m90) cc_final: 0.6675 (m-70) REVERT: e 545 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8036 (t) REVERT: e 599 MET cc_start: 0.8477 (ppp) cc_final: 0.8200 (ppp) REVERT: g 157 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7319 (tp) REVERT: g 226 PHE cc_start: 0.5964 (m-80) cc_final: 0.5429 (m-80) REVERT: g 425 HIS cc_start: 0.7575 (m90) cc_final: 0.7020 (m90) REVERT: g 563 ASP cc_start: 0.7696 (m-30) cc_final: 0.7495 (t0) REVERT: g 570 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8038 (p) REVERT: g 704 SER cc_start: 0.7566 (OUTLIER) cc_final: 0.7203 (t) REVERT: h 9 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7930 (p) REVERT: h 27 MET cc_start: 0.6365 (mmm) cc_final: 0.6104 (mmt) REVERT: h 76 SER cc_start: 0.6891 (OUTLIER) cc_final: 0.6691 (p) REVERT: n 79 ARG cc_start: 0.8574 (mtt-85) cc_final: 0.8288 (mtt180) REVERT: v 56 THR cc_start: 0.3599 (OUTLIER) cc_final: 0.3198 (p) REVERT: o 156 ASP cc_start: 0.6278 (OUTLIER) cc_final: 0.5964 (m-30) REVERT: p 6 PHE cc_start: 0.5925 (p90) cc_final: 0.5101 (m-80) REVERT: p 14 LEU cc_start: 0.8047 (pt) cc_final: 0.7767 (pp) REVERT: q 39 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6993 (tp) REVERT: r 52 MET cc_start: 0.4583 (tpp) cc_final: 0.4168 (ttp) REVERT: r 92 LEU cc_start: 0.3309 (OUTLIER) cc_final: 0.2954 (pt) REVERT: a 153 PHE cc_start: 0.4467 (m-80) cc_final: 0.4254 (m-80) REVERT: a 462 MET cc_start: 0.6816 (mmm) cc_final: 0.6456 (mmm) REVERT: a 583 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7957 (p) REVERT: a 599 MET cc_start: 0.7926 (ppp) cc_final: 0.7568 (ppp) REVERT: a 611 SER cc_start: 0.7640 (OUTLIER) cc_final: 0.7072 (p) REVERT: b 96 PHE cc_start: 0.4788 (p90) cc_final: 0.4435 (p90) REVERT: b 129 MET cc_start: 0.5607 (mmp) cc_final: 0.5322 (mmp) REVERT: b 135 LEU cc_start: 0.7000 (pt) cc_final: 0.6559 (mp) REVERT: b 352 VAL cc_start: 0.8691 (t) cc_final: 0.8373 (t) REVERT: b 384 VAL cc_start: 0.7742 (OUTLIER) cc_final: 0.7532 (m) REVERT: b 450 PHE cc_start: 0.6023 (t80) cc_final: 0.5185 (t80) REVERT: b 695 ARG cc_start: 0.6314 (ptt-90) cc_final: 0.5012 (tpt-90) REVERT: d 43 MET cc_start: 0.6848 (ptp) cc_final: 0.6602 (ptm) REVERT: j 32 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8216 (tp) REVERT: m 43 LEU cc_start: 0.9237 (tp) cc_final: 0.8968 (tt) outliers start: 688 outliers final: 134 residues processed: 2063 average time/residue: 0.8008 time to fit residues: 2869.4664 Evaluate side-chains 1108 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 943 time to evaluate : 6.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain V residue 6 SER Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 621 THR Chi-restraints excluded: chain E residue 699 GLU Chi-restraints excluded: chain E residue 713 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 348 ILE Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 440 LEU Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 522 VAL Chi-restraints excluded: chain G residue 543 ASP Chi-restraints excluded: chain G residue 623 LEU Chi-restraints excluded: chain G residue 635 ILE Chi-restraints excluded: chain G residue 692 SER Chi-restraints excluded: chain G residue 697 LYS Chi-restraints excluded: chain G residue 729 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 159 ILE Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 106 SER Chi-restraints excluded: chain e residue 128 ASN Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 303 VAL Chi-restraints excluded: chain e residue 355 THR Chi-restraints excluded: chain e residue 360 LEU Chi-restraints excluded: chain e residue 431 ILE Chi-restraints excluded: chain e residue 545 VAL Chi-restraints excluded: chain e residue 546 THR Chi-restraints excluded: chain e residue 575 CYS Chi-restraints excluded: chain e residue 590 ASP Chi-restraints excluded: chain e residue 664 SER Chi-restraints excluded: chain e residue 699 GLU Chi-restraints excluded: chain e residue 750 SER Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 157 LEU Chi-restraints excluded: chain g residue 195 VAL Chi-restraints excluded: chain g residue 214 THR Chi-restraints excluded: chain g residue 216 LEU Chi-restraints excluded: chain g residue 345 LEU Chi-restraints excluded: chain g residue 440 LEU Chi-restraints excluded: chain g residue 487 SER Chi-restraints excluded: chain g residue 522 VAL Chi-restraints excluded: chain g residue 570 THR Chi-restraints excluded: chain g residue 659 VAL Chi-restraints excluded: chain g residue 692 SER Chi-restraints excluded: chain g residue 697 LYS Chi-restraints excluded: chain g residue 704 SER Chi-restraints excluded: chain h residue 9 THR Chi-restraints excluded: chain h residue 76 SER Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 56 THR Chi-restraints excluded: chain v residue 59 VAL Chi-restraints excluded: chain o residue 156 ASP Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain q residue 39 LEU Chi-restraints excluded: chain r residue 92 LEU Chi-restraints excluded: chain s residue 101 MET Chi-restraints excluded: chain s residue 151 VAL Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 34 LEU Chi-restraints excluded: chain t residue 38 VAL Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain a residue 365 ILE Chi-restraints excluded: chain a residue 546 THR Chi-restraints excluded: chain a residue 575 CYS Chi-restraints excluded: chain a residue 583 THR Chi-restraints excluded: chain a residue 611 SER Chi-restraints excluded: chain a residue 621 THR Chi-restraints excluded: chain a residue 699 GLU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 216 LEU Chi-restraints excluded: chain b residue 283 LEU Chi-restraints excluded: chain b residue 348 ILE Chi-restraints excluded: chain b residue 377 THR Chi-restraints excluded: chain b residue 384 VAL Chi-restraints excluded: chain b residue 440 LEU Chi-restraints excluded: chain b residue 475 LEU Chi-restraints excluded: chain b residue 522 VAL Chi-restraints excluded: chain b residue 543 ASP Chi-restraints excluded: chain b residue 623 LEU Chi-restraints excluded: chain b residue 635 ILE Chi-restraints excluded: chain b residue 659 VAL Chi-restraints excluded: chain b residue 692 SER Chi-restraints excluded: chain b residue 697 LYS Chi-restraints excluded: chain b residue 729 ILE Chi-restraints excluded: chain c residue 25 LEU Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 21 VAL Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain f residue 34 SER Chi-restraints excluded: chain f residue 43 SER Chi-restraints excluded: chain f residue 156 ASP Chi-restraints excluded: chain f residue 159 ILE Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain m residue 30 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 729 optimal weight: 9.9990 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: 9.9990 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: 4.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN 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 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 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 HIS A 615 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 ** 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 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 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: 99 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2295 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= 0.264 Angle : 0.913 19.276 136125 Z= 0.398 Chirality : 0.050 0.511 11785 Planarity : 0.006 0.106 18332 Dihedral : 21.451 123.493 13724 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.02 % Favored : 87.91 % Rotamer: Outliers : 5.60 % Allowed : 18.18 % Favored : 76.22 % 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: -3.08 (0.08), residues: 8724 helix: -0.78 (0.08), residues: 4218 sheet: -1.31 (0.51), residues: 98 loop : -3.51 (0.08), residues: 4408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP e 87 HIS 0.031 0.003 HIS a 297 PHE 0.045 0.002 PHE a 610 TYR 0.026 0.002 TYR G 626 ARG 0.004 0.001 ARG g 223 *********************** 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 1418 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 401 poor density : 1017 time to evaluate : 6.577 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: A 58 ASP cc_start: 0.7416 (p0) cc_final: 0.7035 (p0) REVERT: A 88 LEU cc_start: 0.8159 (pp) cc_final: 0.7136 (tp) REVERT: A 180 HIS cc_start: 0.6353 (OUTLIER) cc_final: 0.5583 (t-90) REVERT: A 248 SER cc_start: 0.6385 (OUTLIER) cc_final: 0.6179 (t) REVERT: A 298 HIS cc_start: 0.6836 (m90) cc_final: 0.6459 (m-70) REVERT: A 360 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8328 (tt) REVERT: A 599 MET cc_start: 0.8369 (ppp) cc_final: 0.8153 (ppp) REVERT: A 745 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8043 (mm-30) REVERT: B 135 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.5573 (pp) REVERT: B 435 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7538 (t80) REVERT: B 562 CYS cc_start: 0.6723 (OUTLIER) cc_final: 0.5636 (m) REVERT: B 570 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8524 (p) REVERT: B 574 SER cc_start: 0.6845 (OUTLIER) cc_final: 0.6374 (t) REVERT: B 704 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.8020 (t) REVERT: C 9 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7901 (p) REVERT: C 77 MET cc_start: 0.7344 (mmm) cc_final: 0.7050 (mmm) REVERT: D 79 ARG cc_start: 0.8576 (mtt-85) cc_final: 0.8195 (mtt180) REVERT: D 89 TYR cc_start: 0.6903 (m-10) cc_final: 0.6697 (m-80) REVERT: F 118 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6225 (pm20) REVERT: K 52 MET cc_start: 0.4527 (tpp) cc_final: 0.4126 (ttp) REVERT: L 74 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8097 (tt) REVERT: E 91 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7798 (ptt) REVERT: E 197 MET cc_start: 0.7836 (tpp) cc_final: 0.7632 (tpp) REVERT: E 252 GLU cc_start: 0.6136 (mt-10) cc_final: 0.5613 (tp30) REVERT: E 514 VAL cc_start: 0.7293 (OUTLIER) cc_final: 0.7084 (p) REVERT: E 723 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7138 (tp-100) REVERT: G 96 PHE cc_start: 0.5543 (p90) cc_final: 0.5301 (p90) REVERT: G 129 MET cc_start: 0.5906 (mmp) cc_final: 0.5625 (mmp) REVERT: G 135 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6683 (mp) REVERT: G 319 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7493 (m-80) REVERT: G 352 VAL cc_start: 0.8851 (t) cc_final: 0.8476 (t) REVERT: G 380 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6903 (mt0) REVERT: G 450 PHE cc_start: 0.5768 (t80) cc_final: 0.4928 (t80) REVERT: G 695 ARG cc_start: 0.6824 (ptt-90) cc_final: 0.4865 (tpt-90) REVERT: G 697 LYS cc_start: 0.4513 (tmtt) cc_final: 0.4220 (tmtt) REVERT: N 43 MET cc_start: 0.6598 (ptp) cc_final: 0.6351 (ptm) REVERT: N 77 LYS cc_start: 0.5487 (OUTLIER) cc_final: 0.5141 (mtmm) REVERT: W 39 ARG cc_start: 0.7392 (mtm180) cc_final: 0.6950 (mtm180) REVERT: O 164 ARG cc_start: 0.4533 (mpt90) cc_final: 0.3883 (ttp80) REVERT: Q 23 PHE cc_start: 0.7971 (m-80) cc_final: 0.7721 (m-80) REVERT: S 104 ILE cc_start: 0.8920 (pt) cc_final: 0.8690 (mt) REVERT: e 58 ASP cc_start: 0.7344 (p0) cc_final: 0.6953 (p0) REVERT: e 173 MET cc_start: 0.6245 (ptt) cc_final: 0.5071 (ptp) REVERT: e 180 HIS cc_start: 0.6237 (OUTLIER) cc_final: 0.5495 (t-90) REVERT: e 298 HIS cc_start: 0.6901 (m90) cc_final: 0.6500 (m-70) REVERT: e 360 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8426 (tt) REVERT: e 599 MET cc_start: 0.8530 (ppp) cc_final: 0.8146 (ppp) REVERT: g 142 LEU cc_start: 0.7335 (pt) cc_final: 0.6793 (tp) REVERT: g 562 CYS cc_start: 0.7112 (OUTLIER) cc_final: 0.5610 (m) REVERT: g 570 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8303 (p) REVERT: g 574 SER cc_start: 0.6677 (OUTLIER) cc_final: 0.6216 (t) REVERT: g 704 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.7742 (t) REVERT: h 9 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7629 (p) REVERT: n 89 TYR cc_start: 0.7368 (m-80) cc_final: 0.6975 (m-80) REVERT: v 56 THR cc_start: 0.3691 (OUTLIER) cc_final: 0.3459 (p) REVERT: v 62 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5846 (pm20) REVERT: p 6 PHE cc_start: 0.5947 (p90) cc_final: 0.5290 (m-80) REVERT: p 14 LEU cc_start: 0.8032 (pt) cc_final: 0.7799 (pp) REVERT: r 52 MET cc_start: 0.4819 (tpp) cc_final: 0.4549 (ttp) REVERT: a 91 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7701 (ptt) REVERT: a 153 PHE cc_start: 0.4588 (m-80) cc_final: 0.4312 (m-80) REVERT: a 197 MET cc_start: 0.7347 (tpp) cc_final: 0.7036 (tpp) REVERT: a 462 MET cc_start: 0.6885 (mmm) cc_final: 0.6577 (mmm) REVERT: a 514 VAL cc_start: 0.7293 (OUTLIER) cc_final: 0.7041 (p) REVERT: a 599 MET cc_start: 0.8041 (ppp) cc_final: 0.7443 (ppp) REVERT: a 611 SER cc_start: 0.7485 (OUTLIER) cc_final: 0.7029 (p) REVERT: b 96 PHE cc_start: 0.5197 (p90) cc_final: 0.4965 (p90) REVERT: b 129 MET cc_start: 0.5582 (mmp) cc_final: 0.5296 (mmp) REVERT: b 135 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6550 (mp) REVERT: b 450 PHE cc_start: 0.6216 (t80) cc_final: 0.5220 (t80) REVERT: b 695 ARG cc_start: 0.6641 (ptt-90) cc_final: 0.5109 (tpt-90) REVERT: d 127 ASP cc_start: 0.6092 (OUTLIER) cc_final: 0.5786 (p0) REVERT: w 39 ARG cc_start: 0.7302 (mtm180) cc_final: 0.6977 (mtm180) REVERT: l 68 MET cc_start: 0.7999 (mtt) cc_final: 0.7757 (ptp) REVERT: l 104 ILE cc_start: 0.8791 (pt) cc_final: 0.8497 (mt) REVERT: m 47 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7992 (tt) outliers start: 401 outliers final: 224 residues processed: 1292 average time/residue: 0.7678 time to fit residues: 1751.8328 Evaluate side-chains 1109 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 851 time to evaluate : 6.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain V residue 40 PHE Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 61 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 37 PHE Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 520 LYS Chi-restraints excluded: chain E residue 590 ASP Chi-restraints excluded: chain E residue 621 THR Chi-restraints excluded: chain E residue 702 VAL Chi-restraints excluded: chain E residue 723 GLN Chi-restraints excluded: chain E residue 745 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain G residue 380 GLN Chi-restraints excluded: chain G residue 419 LYS Chi-restraints excluded: chain G residue 435 PHE Chi-restraints excluded: chain G residue 440 LEU Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 505 ASN Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 543 ASP Chi-restraints excluded: chain G residue 562 CYS Chi-restraints excluded: chain G residue 574 SER Chi-restraints excluded: chain G residue 635 ILE Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain G residue 662 THR Chi-restraints excluded: chain G residue 729 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 140 ASN Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain O residue 159 ILE Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 78 PHE Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 128 ASN Chi-restraints excluded: chain e residue 180 HIS Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 266 THR Chi-restraints excluded: chain e residue 360 LEU Chi-restraints excluded: chain e residue 400 PHE Chi-restraints excluded: chain e residue 431 ILE Chi-restraints excluded: chain e residue 456 TYR Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 590 ASP Chi-restraints excluded: chain e residue 684 LEU Chi-restraints excluded: chain e residue 750 SER Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 206 HIS Chi-restraints excluded: chain g residue 214 THR Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 216 LEU Chi-restraints excluded: chain g residue 278 LEU Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 315 THR Chi-restraints excluded: chain g residue 345 LEU Chi-restraints excluded: chain g residue 435 PHE Chi-restraints excluded: chain g residue 475 LEU Chi-restraints excluded: chain g residue 522 VAL Chi-restraints excluded: chain g residue 530 ILE Chi-restraints excluded: chain g residue 552 ASP Chi-restraints excluded: chain g residue 562 CYS Chi-restraints excluded: chain g residue 570 THR Chi-restraints excluded: chain g residue 574 SER Chi-restraints excluded: chain g residue 589 THR Chi-restraints excluded: chain g residue 623 LEU Chi-restraints excluded: chain g residue 654 LEU Chi-restraints excluded: chain g residue 658 LEU Chi-restraints excluded: chain g residue 688 THR Chi-restraints excluded: chain g residue 692 SER Chi-restraints excluded: chain g residue 704 SER Chi-restraints excluded: chain h residue 9 THR Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 108 VAL Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 11 LEU Chi-restraints excluded: chain v residue 41 ASP Chi-restraints excluded: chain v residue 56 THR Chi-restraints excluded: chain v residue 59 VAL Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain v residue 62 GLU Chi-restraints excluded: chain o residue 92 LEU Chi-restraints excluded: chain o residue 158 GLU Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain r residue 37 PHE Chi-restraints excluded: chain s residue 88 ASP Chi-restraints excluded: chain s residue 124 VAL Chi-restraints excluded: chain s residue 151 VAL Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain t residue 38 VAL Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 236 ASP Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain a residue 382 THR Chi-restraints excluded: chain a residue 400 PHE Chi-restraints excluded: chain a residue 450 PHE Chi-restraints excluded: chain a residue 514 VAL Chi-restraints excluded: chain a residue 520 LYS Chi-restraints excluded: chain a residue 571 PHE Chi-restraints excluded: chain a residue 583 THR Chi-restraints excluded: chain a residue 590 ASP Chi-restraints excluded: chain a residue 611 SER Chi-restraints excluded: chain a residue 621 THR Chi-restraints excluded: chain a residue 702 VAL Chi-restraints excluded: chain a residue 740 ILE Chi-restraints excluded: chain a residue 745 GLU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 56 ILE Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 141 PHE Chi-restraints excluded: chain b residue 216 LEU Chi-restraints excluded: chain b residue 280 ILE Chi-restraints excluded: chain b residue 283 LEU Chi-restraints excluded: chain b residue 315 THR Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 350 SER Chi-restraints excluded: chain b residue 440 LEU Chi-restraints excluded: chain b residue 475 LEU Chi-restraints excluded: chain b residue 515 ILE Chi-restraints excluded: chain b residue 543 ASP Chi-restraints excluded: chain b residue 562 CYS Chi-restraints excluded: chain b residue 574 SER Chi-restraints excluded: chain b residue 635 ILE Chi-restraints excluded: chain b residue 662 THR Chi-restraints excluded: chain b residue 685 HIS Chi-restraints excluded: chain b residue 729 ILE Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain d residue 69 LEU Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 21 VAL Chi-restraints excluded: chain w residue 30 SER Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain f residue 43 SER Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 34 VAL Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 92 LEU Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 25 GLN Chi-restraints excluded: chain m residue 30 LEU Chi-restraints excluded: chain m residue 47 LEU 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: 8.9990 chunk 653 optimal weight: 5.9990 chunk 534 optimal weight: 7.9990 chunk 216 optimal weight: 40.0000 chunk 786 optimal weight: 8.9990 chunk 849 optimal weight: 2.9990 chunk 700 optimal weight: 0.9990 chunk 779 optimal weight: 5.9990 chunk 267 optimal weight: 6.9990 chunk 630 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 296 HIS ** 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 A 601 ASN A 657 GLN B 34 HIS ** B 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS B 444 ASN ** B 456 GLN ** 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 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 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 654 GLN ** 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 380 GLN G 636 ASN G 644 ASN H 15 GLN ** N 95 GLN ** 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 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 156 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** ** a 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 158 GLN ** b 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 636 ASN ** c 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 95 GLN d 140 ASN m 25 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 95557 Z= 0.283 Angle : 0.867 14.606 136125 Z= 0.384 Chirality : 0.049 0.547 11785 Planarity : 0.006 0.108 18332 Dihedral : 20.217 117.945 13580 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.14 % Favored : 87.83 % Rotamer: Outliers : 5.73 % Allowed : 20.81 % Favored : 73.46 % 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: -2.61 (0.09), residues: 8724 helix: -0.40 (0.08), residues: 4226 sheet: -1.81 (0.39), residues: 172 loop : -3.25 (0.09), residues: 4326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP b 660 HIS 0.024 0.002 HIS b 379 PHE 0.056 0.002 PHE A 85 TYR 0.040 0.002 TYR b 626 ARG 0.009 0.001 ARG j 13 *********************** 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 1349 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 410 poor density : 939 time to evaluate : 6.736 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: A 58 ASP cc_start: 0.7480 (p0) cc_final: 0.7035 (p0) REVERT: A 78 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7661 (m-80) REVERT: A 180 HIS cc_start: 0.6500 (OUTLIER) cc_final: 0.5733 (t-90) REVERT: A 298 HIS cc_start: 0.6941 (m90) cc_final: 0.6347 (m-70) REVERT: A 599 MET cc_start: 0.8420 (ppp) cc_final: 0.8187 (ppp) REVERT: A 601 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7907 (t160) REVERT: A 672 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7509 (pp) REVERT: A 745 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8083 (mm-30) REVERT: B 435 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7629 (t80) REVERT: B 570 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8656 (p) REVERT: B 704 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.8193 (t) REVERT: C 9 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7611 (p) REVERT: D 89 TYR cc_start: 0.7059 (m-10) cc_final: 0.6774 (m-80) REVERT: F 118 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7014 (pt0) REVERT: K 52 MET cc_start: 0.4592 (tpp) cc_final: 0.4318 (ttp) REVERT: L 74 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8401 (tt) REVERT: E 61 THR cc_start: 0.7939 (p) cc_final: 0.7704 (t) REVERT: E 91 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7663 (ptt) REVERT: E 197 MET cc_start: 0.7654 (tpp) cc_final: 0.7342 (tpp) REVERT: E 252 GLU cc_start: 0.5806 (mt-10) cc_final: 0.5438 (tp30) REVERT: E 370 HIS cc_start: 0.6311 (OUTLIER) cc_final: 0.5923 (t-170) REVERT: E 514 VAL cc_start: 0.7263 (OUTLIER) cc_final: 0.7042 (p) REVERT: E 741 TRP cc_start: 0.7660 (p-90) cc_final: 0.7304 (p-90) REVERT: G 96 PHE cc_start: 0.5392 (p90) cc_final: 0.5174 (p90) REVERT: G 129 MET cc_start: 0.5905 (mmp) cc_final: 0.5637 (mmp) REVERT: G 450 PHE cc_start: 0.5804 (t80) cc_final: 0.4847 (t80) REVERT: G 685 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.7204 (t-90) REVERT: G 695 ARG cc_start: 0.7086 (ptt-90) cc_final: 0.5113 (tpt-90) REVERT: N 43 MET cc_start: 0.6589 (ptp) cc_final: 0.6333 (ptm) REVERT: N 77 LYS cc_start: 0.5755 (OUTLIER) cc_final: 0.5395 (mtmm) REVERT: W 39 ARG cc_start: 0.7281 (mtm180) cc_final: 0.6844 (mtm180) REVERT: W 55 GLU cc_start: 0.2686 (tp30) cc_final: 0.1478 (tt0) REVERT: O 164 ARG cc_start: 0.4657 (mpt90) cc_final: 0.4269 (ttp80) REVERT: R 54 LEU cc_start: 0.4109 (OUTLIER) cc_final: 0.3776 (tt) REVERT: S 104 ILE cc_start: 0.8921 (pt) cc_final: 0.8693 (mt) REVERT: e 34 HIS cc_start: 0.3564 (OUTLIER) cc_final: 0.2591 (t70) REVERT: e 58 ASP cc_start: 0.7399 (p0) cc_final: 0.6927 (p0) REVERT: e 81 LEU cc_start: 0.8842 (pp) cc_final: 0.8619 (pp) REVERT: e 173 MET cc_start: 0.6102 (ptt) cc_final: 0.5537 (ptp) REVERT: e 180 HIS cc_start: 0.6367 (OUTLIER) cc_final: 0.5642 (t-90) REVERT: e 298 HIS cc_start: 0.7015 (m90) cc_final: 0.6475 (m-70) REVERT: e 471 MET cc_start: 0.6123 (tmm) cc_final: 0.5167 (tmm) REVERT: e 599 MET cc_start: 0.8446 (ppp) cc_final: 0.8093 (ppp) REVERT: e 672 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7613 (pp) REVERT: g 305 LEU cc_start: 0.7220 (mp) cc_final: 0.6948 (mp) REVERT: g 435 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7361 (t80) REVERT: g 570 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8373 (p) REVERT: g 574 SER cc_start: 0.6787 (OUTLIER) cc_final: 0.6197 (t) REVERT: g 652 MET cc_start: 0.7257 (mmt) cc_final: 0.6810 (mmt) REVERT: g 704 SER cc_start: 0.8184 (OUTLIER) cc_final: 0.7869 (t) REVERT: h 9 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7560 (p) REVERT: n 89 TYR cc_start: 0.7420 (m-80) cc_final: 0.7103 (m-80) REVERT: v 56 THR cc_start: 0.3436 (OUTLIER) cc_final: 0.3062 (p) REVERT: p 1 MET cc_start: 0.6718 (tmm) cc_final: 0.6167 (tmm) REVERT: p 6 PHE cc_start: 0.6009 (p90) cc_final: 0.5210 (m-80) REVERT: r 52 MET cc_start: 0.5002 (tpp) cc_final: 0.4715 (ttp) REVERT: a 91 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7581 (ptt) REVERT: a 153 PHE cc_start: 0.4644 (m-80) cc_final: 0.4223 (m-80) REVERT: a 197 MET cc_start: 0.7769 (tpp) cc_final: 0.7485 (tpp) REVERT: a 333 PHE cc_start: 0.3477 (t80) cc_final: 0.3242 (t80) REVERT: a 344 ASN cc_start: 0.7452 (OUTLIER) cc_final: 0.7150 (p0) REVERT: a 462 MET cc_start: 0.7108 (mmm) cc_final: 0.6745 (mmm) REVERT: a 514 VAL cc_start: 0.7289 (OUTLIER) cc_final: 0.7050 (p) REVERT: a 599 MET cc_start: 0.8038 (ppp) cc_final: 0.7480 (ppp) REVERT: b 129 MET cc_start: 0.5756 (mmp) cc_final: 0.5493 (mmp) REVERT: b 450 PHE cc_start: 0.5728 (t80) cc_final: 0.4661 (t80) REVERT: b 695 ARG cc_start: 0.6797 (ptt-90) cc_final: 0.5232 (tpt-90) REVERT: d 26 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6543 (tm-30) REVERT: d 127 ASP cc_start: 0.5925 (OUTLIER) cc_final: 0.5573 (p0) REVERT: w 39 ARG cc_start: 0.7302 (mtm180) cc_final: 0.6888 (mtm180) REVERT: l 104 ILE cc_start: 0.8836 (pt) cc_final: 0.8551 (mt) outliers start: 410 outliers final: 247 residues processed: 1232 average time/residue: 0.7622 time to fit residues: 1664.1472 Evaluate side-chains 1097 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 821 time to evaluate : 6.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain V residue 40 PHE Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 37 PHE Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain E residue 28 LYS Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 520 LYS Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 565 ASP Chi-restraints excluded: chain E residue 583 THR Chi-restraints excluded: chain E residue 590 ASP Chi-restraints excluded: chain E residue 621 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 327 TYR Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain G residue 419 LYS Chi-restraints excluded: chain G residue 435 PHE Chi-restraints excluded: chain G residue 440 LEU Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 505 ASN Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 562 CYS Chi-restraints excluded: chain G residue 570 THR Chi-restraints excluded: chain G residue 574 SER Chi-restraints excluded: chain G residue 685 HIS Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 138 THR Chi-restraints excluded: chain N residue 140 ASN Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain O residue 159 ILE Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain R residue 37 PHE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 78 PHE Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain e residue 34 HIS Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 180 HIS Chi-restraints excluded: chain e residue 266 THR Chi-restraints excluded: chain e residue 400 PHE Chi-restraints excluded: chain e residue 431 ILE Chi-restraints excluded: chain e residue 456 TYR Chi-restraints excluded: chain e residue 457 ILE Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 590 ASP Chi-restraints excluded: chain e residue 609 HIS Chi-restraints excluded: chain e residue 657 GLN Chi-restraints excluded: chain e residue 672 LEU Chi-restraints excluded: chain e residue 684 LEU Chi-restraints excluded: chain e residue 738 VAL Chi-restraints excluded: chain e residue 750 SER Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain g residue 206 HIS Chi-restraints excluded: chain g residue 214 THR Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 278 LEU Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 315 THR Chi-restraints excluded: chain g residue 376 TYR Chi-restraints excluded: chain g residue 435 PHE Chi-restraints excluded: chain g residue 456 GLN Chi-restraints excluded: chain g residue 475 LEU Chi-restraints excluded: chain g residue 552 ASP Chi-restraints excluded: chain g residue 570 THR Chi-restraints excluded: chain g residue 574 SER Chi-restraints excluded: chain g residue 589 THR Chi-restraints excluded: chain g residue 623 LEU Chi-restraints excluded: chain g residue 651 TRP Chi-restraints excluded: chain g residue 654 LEU Chi-restraints excluded: chain g residue 658 LEU Chi-restraints excluded: chain g residue 688 THR Chi-restraints excluded: chain g residue 692 SER Chi-restraints excluded: chain g residue 704 SER Chi-restraints excluded: chain g residue 722 LEU Chi-restraints excluded: chain h residue 9 THR Chi-restraints excluded: chain n residue 51 MET Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 104 PHE Chi-restraints excluded: chain n residue 108 VAL Chi-restraints excluded: chain v residue 11 LEU Chi-restraints excluded: chain v residue 41 ASP Chi-restraints excluded: chain v residue 56 THR Chi-restraints excluded: chain v residue 59 VAL Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain o residue 34 SER Chi-restraints excluded: chain o residue 156 ASP Chi-restraints excluded: chain o residue 162 SER Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain r residue 34 VAL Chi-restraints excluded: chain r residue 37 PHE Chi-restraints excluded: chain s residue 86 ASP Chi-restraints excluded: chain s residue 88 ASP Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 124 VAL Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain t residue 38 VAL Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 236 ASP Chi-restraints excluded: chain a residue 285 VAL Chi-restraints excluded: chain a residue 344 ASN Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain a residue 400 PHE Chi-restraints excluded: chain a residue 450 PHE Chi-restraints excluded: chain a residue 514 VAL Chi-restraints excluded: chain a residue 526 ILE Chi-restraints excluded: chain a residue 565 ASP Chi-restraints excluded: chain a residue 571 PHE Chi-restraints excluded: chain a residue 583 THR Chi-restraints excluded: chain a residue 590 ASP Chi-restraints excluded: chain a residue 621 THR Chi-restraints excluded: chain a residue 702 VAL Chi-restraints excluded: chain a residue 740 ILE Chi-restraints excluded: chain a residue 745 GLU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 56 ILE Chi-restraints excluded: chain b residue 134 ASP Chi-restraints excluded: chain b residue 141 PHE Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 215 THR Chi-restraints excluded: chain b residue 216 LEU Chi-restraints excluded: chain b residue 315 THR Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 327 TYR Chi-restraints excluded: chain b residue 350 SER Chi-restraints excluded: chain b residue 440 LEU Chi-restraints excluded: chain b residue 443 HIS Chi-restraints excluded: chain b residue 475 LEU Chi-restraints excluded: chain b residue 515 ILE Chi-restraints excluded: chain b residue 562 CYS Chi-restraints excluded: chain b residue 570 THR Chi-restraints excluded: chain b residue 574 SER Chi-restraints excluded: chain b residue 648 VAL Chi-restraints excluded: chain b residue 685 HIS Chi-restraints excluded: chain b residue 688 THR Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 61 PHE Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain c residue 73 THR Chi-restraints excluded: chain d residue 69 LEU Chi-restraints excluded: chain d residue 81 THR Chi-restraints excluded: chain d residue 89 TYR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 21 VAL Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 78 PHE Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 30 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 776 optimal weight: 20.0000 chunk 590 optimal weight: 8.9990 chunk 407 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 375 optimal weight: 30.0000 chunk 527 optimal weight: 40.0000 chunk 788 optimal weight: 10.0000 chunk 835 optimal weight: 2.9990 chunk 412 optimal weight: 1.9990 chunk 747 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 657 GLN ** B 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN ** B 456 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 ** 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 ** 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** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN T 25 GLN ** e 80 GLN ** 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 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 591 HIS ** e 641 ASN ** 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 367 GLN ** 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** ** a 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 369 HIS a 408 HIS ** a 459 ASN ** 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** ** b 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 644 ASN ** c 37 GLN ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 95557 Z= 0.264 Angle : 0.831 13.049 136125 Z= 0.369 Chirality : 0.048 0.466 11785 Planarity : 0.006 0.109 18332 Dihedral : 19.400 117.612 13536 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.90 % Favored : 88.08 % Rotamer: Outliers : 5.93 % Allowed : 23.32 % Favored : 70.75 % 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: -2.39 (0.09), residues: 8724 helix: -0.26 (0.08), residues: 4278 sheet: -1.69 (0.39), residues: 172 loop : -3.12 (0.09), residues: 4274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 660 HIS 0.031 0.002 HIS b 379 PHE 0.042 0.002 PHE a 610 TYR 0.040 0.002 TYR b 626 ARG 0.021 0.001 ARG e 572 *********************** 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 1321 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 424 poor density : 897 time to evaluate : 8.177 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: A 58 ASP cc_start: 0.7497 (p0) cc_final: 0.7079 (p0) REVERT: A 78 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: A 180 HIS cc_start: 0.6561 (OUTLIER) cc_final: 0.5787 (t-90) REVERT: A 298 HIS cc_start: 0.6898 (m90) cc_final: 0.6312 (m-70) REVERT: A 571 PHE cc_start: 0.5121 (OUTLIER) cc_final: 0.2539 (p90) REVERT: A 599 MET cc_start: 0.8452 (ppp) cc_final: 0.8178 (ppp) REVERT: A 745 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8084 (mm-30) REVERT: B 102 ASP cc_start: 0.5537 (OUTLIER) cc_final: 0.4831 (t0) REVERT: B 135 LEU cc_start: 0.5957 (OUTLIER) cc_final: 0.5444 (pp) REVERT: B 387 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7758 (ttm) REVERT: B 570 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8497 (p) REVERT: B 652 MET cc_start: 0.7375 (mmt) cc_final: 0.6974 (mmt) REVERT: D 51 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6420 (mtm) REVERT: F 118 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6967 (pt0) REVERT: F 141 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7079 (pp) REVERT: K 52 MET cc_start: 0.4782 (tpp) cc_final: 0.4471 (ttp) REVERT: K 54 LEU cc_start: 0.2976 (OUTLIER) cc_final: 0.2558 (tt) REVERT: L 74 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8323 (tt) REVERT: E 91 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7638 (ptt) REVERT: E 197 MET cc_start: 0.7839 (tpp) cc_final: 0.7531 (tpp) REVERT: E 252 GLU cc_start: 0.5747 (mt-10) cc_final: 0.5486 (tp30) REVERT: E 370 HIS cc_start: 0.6395 (OUTLIER) cc_final: 0.6027 (t-170) REVERT: E 514 VAL cc_start: 0.7372 (OUTLIER) cc_final: 0.7134 (p) REVERT: G 129 MET cc_start: 0.5948 (mmp) cc_final: 0.5736 (mmp) REVERT: G 380 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6982 (mt0) REVERT: G 443 HIS cc_start: 0.6290 (OUTLIER) cc_final: 0.5909 (t-90) REVERT: G 643 MET cc_start: 0.5610 (tpp) cc_final: 0.5336 (tpt) REVERT: G 685 HIS cc_start: 0.7745 (OUTLIER) cc_final: 0.7432 (t-90) REVERT: G 695 ARG cc_start: 0.6916 (ptt-90) cc_final: 0.5155 (tpt-90) REVERT: N 43 MET cc_start: 0.6573 (ptp) cc_final: 0.6327 (ptm) REVERT: N 77 LYS cc_start: 0.5695 (OUTLIER) cc_final: 0.5358 (mtmm) REVERT: W 39 ARG cc_start: 0.7324 (mtm180) cc_final: 0.6834 (mtm180) REVERT: W 55 GLU cc_start: 0.3119 (tp30) cc_final: 0.1877 (tt0) REVERT: O 164 ARG cc_start: 0.5444 (mpt90) cc_final: 0.4595 (ttp80) REVERT: S 104 ILE cc_start: 0.8884 (pt) cc_final: 0.8668 (mt) REVERT: e 34 HIS cc_start: 0.3449 (OUTLIER) cc_final: 0.2556 (t70) REVERT: e 58 ASP cc_start: 0.7421 (p0) cc_final: 0.6956 (p0) REVERT: e 180 HIS cc_start: 0.6288 (OUTLIER) cc_final: 0.5538 (t-90) REVERT: e 298 HIS cc_start: 0.6894 (m90) cc_final: 0.6279 (m-70) REVERT: e 471 MET cc_start: 0.6026 (tmm) cc_final: 0.5441 (tmm) REVERT: e 571 PHE cc_start: 0.4741 (OUTLIER) cc_final: 0.2375 (p90) REVERT: e 599 MET cc_start: 0.8433 (ppp) cc_final: 0.8066 (ppp) REVERT: e 608 TYR cc_start: 0.7214 (OUTLIER) cc_final: 0.6064 (m-10) REVERT: e 672 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7523 (pp) REVERT: g 414 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6352 (tpp-160) REVERT: g 570 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8656 (p) REVERT: g 574 SER cc_start: 0.6715 (OUTLIER) cc_final: 0.6247 (t) REVERT: g 704 SER cc_start: 0.8252 (OUTLIER) cc_final: 0.8038 (t) REVERT: h 9 THR cc_start: 0.7826 (p) cc_final: 0.7382 (p) REVERT: h 64 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7330 (pt) REVERT: n 89 TYR cc_start: 0.7307 (m-80) cc_final: 0.7019 (m-80) REVERT: o 118 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6424 (pm20) REVERT: p 1 MET cc_start: 0.7053 (tmm) cc_final: 0.6510 (tmm) REVERT: r 52 MET cc_start: 0.4954 (tpp) cc_final: 0.4673 (ttp) REVERT: r 54 LEU cc_start: 0.3339 (OUTLIER) cc_final: 0.2900 (tt) REVERT: a 91 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7387 (ptt) REVERT: a 333 PHE cc_start: 0.3553 (t80) cc_final: 0.3338 (t80) REVERT: a 462 MET cc_start: 0.7143 (mmm) cc_final: 0.6832 (mmt) REVERT: a 514 VAL cc_start: 0.7324 (OUTLIER) cc_final: 0.7083 (p) REVERT: a 599 MET cc_start: 0.8006 (ppp) cc_final: 0.7450 (ppp) REVERT: a 723 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: b 308 LYS cc_start: 0.6320 (OUTLIER) cc_final: 0.5940 (mtpp) REVERT: b 443 HIS cc_start: 0.6195 (OUTLIER) cc_final: 0.5953 (t-90) REVERT: b 450 PHE cc_start: 0.5849 (t80) cc_final: 0.4797 (t80) REVERT: b 643 MET cc_start: 0.5842 (tpp) cc_final: 0.5540 (tpp) REVERT: b 695 ARG cc_start: 0.6816 (ptt-90) cc_final: 0.5196 (tpt-90) REVERT: d 26 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6919 (tm-30) REVERT: d 127 ASP cc_start: 0.5985 (OUTLIER) cc_final: 0.5634 (p0) REVERT: w 39 ARG cc_start: 0.7247 (mtm180) cc_final: 0.6882 (mtm180) REVERT: l 104 ILE cc_start: 0.8927 (pt) cc_final: 0.8643 (mt) outliers start: 424 outliers final: 278 residues processed: 1201 average time/residue: 0.7693 time to fit residues: 1644.2536 Evaluate side-chains 1128 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 813 time to evaluate : 6.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 651 TRP Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain V residue 40 PHE Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 61 ILE Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 37 PHE Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 395 MET Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 565 ASP Chi-restraints excluded: chain E residue 590 ASP Chi-restraints excluded: chain E residue 621 THR Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 702 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 327 TYR Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain G residue 380 GLN Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 419 LYS Chi-restraints excluded: chain G residue 440 LEU Chi-restraints excluded: chain G residue 443 HIS Chi-restraints excluded: chain G residue 452 THR Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 505 ASN Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 562 CYS Chi-restraints excluded: chain G residue 570 THR Chi-restraints excluded: chain G residue 574 SER Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain G residue 662 THR Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain G residue 685 HIS Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain R residue 37 PHE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 78 PHE Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain e residue 34 HIS Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 180 HIS Chi-restraints excluded: chain e residue 232 VAL Chi-restraints excluded: chain e residue 266 THR Chi-restraints excluded: chain e residue 285 VAL Chi-restraints excluded: chain e residue 342 TYR Chi-restraints excluded: chain e residue 364 THR Chi-restraints excluded: chain e residue 400 PHE Chi-restraints excluded: chain e residue 456 TYR Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 571 PHE Chi-restraints excluded: chain e residue 590 ASP Chi-restraints excluded: chain e residue 608 TYR Chi-restraints excluded: chain e residue 609 HIS Chi-restraints excluded: chain e residue 614 MET Chi-restraints excluded: chain e residue 657 GLN Chi-restraints excluded: chain e residue 672 LEU Chi-restraints excluded: chain e residue 684 LEU Chi-restraints excluded: chain e residue 738 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 102 ASP Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 206 HIS Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 278 LEU Chi-restraints excluded: chain g residue 285 ILE Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 315 THR Chi-restraints excluded: chain g residue 376 TYR Chi-restraints excluded: chain g residue 382 ILE Chi-restraints excluded: chain g residue 414 ARG Chi-restraints excluded: chain g residue 452 THR Chi-restraints excluded: chain g residue 456 GLN Chi-restraints excluded: chain g residue 552 ASP Chi-restraints excluded: chain g residue 570 THR Chi-restraints excluded: chain g residue 574 SER Chi-restraints excluded: chain g residue 577 ASP Chi-restraints excluded: chain g residue 589 THR Chi-restraints excluded: chain g residue 623 LEU Chi-restraints excluded: chain g residue 651 TRP Chi-restraints excluded: chain g residue 654 LEU Chi-restraints excluded: chain g residue 658 LEU Chi-restraints excluded: chain g residue 688 THR Chi-restraints excluded: chain g residue 704 SER Chi-restraints excluded: chain g residue 722 LEU Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain n residue 51 MET Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 104 PHE Chi-restraints excluded: chain n residue 108 VAL Chi-restraints excluded: chain v residue 11 LEU Chi-restraints excluded: chain v residue 41 ASP Chi-restraints excluded: chain v residue 43 VAL Chi-restraints excluded: chain v residue 56 THR Chi-restraints excluded: chain v residue 59 VAL Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain o residue 156 ASP Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain r residue 37 PHE Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 54 LEU Chi-restraints excluded: chain s residue 86 ASP Chi-restraints excluded: chain s residue 88 ASP Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 124 VAL Chi-restraints excluded: chain s residue 163 ASN Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain t residue 38 VAL Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 74 PHE Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 140 ILE Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 198 LEU Chi-restraints excluded: chain a residue 236 ASP Chi-restraints excluded: chain a residue 285 VAL Chi-restraints excluded: chain a residue 362 SER Chi-restraints excluded: chain a residue 400 PHE Chi-restraints excluded: chain a residue 450 PHE Chi-restraints excluded: chain a residue 514 VAL Chi-restraints excluded: chain a residue 526 ILE Chi-restraints excluded: chain a residue 565 ASP Chi-restraints excluded: chain a residue 571 PHE Chi-restraints excluded: chain a residue 583 THR Chi-restraints excluded: chain a residue 590 ASP Chi-restraints excluded: chain a residue 621 THR Chi-restraints excluded: chain a residue 672 LEU Chi-restraints excluded: chain a residue 702 VAL Chi-restraints excluded: chain a residue 721 ILE Chi-restraints excluded: chain a residue 723 GLN Chi-restraints excluded: chain a residue 740 ILE Chi-restraints excluded: chain a residue 745 GLU Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 56 ILE Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 141 PHE Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 210 ASP Chi-restraints excluded: chain b residue 216 LEU Chi-restraints excluded: chain b residue 280 ILE Chi-restraints excluded: chain b residue 308 LYS Chi-restraints excluded: chain b residue 315 THR Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 327 TYR Chi-restraints excluded: chain b residue 350 SER Chi-restraints excluded: chain b residue 384 VAL Chi-restraints excluded: chain b residue 440 LEU Chi-restraints excluded: chain b residue 443 HIS Chi-restraints excluded: chain b residue 475 LEU Chi-restraints excluded: chain b residue 515 ILE Chi-restraints excluded: chain b residue 536 VAL Chi-restraints excluded: chain b residue 562 CYS Chi-restraints excluded: chain b residue 570 THR Chi-restraints excluded: chain b residue 574 SER Chi-restraints excluded: chain b residue 648 VAL Chi-restraints excluded: chain b residue 662 THR Chi-restraints excluded: chain b residue 680 THR Chi-restraints excluded: chain b residue 685 HIS Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 61 PHE Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain d residue 69 LEU Chi-restraints excluded: chain d residue 81 THR Chi-restraints excluded: chain d residue 89 TYR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 21 VAL Chi-restraints excluded: chain w residue 30 SER Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 37 SER Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 37 PHE Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 47 ILE Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 30 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 695 optimal weight: 20.0000 chunk 474 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 621 optimal weight: 0.9990 chunk 344 optimal weight: 6.9990 chunk 712 optimal weight: 10.0000 chunk 577 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 426 optimal weight: 10.0000 chunk 749 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 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 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 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 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 113 GLN D 125 ASN ** L 128 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 459 ASN E 641 ASN ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 ASN T 25 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 369 HIS ** 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 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 95 GLN ** n 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 ASN o 55 GLN ** a 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 370 HIS a 459 ASN a 591 HIS a 641 ASN ** b 306 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** c 37 GLN ** d 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 95557 Z= 0.258 Angle : 0.818 13.168 136125 Z= 0.364 Chirality : 0.048 0.479 11785 Planarity : 0.006 0.113 18332 Dihedral : 18.902 116.161 13516 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 6.53 % Allowed : 24.15 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -2.24 (0.09), residues: 8724 helix: -0.14 (0.08), residues: 4302 sheet: -1.32 (0.40), residues: 174 loop : -3.06 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP e 680 HIS 0.014 0.002 HIS g 425 PHE 0.033 0.002 PHE a 610 TYR 0.048 0.002 TYR b 626 ARG 0.006 0.001 ARG b 695 *********************** 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 1352 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 467 poor density : 885 time to evaluate : 6.597 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: A 58 ASP cc_start: 0.7470 (p0) cc_final: 0.6982 (p0) REVERT: A 78 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: A 180 HIS cc_start: 0.6580 (OUTLIER) cc_final: 0.5796 (t-90) REVERT: A 415 ARG cc_start: 0.7758 (mmt90) cc_final: 0.7321 (mmt-90) REVERT: A 599 MET cc_start: 0.8437 (ppp) cc_final: 0.8154 (ppp) REVERT: A 608 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6006 (m-10) REVERT: A 672 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7416 (pp) REVERT: A 745 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8264 (tp30) REVERT: B 102 ASP cc_start: 0.5630 (OUTLIER) cc_final: 0.4988 (t0) REVERT: B 294 ASN cc_start: 0.7946 (p0) cc_final: 0.7185 (t0) REVERT: B 570 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8503 (p) REVERT: B 703 MET cc_start: 0.7518 (mtp) cc_final: 0.7274 (mtp) REVERT: C 9 THR cc_start: 0.7935 (p) cc_final: 0.7535 (p) REVERT: D 51 MET cc_start: 0.6945 (mtp) cc_final: 0.6417 (mtm) REVERT: D 136 MET cc_start: 0.3703 (tpp) cc_final: 0.3317 (tpp) REVERT: F 118 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7093 (pt0) REVERT: K 52 MET cc_start: 0.4705 (tpp) cc_final: 0.4396 (ttp) REVERT: K 54 LEU cc_start: 0.2983 (OUTLIER) cc_final: 0.2560 (tt) REVERT: L 74 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8302 (tt) REVERT: E 91 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7651 (ptt) REVERT: E 197 MET cc_start: 0.7730 (tpp) cc_final: 0.7517 (tpp) REVERT: E 252 GLU cc_start: 0.5639 (mt-10) cc_final: 0.5408 (tp30) REVERT: E 370 HIS cc_start: 0.6364 (OUTLIER) cc_final: 0.6010 (t-170) REVERT: E 462 MET cc_start: 0.7183 (mmm) cc_final: 0.6876 (mmm) REVERT: E 514 VAL cc_start: 0.7391 (OUTLIER) cc_final: 0.7168 (p) REVERT: G 129 MET cc_start: 0.5935 (mmp) cc_final: 0.5720 (mmp) REVERT: G 380 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6948 (mt0) REVERT: G 443 HIS cc_start: 0.6062 (OUTLIER) cc_final: 0.5594 (t-90) REVERT: G 450 PHE cc_start: 0.5250 (t80) cc_final: 0.4234 (t80) REVERT: G 695 ARG cc_start: 0.6789 (ptt-90) cc_final: 0.5119 (tpt-90) REVERT: G 703 MET cc_start: 0.7731 (mtm) cc_final: 0.7446 (mtp) REVERT: N 43 MET cc_start: 0.6552 (ptp) cc_final: 0.6307 (ptm) REVERT: N 77 LYS cc_start: 0.5739 (OUTLIER) cc_final: 0.5381 (mtmm) REVERT: N 89 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: W 55 GLU cc_start: 0.3270 (tp30) cc_final: 0.2090 (tt0) REVERT: O 65 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6647 (pt) REVERT: O 164 ARG cc_start: 0.5443 (mpt90) cc_final: 0.4510 (ttp80) REVERT: R 54 LEU cc_start: 0.3873 (OUTLIER) cc_final: 0.3515 (tt) REVERT: S 104 ILE cc_start: 0.8867 (pt) cc_final: 0.8645 (mt) REVERT: e 58 ASP cc_start: 0.7384 (p0) cc_final: 0.6947 (p0) REVERT: e 167 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6865 (tt) REVERT: e 180 HIS cc_start: 0.6410 (OUTLIER) cc_final: 0.5547 (t-90) REVERT: e 415 ARG cc_start: 0.7717 (mmt90) cc_final: 0.7280 (mmt-90) REVERT: e 471 MET cc_start: 0.6185 (tmm) cc_final: 0.5277 (tmm) REVERT: e 599 MET cc_start: 0.8395 (ppp) cc_final: 0.7999 (ppp) REVERT: e 608 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6018 (m-10) REVERT: e 672 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7486 (pp) REVERT: g 102 ASP cc_start: 0.5768 (OUTLIER) cc_final: 0.5151 (t0) REVERT: g 294 ASN cc_start: 0.8003 (p0) cc_final: 0.7205 (t0) REVERT: g 414 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6312 (tpp-160) REVERT: g 452 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7358 (t) REVERT: g 570 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8517 (p) REVERT: g 703 MET cc_start: 0.7423 (mtp) cc_final: 0.7207 (mtp) REVERT: h 9 THR cc_start: 0.7910 (p) cc_final: 0.7431 (p) REVERT: n 82 ASP cc_start: 0.4720 (OUTLIER) cc_final: 0.4092 (t0) REVERT: n 89 TYR cc_start: 0.7261 (m-80) cc_final: 0.6994 (m-80) REVERT: o 118 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6515 (pm20) REVERT: p 1 MET cc_start: 0.7054 (tmm) cc_final: 0.6510 (tmm) REVERT: r 52 MET cc_start: 0.4846 (tpp) cc_final: 0.4618 (ttp) REVERT: r 54 LEU cc_start: 0.3352 (OUTLIER) cc_final: 0.2920 (tt) REVERT: a 91 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7313 (ptt) REVERT: a 514 VAL cc_start: 0.7378 (OUTLIER) cc_final: 0.7146 (p) REVERT: a 599 MET cc_start: 0.7946 (ppp) cc_final: 0.7425 (ppp) REVERT: a 723 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: b 308 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5946 (mtpp) REVERT: b 443 HIS cc_start: 0.6231 (OUTLIER) cc_final: 0.5895 (t-90) REVERT: b 450 PHE cc_start: 0.5677 (t80) cc_final: 0.4758 (t80) REVERT: b 695 ARG cc_start: 0.6973 (ptt-90) cc_final: 0.5415 (tpt-90) REVERT: b 703 MET cc_start: 0.7916 (mtm) cc_final: 0.7631 (mtp) REVERT: d 93 GLU cc_start: 0.3015 (mp0) cc_final: 0.2543 (mp0) REVERT: d 127 ASP cc_start: 0.6008 (OUTLIER) cc_final: 0.5663 (p0) REVERT: w 55 GLU cc_start: 0.2063 (mm-30) cc_final: 0.0908 (tt0) REVERT: j 42 ASP cc_start: 0.4526 (OUTLIER) cc_final: 0.4276 (t0) REVERT: l 104 ILE cc_start: 0.8940 (pt) cc_final: 0.8653 (mt) REVERT: l 171 PHE cc_start: 0.6272 (p90) cc_final: 0.6032 (t80) outliers start: 467 outliers final: 317 residues processed: 1238 average time/residue: 0.7590 time to fit residues: 1669.2445 Evaluate side-chains 1163 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 810 time to evaluate : 7.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 643 MET Chi-restraints excluded: chain B residue 651 TRP Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain V residue 40 PHE Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 61 ILE Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 37 PHE Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain E residue 28 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 395 MET Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 565 ASP Chi-restraints excluded: chain E residue 583 THR Chi-restraints excluded: chain E residue 590 ASP Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 621 THR Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 721 ILE Chi-restraints excluded: chain E residue 740 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 327 TYR Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain G residue 380 GLN Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 419 LYS Chi-restraints excluded: chain G residue 435 PHE Chi-restraints excluded: chain G residue 440 LEU Chi-restraints excluded: chain G residue 443 HIS Chi-restraints excluded: chain G residue 452 THR Chi-restraints excluded: chain G residue 505 ASN Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain G residue 562 CYS Chi-restraints excluded: chain G residue 570 THR Chi-restraints excluded: chain G residue 574 SER Chi-restraints excluded: chain G residue 577 ASP Chi-restraints excluded: chain G residue 580 TYR Chi-restraints excluded: chain G residue 623 LEU Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain G residue 662 THR Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 89 TYR Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 138 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain R residue 37 PHE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 78 PHE Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain e residue 128 ASN Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 167 LEU Chi-restraints excluded: chain e residue 180 HIS Chi-restraints excluded: chain e residue 232 VAL Chi-restraints excluded: chain e residue 266 THR Chi-restraints excluded: chain e residue 274 ASP Chi-restraints excluded: chain e residue 285 VAL Chi-restraints excluded: chain e residue 303 VAL Chi-restraints excluded: chain e residue 305 PHE Chi-restraints excluded: chain e residue 342 TYR Chi-restraints excluded: chain e residue 364 THR Chi-restraints excluded: chain e residue 400 PHE Chi-restraints excluded: chain e residue 431 ILE Chi-restraints excluded: chain e residue 456 TYR Chi-restraints excluded: chain e residue 461 THR Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 571 PHE Chi-restraints excluded: chain e residue 590 ASP Chi-restraints excluded: chain e residue 608 TYR Chi-restraints excluded: chain e residue 657 GLN Chi-restraints excluded: chain e residue 672 LEU Chi-restraints excluded: chain e residue 684 LEU Chi-restraints excluded: chain e residue 738 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 102 ASP Chi-restraints excluded: chain g residue 206 HIS Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 278 LEU Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 376 TYR Chi-restraints excluded: chain g residue 382 ILE Chi-restraints excluded: chain g residue 414 ARG Chi-restraints excluded: chain g residue 427 SER Chi-restraints excluded: chain g residue 452 THR Chi-restraints excluded: chain g residue 456 GLN Chi-restraints excluded: chain g residue 536 VAL Chi-restraints excluded: chain g residue 570 THR Chi-restraints excluded: chain g residue 574 SER Chi-restraints excluded: chain g residue 577 ASP Chi-restraints excluded: chain g residue 589 THR Chi-restraints excluded: chain g residue 619 LEU Chi-restraints excluded: chain g residue 623 LEU Chi-restraints excluded: chain g residue 654 LEU Chi-restraints excluded: chain g residue 658 LEU Chi-restraints excluded: chain g residue 680 THR Chi-restraints excluded: chain g residue 688 THR Chi-restraints excluded: chain g residue 713 LEU Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 108 VAL Chi-restraints excluded: chain v residue 11 LEU Chi-restraints excluded: chain v residue 41 ASP Chi-restraints excluded: chain v residue 43 VAL Chi-restraints excluded: chain v residue 56 THR Chi-restraints excluded: chain o residue 52 ASN Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain o residue 147 LEU Chi-restraints excluded: chain o residue 156 ASP Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain r residue 37 PHE Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 54 LEU Chi-restraints excluded: chain r residue 77 ILE Chi-restraints excluded: chain s residue 86 ASP Chi-restraints excluded: chain s residue 88 ASP Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 163 ASN Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain t residue 38 VAL Chi-restraints excluded: chain a residue 60 ASP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 74 PHE Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 140 ILE Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 236 ASP Chi-restraints excluded: chain a residue 254 TYR Chi-restraints excluded: chain a residue 277 THR Chi-restraints excluded: chain a residue 285 VAL Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 362 SER Chi-restraints excluded: chain a residue 400 PHE Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 450 PHE Chi-restraints excluded: chain a residue 514 VAL Chi-restraints excluded: chain a residue 526 ILE Chi-restraints excluded: chain a residue 565 ASP Chi-restraints excluded: chain a residue 583 THR Chi-restraints excluded: chain a residue 590 ASP Chi-restraints excluded: chain a residue 621 THR Chi-restraints excluded: chain a residue 647 LEU Chi-restraints excluded: chain a residue 672 LEU Chi-restraints excluded: chain a residue 702 VAL Chi-restraints excluded: chain a residue 721 ILE Chi-restraints excluded: chain a residue 723 GLN Chi-restraints excluded: chain a residue 740 ILE Chi-restraints excluded: chain a residue 743 PHE Chi-restraints excluded: chain a residue 745 GLU Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 56 ILE Chi-restraints excluded: chain b residue 134 ASP Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 141 PHE Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 215 THR Chi-restraints excluded: chain b residue 216 LEU Chi-restraints excluded: chain b residue 308 LYS Chi-restraints excluded: chain b residue 315 THR Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 327 TYR Chi-restraints excluded: chain b residue 349 THR Chi-restraints excluded: chain b residue 350 SER Chi-restraints excluded: chain b residue 384 VAL Chi-restraints excluded: chain b residue 440 LEU Chi-restraints excluded: chain b residue 443 HIS Chi-restraints excluded: chain b residue 475 LEU Chi-restraints excluded: chain b residue 515 ILE Chi-restraints excluded: chain b residue 536 VAL Chi-restraints excluded: chain b residue 562 CYS Chi-restraints excluded: chain b residue 570 THR Chi-restraints excluded: chain b residue 574 SER Chi-restraints excluded: chain b residue 580 TYR Chi-restraints excluded: chain b residue 623 LEU Chi-restraints excluded: chain b residue 648 VAL Chi-restraints excluded: chain b residue 662 THR Chi-restraints excluded: chain b residue 680 THR Chi-restraints excluded: chain b residue 685 HIS Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 53 CYS Chi-restraints excluded: chain c residue 61 PHE Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain d residue 69 LEU Chi-restraints excluded: chain d residue 81 THR Chi-restraints excluded: chain d residue 89 TYR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 21 VAL Chi-restraints excluded: chain w residue 30 SER Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 57 GLU Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 10 ILE Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 37 SER Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 42 ASP Chi-restraints excluded: chain k residue 37 PHE Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 47 ILE Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 78 PHE Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 30 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 280 optimal weight: 6.9990 chunk 752 optimal weight: 10.0000 chunk 165 optimal weight: 0.0170 chunk 490 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 chunk 835 optimal weight: 9.9990 chunk 693 optimal weight: 0.0870 chunk 387 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 chunk 438 optimal weight: 5.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** 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 456 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 128 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 ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 GLN E 369 HIS E 601 ASN ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** O 46 ASN O 55 GLN T 25 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 422 ASN ** 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 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 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 352 GLN ** b 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 380 GLN ** b 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 95557 Z= 0.192 Angle : 0.763 12.695 136125 Z= 0.339 Chirality : 0.046 0.463 11785 Planarity : 0.005 0.109 18332 Dihedral : 18.343 114.103 13508 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 5.58 % Allowed : 25.63 % Favored : 68.80 % 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: -1.94 (0.09), residues: 8724 helix: 0.10 (0.08), residues: 4274 sheet: -1.35 (0.36), residues: 222 loop : -2.88 (0.09), residues: 4228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP e 680 HIS 0.023 0.002 HIS B 156 PHE 0.058 0.002 PHE E 74 TYR 0.039 0.002 TYR b 626 ARG 0.006 0.000 ARG n 52 *********************** 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 1310 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 399 poor density : 911 time to evaluate : 6.598 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: A 58 ASP cc_start: 0.7252 (p0) cc_final: 0.6795 (p0) REVERT: A 78 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7241 (m-80) REVERT: A 180 HIS cc_start: 0.6582 (OUTLIER) cc_final: 0.5721 (t-90) REVERT: A 298 HIS cc_start: 0.6803 (m90) cc_final: 0.6597 (m-70) REVERT: A 415 ARG cc_start: 0.7726 (mmt90) cc_final: 0.7270 (mmt-90) REVERT: A 599 MET cc_start: 0.8219 (ppp) cc_final: 0.7952 (ppp) REVERT: A 608 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.6087 (m-10) REVERT: A 745 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8312 (tp30) REVERT: B 102 ASP cc_start: 0.5310 (OUTLIER) cc_final: 0.4928 (t0) REVERT: B 294 ASN cc_start: 0.7852 (p0) cc_final: 0.7106 (t0) REVERT: B 703 MET cc_start: 0.7449 (mtp) cc_final: 0.7215 (mtp) REVERT: C 9 THR cc_start: 0.7876 (p) cc_final: 0.7466 (p) REVERT: C 77 MET cc_start: 0.6945 (mmm) cc_final: 0.6542 (mmm) REVERT: D 51 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.6264 (mtm) REVERT: D 136 MET cc_start: 0.3713 (tpp) cc_final: 0.3351 (tpp) REVERT: F 118 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7084 (pt0) REVERT: K 52 MET cc_start: 0.4488 (tpp) cc_final: 0.4189 (ttp) REVERT: K 54 LEU cc_start: 0.2933 (OUTLIER) cc_final: 0.2538 (tt) REVERT: L 74 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8243 (tt) REVERT: E 91 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7552 (ptt) REVERT: E 310 HIS cc_start: 0.4746 (m90) cc_final: 0.4085 (m-70) REVERT: E 370 HIS cc_start: 0.6322 (OUTLIER) cc_final: 0.6058 (t-170) REVERT: E 462 MET cc_start: 0.7325 (mmm) cc_final: 0.7005 (mmm) REVERT: E 514 VAL cc_start: 0.7442 (OUTLIER) cc_final: 0.7203 (p) REVERT: E 646 TRP cc_start: 0.6667 (OUTLIER) cc_final: 0.3829 (m100) REVERT: G 443 HIS cc_start: 0.6113 (OUTLIER) cc_final: 0.5713 (t-90) REVERT: G 450 PHE cc_start: 0.5178 (t80) cc_final: 0.4165 (t80) REVERT: G 695 ARG cc_start: 0.6738 (ptt-90) cc_final: 0.5050 (tpt-90) REVERT: H 27 MET cc_start: 0.5077 (tpp) cc_final: 0.4721 (tpp) REVERT: N 77 LYS cc_start: 0.5767 (OUTLIER) cc_final: 0.5439 (mtmm) REVERT: N 89 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: W 55 GLU cc_start: 0.3505 (tp30) cc_final: 0.2654 (tt0) REVERT: O 65 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6568 (pt) REVERT: O 164 ARG cc_start: 0.5351 (mpt90) cc_final: 0.4433 (ttp80) REVERT: Q 23 PHE cc_start: 0.7623 (m-80) cc_final: 0.7398 (m-80) REVERT: R 54 LEU cc_start: 0.3893 (OUTLIER) cc_final: 0.3530 (tt) REVERT: e 58 ASP cc_start: 0.7242 (p0) cc_final: 0.6864 (p0) REVERT: e 180 HIS cc_start: 0.6353 (OUTLIER) cc_final: 0.5497 (t-90) REVERT: e 298 HIS cc_start: 0.6757 (m90) cc_final: 0.6553 (m-70) REVERT: e 415 ARG cc_start: 0.7627 (mmt90) cc_final: 0.7260 (mmt90) REVERT: e 471 MET cc_start: 0.6147 (tmm) cc_final: 0.5210 (tmm) REVERT: e 571 PHE cc_start: 0.4773 (OUTLIER) cc_final: 0.2465 (p90) REVERT: e 589 TRP cc_start: 0.6531 (OUTLIER) cc_final: 0.4583 (p-90) REVERT: e 599 MET cc_start: 0.8124 (ppp) cc_final: 0.7908 (ppp) REVERT: e 601 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7839 (t0) REVERT: e 608 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.5996 (m-10) REVERT: e 638 MET cc_start: 0.6636 (pmm) cc_final: 0.6313 (pmm) REVERT: e 672 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7570 (pp) REVERT: g 37 MET cc_start: 0.5261 (ptp) cc_final: 0.4982 (ptm) REVERT: g 102 ASP cc_start: 0.5686 (OUTLIER) cc_final: 0.5280 (t0) REVERT: g 294 ASN cc_start: 0.7820 (p0) cc_final: 0.7071 (t0) REVERT: g 414 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6215 (tpp-160) REVERT: g 452 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7229 (t) REVERT: g 570 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8580 (p) REVERT: h 9 THR cc_start: 0.7844 (p) cc_final: 0.7354 (p) REVERT: n 25 ARG cc_start: 0.5083 (OUTLIER) cc_final: 0.4576 (mmp-170) REVERT: n 82 ASP cc_start: 0.4710 (OUTLIER) cc_final: 0.4082 (t0) REVERT: n 89 TYR cc_start: 0.7289 (m-80) cc_final: 0.6913 (m-80) REVERT: p 1 MET cc_start: 0.7014 (tmm) cc_final: 0.6485 (tmm) REVERT: r 52 MET cc_start: 0.4637 (tpp) cc_final: 0.4391 (ttp) REVERT: r 54 LEU cc_start: 0.3323 (OUTLIER) cc_final: 0.2936 (tt) REVERT: s 128 ASN cc_start: 0.7407 (p0) cc_final: 0.7164 (p0) REVERT: s 151 VAL cc_start: 0.8697 (t) cc_final: 0.8419 (p) REVERT: a 91 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7211 (ptt) REVERT: a 462 MET cc_start: 0.7798 (mmt) cc_final: 0.7144 (mmm) REVERT: a 514 VAL cc_start: 0.7343 (OUTLIER) cc_final: 0.7119 (p) REVERT: a 599 MET cc_start: 0.7852 (ppp) cc_final: 0.7276 (ppp) REVERT: a 646 TRP cc_start: 0.6767 (OUTLIER) cc_final: 0.4116 (m100) REVERT: b 282 VAL cc_start: 0.8736 (m) cc_final: 0.8497 (t) REVERT: b 308 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5855 (mtpp) REVERT: b 443 HIS cc_start: 0.6021 (OUTLIER) cc_final: 0.5552 (t-90) REVERT: b 695 ARG cc_start: 0.6873 (ptt-90) cc_final: 0.5280 (tpt-90) REVERT: d 93 GLU cc_start: 0.3001 (mp0) cc_final: 0.2667 (mp0) REVERT: d 127 ASP cc_start: 0.5993 (OUTLIER) cc_final: 0.5636 (p0) REVERT: w 55 GLU cc_start: 0.1885 (mm-30) cc_final: 0.0768 (tt0) REVERT: l 104 ILE cc_start: 0.8869 (pt) cc_final: 0.8645 (mt) REVERT: l 131 ASP cc_start: 0.5732 (p0) cc_final: 0.5378 (p0) outliers start: 399 outliers final: 277 residues processed: 1208 average time/residue: 0.7518 time to fit residues: 1616.0788 Evaluate side-chains 1149 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 836 time to evaluate : 7.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 651 TRP Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain V residue 40 PHE Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 61 ILE Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 37 PHE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 241 HIS Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 395 MET Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 565 ASP Chi-restraints excluded: chain E residue 590 ASP Chi-restraints excluded: chain E residue 621 THR Chi-restraints excluded: chain E residue 646 TRP Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 702 VAL Chi-restraints excluded: chain E residue 721 ILE Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 327 TYR Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 435 PHE Chi-restraints excluded: chain G residue 440 LEU Chi-restraints excluded: chain G residue 443 HIS Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 505 ASN Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 562 CYS Chi-restraints excluded: chain G residue 570 THR Chi-restraints excluded: chain G residue 574 SER Chi-restraints excluded: chain G residue 577 ASP Chi-restraints excluded: chain G residue 580 TYR Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain G residue 662 THR Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 89 TYR Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 138 THR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain R residue 37 PHE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 78 PHE Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain e residue 34 HIS Chi-restraints excluded: chain e residue 128 ASN Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 180 HIS Chi-restraints excluded: chain e residue 232 VAL Chi-restraints excluded: chain e residue 274 ASP Chi-restraints excluded: chain e residue 285 VAL Chi-restraints excluded: chain e residue 303 VAL Chi-restraints excluded: chain e residue 305 PHE Chi-restraints excluded: chain e residue 342 TYR Chi-restraints excluded: chain e residue 364 THR Chi-restraints excluded: chain e residue 400 PHE Chi-restraints excluded: chain e residue 431 ILE Chi-restraints excluded: chain e residue 456 TYR Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 571 PHE Chi-restraints excluded: chain e residue 589 TRP Chi-restraints excluded: chain e residue 590 ASP Chi-restraints excluded: chain e residue 601 ASN Chi-restraints excluded: chain e residue 608 TYR Chi-restraints excluded: chain e residue 614 MET Chi-restraints excluded: chain e residue 657 GLN Chi-restraints excluded: chain e residue 672 LEU Chi-restraints excluded: chain e residue 683 SER Chi-restraints excluded: chain e residue 684 LEU Chi-restraints excluded: chain e residue 734 LEU Chi-restraints excluded: chain e residue 738 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 102 ASP Chi-restraints excluded: chain g residue 142 LEU Chi-restraints excluded: chain g residue 206 HIS Chi-restraints excluded: chain g residue 214 THR Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 278 LEU Chi-restraints excluded: chain g residue 285 ILE Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 349 THR Chi-restraints excluded: chain g residue 376 TYR Chi-restraints excluded: chain g residue 414 ARG Chi-restraints excluded: chain g residue 427 SER Chi-restraints excluded: chain g residue 452 THR Chi-restraints excluded: chain g residue 456 GLN Chi-restraints excluded: chain g residue 570 THR Chi-restraints excluded: chain g residue 574 SER Chi-restraints excluded: chain g residue 623 LEU Chi-restraints excluded: chain g residue 680 THR Chi-restraints excluded: chain g residue 688 THR Chi-restraints excluded: chain n residue 25 ARG Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 108 VAL Chi-restraints excluded: chain v residue 11 LEU Chi-restraints excluded: chain v residue 41 ASP Chi-restraints excluded: chain v residue 43 VAL Chi-restraints excluded: chain v residue 56 THR Chi-restraints excluded: chain o residue 47 THR Chi-restraints excluded: chain o residue 52 ASN Chi-restraints excluded: chain o residue 147 LEU Chi-restraints excluded: chain o residue 156 ASP Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain r residue 54 LEU Chi-restraints excluded: chain s residue 86 ASP Chi-restraints excluded: chain s residue 88 ASP Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 163 ASN Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain t residue 38 VAL Chi-restraints excluded: chain a residue 60 ASP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 74 PHE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 236 ASP Chi-restraints excluded: chain a residue 254 TYR Chi-restraints excluded: chain a residue 277 THR Chi-restraints excluded: chain a residue 285 VAL Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 395 MET Chi-restraints excluded: chain a residue 400 PHE Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 450 PHE Chi-restraints excluded: chain a residue 514 VAL Chi-restraints excluded: chain a residue 526 ILE Chi-restraints excluded: chain a residue 562 LEU Chi-restraints excluded: chain a residue 565 ASP Chi-restraints excluded: chain a residue 571 PHE Chi-restraints excluded: chain a residue 583 THR Chi-restraints excluded: chain a residue 590 ASP Chi-restraints excluded: chain a residue 621 THR Chi-restraints excluded: chain a residue 646 TRP Chi-restraints excluded: chain a residue 647 LEU Chi-restraints excluded: chain a residue 672 LEU Chi-restraints excluded: chain a residue 702 VAL Chi-restraints excluded: chain a residue 743 PHE Chi-restraints excluded: chain a residue 745 GLU Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 134 ASP Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 141 PHE Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 210 ASP Chi-restraints excluded: chain b residue 216 LEU Chi-restraints excluded: chain b residue 308 LYS Chi-restraints excluded: chain b residue 315 THR Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 327 TYR Chi-restraints excluded: chain b residue 350 SER Chi-restraints excluded: chain b residue 384 VAL Chi-restraints excluded: chain b residue 440 LEU Chi-restraints excluded: chain b residue 443 HIS Chi-restraints excluded: chain b residue 515 ILE Chi-restraints excluded: chain b residue 562 CYS Chi-restraints excluded: chain b residue 570 THR Chi-restraints excluded: chain b residue 574 SER Chi-restraints excluded: chain b residue 577 ASP Chi-restraints excluded: chain b residue 580 TYR Chi-restraints excluded: chain b residue 623 LEU Chi-restraints excluded: chain b residue 648 VAL Chi-restraints excluded: chain b residue 662 THR Chi-restraints excluded: chain b residue 680 THR Chi-restraints excluded: chain b residue 685 HIS Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 53 CYS Chi-restraints excluded: chain c residue 61 PHE Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain d residue 69 LEU Chi-restraints excluded: chain d residue 81 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 89 TYR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 21 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 30 SER Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 10 ILE Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 37 PHE Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 47 ILE Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 78 PHE Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 30 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 805 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 476 optimal weight: 7.9990 chunk 610 optimal weight: 9.9990 chunk 472 optimal weight: 3.9990 chunk 703 optimal weight: 9.9990 chunk 466 optimal weight: 5.9990 chunk 832 optimal weight: 0.4980 chunk 521 optimal weight: 4.9990 chunk 507 optimal weight: 6.9990 chunk 384 optimal weight: 0.0980 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 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** ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 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 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 355 HIS ** 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 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 GLN ** 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 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** ** a 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 380 GLN ** b 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 95557 Z= 0.197 Angle : 0.755 12.560 136125 Z= 0.336 Chirality : 0.045 0.476 11785 Planarity : 0.005 0.110 18332 Dihedral : 17.991 113.197 13501 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 5.52 % Allowed : 26.29 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -1.83 (0.09), residues: 8724 helix: 0.18 (0.08), residues: 4286 sheet: -1.46 (0.38), residues: 194 loop : -2.81 (0.09), residues: 4244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP e 680 HIS 0.015 0.001 HIS e 201 PHE 0.042 0.002 PHE e 447 TYR 0.033 0.002 TYR G 626 ARG 0.008 0.000 ARG b 624 *********************** 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 1280 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 395 poor density : 885 time to evaluate : 6.663 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: A 58 ASP cc_start: 0.7336 (p0) cc_final: 0.6868 (p0) REVERT: A 78 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: A 180 HIS cc_start: 0.6548 (OUTLIER) cc_final: 0.5735 (t-90) REVERT: A 415 ARG cc_start: 0.7609 (mmt90) cc_final: 0.7156 (mmt-90) REVERT: A 599 MET cc_start: 0.8175 (ppp) cc_final: 0.7957 (ppp) REVERT: A 608 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6026 (m-10) REVERT: A 745 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8352 (tp30) REVERT: B 102 ASP cc_start: 0.5350 (OUTLIER) cc_final: 0.4961 (t0) REVERT: B 294 ASN cc_start: 0.7857 (p0) cc_final: 0.7062 (t0) REVERT: C 9 THR cc_start: 0.7892 (p) cc_final: 0.7495 (p) REVERT: C 77 MET cc_start: 0.7157 (mmm) cc_final: 0.6855 (mmm) REVERT: D 51 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6332 (mtm) REVERT: K 52 MET cc_start: 0.4457 (tpp) cc_final: 0.4072 (ttp) REVERT: K 54 LEU cc_start: 0.3255 (OUTLIER) cc_final: 0.2873 (tt) REVERT: L 74 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8308 (tt) REVERT: E 91 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7467 (ptt) REVERT: E 310 HIS cc_start: 0.4850 (m90) cc_final: 0.3941 (m-70) REVERT: E 370 HIS cc_start: 0.6382 (OUTLIER) cc_final: 0.6050 (t-170) REVERT: E 462 MET cc_start: 0.7351 (mmm) cc_final: 0.7050 (mmm) REVERT: E 514 VAL cc_start: 0.7440 (OUTLIER) cc_final: 0.7219 (p) REVERT: E 638 MET cc_start: 0.5285 (tmm) cc_final: 0.3988 (ptt) REVERT: E 646 TRP cc_start: 0.6774 (OUTLIER) cc_final: 0.3934 (m100) REVERT: G 443 HIS cc_start: 0.6024 (OUTLIER) cc_final: 0.5677 (t-90) REVERT: G 450 PHE cc_start: 0.5206 (t80) cc_final: 0.4333 (t80) REVERT: G 695 ARG cc_start: 0.6822 (ptt-90) cc_final: 0.5201 (tpt-90) REVERT: H 27 MET cc_start: 0.5192 (tpp) cc_final: 0.4826 (tpp) REVERT: N 77 LYS cc_start: 0.5598 (OUTLIER) cc_final: 0.5247 (mtmm) REVERT: W 55 GLU cc_start: 0.3590 (tp30) cc_final: 0.2926 (tt0) REVERT: O 65 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6536 (pt) REVERT: R 54 LEU cc_start: 0.3969 (OUTLIER) cc_final: 0.3581 (tt) REVERT: e 58 ASP cc_start: 0.7234 (p0) cc_final: 0.6843 (p0) REVERT: e 180 HIS cc_start: 0.6323 (OUTLIER) cc_final: 0.5504 (t-90) REVERT: e 298 HIS cc_start: 0.6704 (m90) cc_final: 0.6503 (m-70) REVERT: e 415 ARG cc_start: 0.7503 (mmt90) cc_final: 0.7141 (mmt90) REVERT: e 471 MET cc_start: 0.6144 (tmm) cc_final: 0.5245 (tmm) REVERT: e 571 PHE cc_start: 0.4788 (OUTLIER) cc_final: 0.2485 (p90) REVERT: e 589 TRP cc_start: 0.6690 (OUTLIER) cc_final: 0.4801 (p-90) REVERT: e 590 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: e 608 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6093 (m-10) REVERT: e 638 MET cc_start: 0.6671 (pmm) cc_final: 0.6399 (pmm) REVERT: e 672 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7564 (pp) REVERT: g 37 MET cc_start: 0.5448 (ptp) cc_final: 0.5120 (ptm) REVERT: g 102 ASP cc_start: 0.5687 (OUTLIER) cc_final: 0.5300 (t0) REVERT: g 294 ASN cc_start: 0.7880 (p0) cc_final: 0.7086 (t0) REVERT: g 414 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6227 (tpp-160) REVERT: g 452 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7362 (t) REVERT: h 9 THR cc_start: 0.7771 (p) cc_final: 0.7289 (p) REVERT: n 82 ASP cc_start: 0.4685 (OUTLIER) cc_final: 0.3920 (t0) REVERT: n 89 TYR cc_start: 0.7293 (m-80) cc_final: 0.7072 (m-80) REVERT: p 1 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6410 (tmm) REVERT: r 52 MET cc_start: 0.4592 (tpp) cc_final: 0.4350 (ttp) REVERT: r 54 LEU cc_start: 0.3331 (OUTLIER) cc_final: 0.2953 (tt) REVERT: a 91 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7158 (ptt) REVERT: a 397 ILE cc_start: 0.8529 (mm) cc_final: 0.8082 (tp) REVERT: a 462 MET cc_start: 0.7753 (mmt) cc_final: 0.7139 (mmm) REVERT: a 514 VAL cc_start: 0.7357 (OUTLIER) cc_final: 0.7137 (p) REVERT: a 599 MET cc_start: 0.7838 (ppp) cc_final: 0.7414 (ppp) REVERT: a 646 TRP cc_start: 0.6723 (OUTLIER) cc_final: 0.4069 (m100) REVERT: a 723 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: b 282 VAL cc_start: 0.8735 (m) cc_final: 0.8491 (t) REVERT: b 443 HIS cc_start: 0.5990 (OUTLIER) cc_final: 0.5582 (t-90) REVERT: b 695 ARG cc_start: 0.6895 (ptt-90) cc_final: 0.5287 (tpt-90) REVERT: d 127 ASP cc_start: 0.6028 (OUTLIER) cc_final: 0.5691 (p0) REVERT: w 55 GLU cc_start: 0.1857 (mm-30) cc_final: 0.0756 (tt0) REVERT: k 54 LEU cc_start: 0.3967 (OUTLIER) cc_final: 0.3652 (tt) REVERT: l 131 ASP cc_start: 0.5695 (p0) cc_final: 0.5287 (p0) outliers start: 395 outliers final: 291 residues processed: 1177 average time/residue: 0.7512 time to fit residues: 1577.2461 Evaluate side-chains 1152 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 827 time to evaluate : 6.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 651 TRP Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain V residue 40 PHE Chi-restraints excluded: chain V residue 61 ILE Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 241 HIS Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 395 MET Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 565 ASP Chi-restraints excluded: chain E residue 590 ASP Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 646 TRP Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 702 VAL Chi-restraints excluded: chain E residue 721 ILE Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 327 TYR Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 435 PHE Chi-restraints excluded: chain G residue 440 LEU Chi-restraints excluded: chain G residue 443 HIS Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 505 ASN Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 562 CYS Chi-restraints excluded: chain G residue 570 THR Chi-restraints excluded: chain G residue 574 SER Chi-restraints excluded: chain G residue 577 ASP Chi-restraints excluded: chain G residue 580 TYR Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain G residue 662 THR Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 138 THR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain R residue 37 PHE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 78 PHE Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain e residue 34 HIS Chi-restraints excluded: chain e residue 128 ASN Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 180 HIS Chi-restraints excluded: chain e residue 232 VAL Chi-restraints excluded: chain e residue 266 THR Chi-restraints excluded: chain e residue 274 ASP Chi-restraints excluded: chain e residue 285 VAL Chi-restraints excluded: chain e residue 303 VAL Chi-restraints excluded: chain e residue 305 PHE Chi-restraints excluded: chain e residue 364 THR Chi-restraints excluded: chain e residue 400 PHE Chi-restraints excluded: chain e residue 431 ILE Chi-restraints excluded: chain e residue 456 TYR Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 571 PHE Chi-restraints excluded: chain e residue 589 TRP Chi-restraints excluded: chain e residue 590 ASP Chi-restraints excluded: chain e residue 608 TYR Chi-restraints excluded: chain e residue 614 MET Chi-restraints excluded: chain e residue 647 LEU Chi-restraints excluded: chain e residue 657 GLN Chi-restraints excluded: chain e residue 672 LEU Chi-restraints excluded: chain e residue 683 SER Chi-restraints excluded: chain e residue 684 LEU Chi-restraints excluded: chain e residue 713 THR Chi-restraints excluded: chain e residue 721 ILE Chi-restraints excluded: chain e residue 738 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 102 ASP Chi-restraints excluded: chain g residue 142 LEU Chi-restraints excluded: chain g residue 178 HIS Chi-restraints excluded: chain g residue 206 HIS Chi-restraints excluded: chain g residue 214 THR Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 278 LEU Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 349 THR Chi-restraints excluded: chain g residue 376 TYR Chi-restraints excluded: chain g residue 397 PHE Chi-restraints excluded: chain g residue 414 ARG Chi-restraints excluded: chain g residue 427 SER Chi-restraints excluded: chain g residue 452 THR Chi-restraints excluded: chain g residue 456 GLN Chi-restraints excluded: chain g residue 457 ILE Chi-restraints excluded: chain g residue 552 ASP Chi-restraints excluded: chain g residue 574 SER Chi-restraints excluded: chain g residue 623 LEU Chi-restraints excluded: chain g residue 680 THR Chi-restraints excluded: chain g residue 688 THR Chi-restraints excluded: chain g residue 694 VAL Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 108 VAL Chi-restraints excluded: chain v residue 43 VAL Chi-restraints excluded: chain v residue 56 THR Chi-restraints excluded: chain o residue 47 THR Chi-restraints excluded: chain o residue 52 ASN Chi-restraints excluded: chain o residue 147 LEU Chi-restraints excluded: chain o residue 156 ASP Chi-restraints excluded: chain o residue 162 SER Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain q residue 32 LEU Chi-restraints excluded: chain r residue 37 PHE Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 54 LEU Chi-restraints excluded: chain r residue 77 ILE Chi-restraints excluded: chain s residue 86 ASP Chi-restraints excluded: chain s residue 88 ASP Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 163 ASN Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain t residue 38 VAL Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 60 ASP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 254 TYR Chi-restraints excluded: chain a residue 277 THR Chi-restraints excluded: chain a residue 285 VAL Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 362 SER Chi-restraints excluded: chain a residue 395 MET Chi-restraints excluded: chain a residue 400 PHE Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 450 PHE Chi-restraints excluded: chain a residue 503 LEU Chi-restraints excluded: chain a residue 514 VAL Chi-restraints excluded: chain a residue 562 LEU Chi-restraints excluded: chain a residue 565 ASP Chi-restraints excluded: chain a residue 583 THR Chi-restraints excluded: chain a residue 590 ASP Chi-restraints excluded: chain a residue 646 TRP Chi-restraints excluded: chain a residue 672 LEU Chi-restraints excluded: chain a residue 684 LEU Chi-restraints excluded: chain a residue 702 VAL Chi-restraints excluded: chain a residue 723 GLN Chi-restraints excluded: chain a residue 745 GLU Chi-restraints excluded: chain b residue 134 ASP Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 141 PHE Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 210 ASP Chi-restraints excluded: chain b residue 216 LEU Chi-restraints excluded: chain b residue 301 ILE Chi-restraints excluded: chain b residue 315 THR Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 327 TYR Chi-restraints excluded: chain b residue 350 SER Chi-restraints excluded: chain b residue 384 VAL Chi-restraints excluded: chain b residue 440 LEU Chi-restraints excluded: chain b residue 443 HIS Chi-restraints excluded: chain b residue 515 ILE Chi-restraints excluded: chain b residue 562 CYS Chi-restraints excluded: chain b residue 570 THR Chi-restraints excluded: chain b residue 574 SER Chi-restraints excluded: chain b residue 577 ASP Chi-restraints excluded: chain b residue 580 TYR Chi-restraints excluded: chain b residue 623 LEU Chi-restraints excluded: chain b residue 648 VAL Chi-restraints excluded: chain b residue 662 THR Chi-restraints excluded: chain b residue 680 THR Chi-restraints excluded: chain b residue 685 HIS Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 53 CYS Chi-restraints excluded: chain c residue 61 PHE Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain d residue 69 LEU Chi-restraints excluded: chain d residue 81 THR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 21 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 30 SER Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 10 ILE Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 37 PHE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 47 ILE Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 78 PHE Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 30 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 515 optimal weight: 20.0000 chunk 332 optimal weight: 10.0000 chunk 497 optimal weight: 6.9990 chunk 250 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 529 optimal weight: 0.4980 chunk 567 optimal weight: 10.0000 chunk 411 optimal weight: 0.2980 chunk 77 optimal weight: 8.9990 chunk 654 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 456 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** ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** L 128 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 225 ASN ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 654 GLN ** G 355 HIS ** 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** T 25 GLN ** 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 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** ** a 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 95557 Z= 0.209 Angle : 0.763 20.564 136125 Z= 0.340 Chirality : 0.046 0.439 11785 Planarity : 0.005 0.110 18332 Dihedral : 17.667 111.543 13494 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 5.42 % Allowed : 26.94 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 2.05 % 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: -1.73 (0.09), residues: 8724 helix: 0.22 (0.08), residues: 4292 sheet: -1.67 (0.33), residues: 242 loop : -2.70 (0.09), residues: 4190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP e 443 HIS 0.013 0.002 HIS e 201 PHE 0.067 0.002 PHE E 74 TYR 0.033 0.002 TYR b 626 ARG 0.006 0.000 ARG b 624 *********************** 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 1247 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 859 time to evaluate : 6.668 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: A 58 ASP cc_start: 0.7275 (p0) cc_final: 0.6737 (p0) REVERT: A 78 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7289 (m-80) REVERT: A 180 HIS cc_start: 0.6538 (OUTLIER) cc_final: 0.5725 (t-90) REVERT: A 415 ARG cc_start: 0.7506 (mmt90) cc_final: 0.7089 (mmt90) REVERT: A 571 PHE cc_start: 0.4997 (OUTLIER) cc_final: 0.2381 (p90) REVERT: A 608 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6030 (m-10) REVERT: A 745 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8358 (tp30) REVERT: B 102 ASP cc_start: 0.5514 (OUTLIER) cc_final: 0.5129 (t0) REVERT: B 294 ASN cc_start: 0.7830 (p0) cc_final: 0.6997 (t0) REVERT: B 435 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7534 (t80) REVERT: C 9 THR cc_start: 0.7889 (p) cc_final: 0.7463 (p) REVERT: C 77 MET cc_start: 0.7479 (mmm) cc_final: 0.7155 (mmm) REVERT: D 51 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6332 (mtm) REVERT: K 52 MET cc_start: 0.4329 (tpp) cc_final: 0.4055 (ttp) REVERT: K 54 LEU cc_start: 0.3254 (OUTLIER) cc_final: 0.2879 (tt) REVERT: E 91 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7473 (ptt) REVERT: E 370 HIS cc_start: 0.6355 (OUTLIER) cc_final: 0.6069 (t-170) REVERT: E 462 MET cc_start: 0.7441 (mmm) cc_final: 0.7162 (mmm) REVERT: E 514 VAL cc_start: 0.7505 (OUTLIER) cc_final: 0.7285 (p) REVERT: E 638 MET cc_start: 0.5251 (tmm) cc_final: 0.3948 (ptt) REVERT: E 646 TRP cc_start: 0.6879 (OUTLIER) cc_final: 0.4019 (m100) REVERT: G 351 LEU cc_start: 0.8658 (tp) cc_final: 0.8276 (tt) REVERT: G 443 HIS cc_start: 0.6077 (OUTLIER) cc_final: 0.5773 (t-90) REVERT: G 450 PHE cc_start: 0.5277 (t80) cc_final: 0.4534 (t80) REVERT: G 695 ARG cc_start: 0.6830 (ptt-90) cc_final: 0.5213 (tpt-90) REVERT: H 27 MET cc_start: 0.5164 (tpp) cc_final: 0.4797 (tpp) REVERT: N 43 MET cc_start: 0.7268 (ppp) cc_final: 0.7011 (pmm) REVERT: N 77 LYS cc_start: 0.5618 (OUTLIER) cc_final: 0.5293 (mtmm) REVERT: W 55 GLU cc_start: 0.3686 (tp30) cc_final: 0.3082 (tt0) REVERT: O 65 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6548 (pt) REVERT: R 54 LEU cc_start: 0.4024 (OUTLIER) cc_final: 0.3617 (tt) REVERT: e 58 ASP cc_start: 0.7254 (p0) cc_final: 0.6863 (p0) REVERT: e 180 HIS cc_start: 0.6338 (OUTLIER) cc_final: 0.5518 (t-90) REVERT: e 298 HIS cc_start: 0.6821 (m90) cc_final: 0.6614 (m-70) REVERT: e 415 ARG cc_start: 0.7440 (mmt90) cc_final: 0.7073 (mmt90) REVERT: e 471 MET cc_start: 0.6164 (tmm) cc_final: 0.5287 (tmm) REVERT: e 571 PHE cc_start: 0.4767 (OUTLIER) cc_final: 0.2287 (p90) REVERT: e 599 MET cc_start: 0.7979 (ppp) cc_final: 0.7641 (ppp) REVERT: e 608 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6072 (m-10) REVERT: e 672 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7415 (pp) REVERT: g 102 ASP cc_start: 0.5726 (OUTLIER) cc_final: 0.5308 (t0) REVERT: g 294 ASN cc_start: 0.7917 (p0) cc_final: 0.7021 (t0) REVERT: g 414 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6320 (tpp-160) REVERT: g 452 THR cc_start: 0.7588 (OUTLIER) cc_final: 0.7380 (t) REVERT: g 652 MET cc_start: 0.6934 (mmt) cc_final: 0.6710 (mtm) REVERT: g 723 THR cc_start: 0.7867 (p) cc_final: 0.7593 (t) REVERT: h 9 THR cc_start: 0.7784 (p) cc_final: 0.7289 (p) REVERT: n 82 ASP cc_start: 0.4868 (OUTLIER) cc_final: 0.4031 (t0) REVERT: n 89 TYR cc_start: 0.7350 (m-80) cc_final: 0.7117 (m-80) REVERT: p 1 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6473 (tmm) REVERT: r 54 LEU cc_start: 0.3327 (OUTLIER) cc_final: 0.2952 (tt) REVERT: a 91 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.7141 (ptt) REVERT: a 397 ILE cc_start: 0.8437 (mm) cc_final: 0.8085 (tp) REVERT: a 462 MET cc_start: 0.7704 (mmt) cc_final: 0.7109 (mmm) REVERT: a 514 VAL cc_start: 0.7418 (OUTLIER) cc_final: 0.7197 (p) REVERT: a 599 MET cc_start: 0.7775 (ppp) cc_final: 0.7371 (ppp) REVERT: a 638 MET cc_start: 0.5062 (tmm) cc_final: 0.4014 (ptt) REVERT: a 646 TRP cc_start: 0.6738 (OUTLIER) cc_final: 0.3905 (m100) REVERT: a 723 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: b 282 VAL cc_start: 0.8706 (m) cc_final: 0.8493 (t) REVERT: b 443 HIS cc_start: 0.6012 (OUTLIER) cc_final: 0.5414 (t-90) REVERT: b 695 ARG cc_start: 0.6899 (ptt-90) cc_final: 0.5282 (tpt-90) REVERT: d 89 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6387 (m-10) REVERT: d 93 GLU cc_start: 0.3483 (mp0) cc_final: 0.3237 (mp0) REVERT: d 127 ASP cc_start: 0.5979 (OUTLIER) cc_final: 0.5656 (p0) REVERT: w 55 GLU cc_start: 0.2148 (mm-30) cc_final: 0.1092 (tt0) REVERT: k 48 VAL cc_start: 0.5608 (m) cc_final: 0.5399 (m) REVERT: k 54 LEU cc_start: 0.3833 (OUTLIER) cc_final: 0.3502 (tt) REVERT: l 131 ASP cc_start: 0.5604 (p0) cc_final: 0.5198 (p0) outliers start: 388 outliers final: 305 residues processed: 1153 average time/residue: 0.7667 time to fit residues: 1575.0738 Evaluate side-chains 1151 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 812 time to evaluate : 6.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 651 TRP Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain V residue 40 PHE Chi-restraints excluded: chain V residue 61 ILE Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 40 TYR Chi-restraints excluded: chain K residue 37 PHE Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain E residue 28 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 87 TRP Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 241 HIS Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 395 MET Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 565 ASP Chi-restraints excluded: chain E residue 590 ASP Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 646 TRP Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 702 VAL Chi-restraints excluded: chain E residue 721 ILE Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 327 TYR Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 435 PHE Chi-restraints excluded: chain G residue 440 LEU Chi-restraints excluded: chain G residue 443 HIS Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 505 ASN Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 562 CYS Chi-restraints excluded: chain G residue 570 THR Chi-restraints excluded: chain G residue 574 SER Chi-restraints excluded: chain G residue 577 ASP Chi-restraints excluded: chain G residue 580 TYR Chi-restraints excluded: chain G residue 634 LEU Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain G residue 662 THR Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain R residue 37 PHE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 78 PHE Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain e residue 34 HIS Chi-restraints excluded: chain e residue 128 ASN Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 180 HIS Chi-restraints excluded: chain e residue 232 VAL Chi-restraints excluded: chain e residue 266 THR Chi-restraints excluded: chain e residue 274 ASP Chi-restraints excluded: chain e residue 285 VAL Chi-restraints excluded: chain e residue 305 PHE Chi-restraints excluded: chain e residue 342 TYR Chi-restraints excluded: chain e residue 364 THR Chi-restraints excluded: chain e residue 374 MET Chi-restraints excluded: chain e residue 400 PHE Chi-restraints excluded: chain e residue 431 ILE Chi-restraints excluded: chain e residue 456 TYR Chi-restraints excluded: chain e residue 461 THR Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 571 PHE Chi-restraints excluded: chain e residue 608 TYR Chi-restraints excluded: chain e residue 614 MET Chi-restraints excluded: chain e residue 657 GLN Chi-restraints excluded: chain e residue 672 LEU Chi-restraints excluded: chain e residue 683 SER Chi-restraints excluded: chain e residue 684 LEU Chi-restraints excluded: chain e residue 713 THR Chi-restraints excluded: chain e residue 721 ILE Chi-restraints excluded: chain e residue 734 LEU Chi-restraints excluded: chain e residue 738 VAL Chi-restraints excluded: chain e residue 744 PHE Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 102 ASP Chi-restraints excluded: chain g residue 142 LEU Chi-restraints excluded: chain g residue 178 HIS Chi-restraints excluded: chain g residue 206 HIS Chi-restraints excluded: chain g residue 214 THR Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 236 ASN Chi-restraints excluded: chain g residue 278 LEU Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 349 THR Chi-restraints excluded: chain g residue 365 MET Chi-restraints excluded: chain g residue 376 TYR Chi-restraints excluded: chain g residue 397 PHE Chi-restraints excluded: chain g residue 414 ARG Chi-restraints excluded: chain g residue 452 THR Chi-restraints excluded: chain g residue 456 GLN Chi-restraints excluded: chain g residue 457 ILE Chi-restraints excluded: chain g residue 552 ASP Chi-restraints excluded: chain g residue 574 SER Chi-restraints excluded: chain g residue 623 LEU Chi-restraints excluded: chain g residue 654 LEU Chi-restraints excluded: chain g residue 680 THR Chi-restraints excluded: chain g residue 688 THR Chi-restraints excluded: chain g residue 694 VAL Chi-restraints excluded: chain h residue 44 THR Chi-restraints excluded: chain h residue 53 CYS Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 108 VAL Chi-restraints excluded: chain v residue 43 VAL Chi-restraints excluded: chain v residue 56 THR Chi-restraints excluded: chain o residue 47 THR Chi-restraints excluded: chain o residue 52 ASN Chi-restraints excluded: chain o residue 53 SER Chi-restraints excluded: chain o residue 147 LEU Chi-restraints excluded: chain o residue 156 ASP Chi-restraints excluded: chain o residue 162 SER Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain q residue 32 LEU Chi-restraints excluded: chain q residue 40 TYR Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 54 LEU Chi-restraints excluded: chain r residue 77 ILE Chi-restraints excluded: chain s residue 86 ASP Chi-restraints excluded: chain s residue 88 ASP Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 163 ASN Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 60 ASP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 140 ILE Chi-restraints excluded: chain a residue 198 LEU Chi-restraints excluded: chain a residue 254 TYR Chi-restraints excluded: chain a residue 277 THR Chi-restraints excluded: chain a residue 285 VAL Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 362 SER Chi-restraints excluded: chain a residue 400 PHE Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 450 PHE Chi-restraints excluded: chain a residue 503 LEU Chi-restraints excluded: chain a residue 514 VAL Chi-restraints excluded: chain a residue 526 ILE Chi-restraints excluded: chain a residue 562 LEU Chi-restraints excluded: chain a residue 565 ASP Chi-restraints excluded: chain a residue 583 THR Chi-restraints excluded: chain a residue 590 ASP Chi-restraints excluded: chain a residue 646 TRP Chi-restraints excluded: chain a residue 672 LEU Chi-restraints excluded: chain a residue 684 LEU Chi-restraints excluded: chain a residue 702 VAL Chi-restraints excluded: chain a residue 723 GLN Chi-restraints excluded: chain a residue 743 PHE Chi-restraints excluded: chain a residue 745 GLU Chi-restraints excluded: chain b residue 134 ASP Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 141 PHE Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 210 ASP Chi-restraints excluded: chain b residue 301 ILE Chi-restraints excluded: chain b residue 315 THR Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain b residue 327 TYR Chi-restraints excluded: chain b residue 350 SER Chi-restraints excluded: chain b residue 384 VAL Chi-restraints excluded: chain b residue 440 LEU Chi-restraints excluded: chain b residue 443 HIS Chi-restraints excluded: chain b residue 515 ILE Chi-restraints excluded: chain b residue 562 CYS Chi-restraints excluded: chain b residue 570 THR Chi-restraints excluded: chain b residue 574 SER Chi-restraints excluded: chain b residue 577 ASP Chi-restraints excluded: chain b residue 580 TYR Chi-restraints excluded: chain b residue 622 TRP Chi-restraints excluded: chain b residue 623 LEU Chi-restraints excluded: chain b residue 648 VAL Chi-restraints excluded: chain b residue 662 THR Chi-restraints excluded: chain b residue 680 THR Chi-restraints excluded: chain b residue 685 HIS Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 53 CYS Chi-restraints excluded: chain c residue 61 PHE Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain d residue 40 VAL Chi-restraints excluded: chain d residue 69 LEU Chi-restraints excluded: chain d residue 81 THR Chi-restraints excluded: chain d residue 89 TYR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 30 SER Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 10 ILE Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 37 SER Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 37 PHE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 47 ILE Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 78 PHE Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 30 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 757 optimal weight: 0.9990 chunk 797 optimal weight: 0.0470 chunk 727 optimal weight: 0.6980 chunk 776 optimal weight: 10.0000 chunk 467 optimal weight: 0.9990 chunk 338 optimal weight: 0.7980 chunk 609 optimal weight: 5.9990 chunk 238 optimal weight: 0.9990 chunk 701 optimal weight: 9.9990 chunk 733 optimal weight: 9.9990 chunk 773 optimal weight: 3.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS A 408 HIS ** 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 456 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** L 128 ASN ** E 80 GLN ** 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** E 352 GLN E 422 ASN ** E 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 355 HIS ** G 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 685 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 408 HIS ** 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 531 HIS ** 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** a 568 ASN ** a 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 355 HIS ** b 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 95557 Z= 0.167 Angle : 0.730 20.243 136125 Z= 0.324 Chirality : 0.044 0.397 11785 Planarity : 0.005 0.107 18332 Dihedral : 17.258 109.861 13485 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 3.95 % Allowed : 28.72 % Favored : 67.33 % 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: -1.51 (0.09), residues: 8724 helix: 0.36 (0.08), residues: 4296 sheet: -1.08 (0.37), residues: 196 loop : -2.56 (0.09), residues: 4232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP e 680 HIS 0.020 0.001 HIS b 379 PHE 0.066 0.001 PHE b 284 TYR 0.029 0.001 TYR e 160 ARG 0.006 0.000 ARG b 624 *********************** 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 1248 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 965 time to evaluate : 6.634 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: A 58 ASP cc_start: 0.7093 (p0) cc_final: 0.6529 (p0) REVERT: A 78 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.7180 (m-80) REVERT: A 180 HIS cc_start: 0.5883 (OUTLIER) cc_final: 0.5531 (t70) REVERT: A 298 HIS cc_start: 0.6659 (m-70) cc_final: 0.6361 (m-70) REVERT: A 599 MET cc_start: 0.7954 (ppp) cc_final: 0.7732 (ppp) REVERT: A 608 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.5943 (m-10) REVERT: B 49 THR cc_start: 0.8073 (p) cc_final: 0.7872 (p) REVERT: B 294 ASN cc_start: 0.7812 (p0) cc_final: 0.6876 (t0) REVERT: B 435 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7628 (t80) REVERT: B 593 VAL cc_start: 0.8451 (p) cc_final: 0.8001 (p) REVERT: B 723 THR cc_start: 0.7859 (p) cc_final: 0.7604 (t) REVERT: C 9 THR cc_start: 0.7766 (p) cc_final: 0.7374 (p) REVERT: C 77 MET cc_start: 0.7426 (mmm) cc_final: 0.7183 (mmm) REVERT: D 51 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6171 (mtm) REVERT: L 74 LEU cc_start: 0.8918 (tp) cc_final: 0.8558 (tt) REVERT: E 91 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.7108 (ptt) REVERT: E 370 HIS cc_start: 0.6198 (OUTLIER) cc_final: 0.5807 (t-170) REVERT: E 462 MET cc_start: 0.7353 (mmm) cc_final: 0.7104 (mmm) REVERT: E 514 VAL cc_start: 0.7463 (OUTLIER) cc_final: 0.7251 (p) REVERT: E 599 MET cc_start: 0.7881 (ppp) cc_final: 0.7113 (ppp) REVERT: E 638 MET cc_start: 0.5274 (tmm) cc_final: 0.3890 (ptt) REVERT: E 646 TRP cc_start: 0.6861 (OUTLIER) cc_final: 0.4007 (m100) REVERT: G 304 MET cc_start: 0.6748 (mmm) cc_final: 0.5898 (mmm) REVERT: G 443 HIS cc_start: 0.5796 (OUTLIER) cc_final: 0.5378 (t-90) REVERT: G 450 PHE cc_start: 0.5343 (t80) cc_final: 0.5087 (t80) REVERT: G 620 MET cc_start: 0.4130 (ttm) cc_final: 0.3911 (ttm) REVERT: G 695 ARG cc_start: 0.6741 (ptt-90) cc_final: 0.5094 (tpt-90) REVERT: H 27 MET cc_start: 0.4912 (tpp) cc_final: 0.4535 (tpp) REVERT: N 77 LYS cc_start: 0.5707 (OUTLIER) cc_final: 0.5393 (mtmm) REVERT: N 89 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: W 55 GLU cc_start: 0.3513 (tp30) cc_final: 0.3077 (tt0) REVERT: e 58 ASP cc_start: 0.7047 (p0) cc_final: 0.6698 (p0) REVERT: e 298 HIS cc_start: 0.6908 (m90) cc_final: 0.6571 (m-70) REVERT: e 471 MET cc_start: 0.5876 (tmm) cc_final: 0.5269 (tmm) REVERT: e 599 MET cc_start: 0.7861 (ppp) cc_final: 0.7602 (ppp) REVERT: e 608 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.6035 (m-10) REVERT: e 672 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7402 (pp) REVERT: g 294 ASN cc_start: 0.7936 (p0) cc_final: 0.7016 (t0) REVERT: g 414 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6210 (tpp-160) REVERT: g 574 SER cc_start: 0.6150 (OUTLIER) cc_final: 0.5716 (t) REVERT: g 593 VAL cc_start: 0.8422 (p) cc_final: 0.7920 (p) REVERT: g 652 MET cc_start: 0.6912 (mmt) cc_final: 0.6564 (mtm) REVERT: h 9 THR cc_start: 0.7762 (p) cc_final: 0.7304 (p) REVERT: n 51 MET cc_start: 0.6833 (mtp) cc_final: 0.5447 (mtm) REVERT: n 82 ASP cc_start: 0.4632 (OUTLIER) cc_final: 0.3804 (t0) REVERT: n 89 TYR cc_start: 0.7316 (m-80) cc_final: 0.7069 (m-80) REVERT: n 136 MET cc_start: 0.3710 (mmm) cc_final: 0.3381 (tpp) REVERT: o 91 ILE cc_start: 0.8729 (tp) cc_final: 0.8504 (tp) REVERT: p 1 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6585 (tmm) REVERT: a 462 MET cc_start: 0.7556 (mmt) cc_final: 0.6993 (mmm) REVERT: a 568 ASN cc_start: 0.7276 (OUTLIER) cc_final: 0.6820 (t0) REVERT: a 599 MET cc_start: 0.7666 (ppp) cc_final: 0.7263 (ppp) REVERT: a 638 MET cc_start: 0.5085 (tmm) cc_final: 0.3930 (ptt) REVERT: a 646 TRP cc_start: 0.6677 (OUTLIER) cc_final: 0.3917 (m100) REVERT: a 723 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: b 443 HIS cc_start: 0.5784 (OUTLIER) cc_final: 0.5234 (t-90) REVERT: b 695 ARG cc_start: 0.6722 (ptt-90) cc_final: 0.5081 (tpt-90) REVERT: c 27 MET cc_start: 0.4613 (tpp) cc_final: 0.3051 (tpp) REVERT: d 89 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6328 (m-10) REVERT: d 93 GLU cc_start: 0.3491 (mp0) cc_final: 0.3016 (mp0) REVERT: d 127 ASP cc_start: 0.5937 (OUTLIER) cc_final: 0.5610 (p0) REVERT: w 55 GLU cc_start: 0.2349 (mm-30) cc_final: 0.1351 (tt0) REVERT: l 131 ASP cc_start: 0.5589 (p0) cc_final: 0.5215 (p0) outliers start: 283 outliers final: 215 residues processed: 1168 average time/residue: 0.7723 time to fit residues: 1597.1302 Evaluate side-chains 1111 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 872 time to evaluate : 6.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 651 TRP Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain V residue 40 PHE Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain E residue 28 LYS Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 87 TRP Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 241 HIS Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 646 TRP Chi-restraints excluded: chain E residue 702 VAL Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain G residue 327 TYR Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 435 PHE Chi-restraints excluded: chain G residue 443 HIS Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 505 ASN Chi-restraints excluded: chain G residue 562 CYS Chi-restraints excluded: chain G residue 577 ASP Chi-restraints excluded: chain G residue 580 TYR Chi-restraints excluded: chain G residue 634 LEU Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 89 TYR Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain R residue 37 PHE Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain e residue 34 HIS Chi-restraints excluded: chain e residue 128 ASN Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 180 HIS Chi-restraints excluded: chain e residue 232 VAL Chi-restraints excluded: chain e residue 266 THR Chi-restraints excluded: chain e residue 274 ASP Chi-restraints excluded: chain e residue 285 VAL Chi-restraints excluded: chain e residue 303 VAL Chi-restraints excluded: chain e residue 305 PHE Chi-restraints excluded: chain e residue 342 TYR Chi-restraints excluded: chain e residue 400 PHE Chi-restraints excluded: chain e residue 456 TYR Chi-restraints excluded: chain e residue 461 THR Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 608 TYR Chi-restraints excluded: chain e residue 614 MET Chi-restraints excluded: chain e residue 672 LEU Chi-restraints excluded: chain e residue 683 SER Chi-restraints excluded: chain e residue 684 LEU Chi-restraints excluded: chain e residue 713 THR Chi-restraints excluded: chain e residue 738 VAL Chi-restraints excluded: chain e residue 744 PHE Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 142 LEU Chi-restraints excluded: chain g residue 206 HIS Chi-restraints excluded: chain g residue 214 THR Chi-restraints excluded: chain g residue 349 THR Chi-restraints excluded: chain g residue 365 MET Chi-restraints excluded: chain g residue 376 TYR Chi-restraints excluded: chain g residue 414 ARG Chi-restraints excluded: chain g residue 456 GLN Chi-restraints excluded: chain g residue 552 ASP Chi-restraints excluded: chain g residue 574 SER Chi-restraints excluded: chain g residue 623 LEU Chi-restraints excluded: chain g residue 654 LEU Chi-restraints excluded: chain g residue 680 THR Chi-restraints excluded: chain h residue 44 THR Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 108 VAL Chi-restraints excluded: chain v residue 43 VAL Chi-restraints excluded: chain o residue 47 THR Chi-restraints excluded: chain o residue 53 SER Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain q residue 32 LEU Chi-restraints excluded: chain s residue 88 ASP Chi-restraints excluded: chain s residue 163 ASN Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain a residue 60 ASP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 254 TYR Chi-restraints excluded: chain a residue 274 ASP Chi-restraints excluded: chain a residue 285 VAL Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 400 PHE Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 450 PHE Chi-restraints excluded: chain a residue 562 LEU Chi-restraints excluded: chain a residue 568 ASN Chi-restraints excluded: chain a residue 583 THR Chi-restraints excluded: chain a residue 590 ASP Chi-restraints excluded: chain a residue 646 TRP Chi-restraints excluded: chain a residue 684 LEU Chi-restraints excluded: chain a residue 702 VAL Chi-restraints excluded: chain a residue 723 GLN Chi-restraints excluded: chain a residue 745 GLU Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 141 PHE Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 301 ILE Chi-restraints excluded: chain b residue 315 THR Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 327 TYR Chi-restraints excluded: chain b residue 350 SER Chi-restraints excluded: chain b residue 384 VAL Chi-restraints excluded: chain b residue 440 LEU Chi-restraints excluded: chain b residue 443 HIS Chi-restraints excluded: chain b residue 562 CYS Chi-restraints excluded: chain b residue 570 THR Chi-restraints excluded: chain b residue 574 SER Chi-restraints excluded: chain b residue 580 TYR Chi-restraints excluded: chain b residue 622 TRP Chi-restraints excluded: chain b residue 623 LEU Chi-restraints excluded: chain b residue 648 VAL Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 53 CYS Chi-restraints excluded: chain c residue 61 PHE Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain d residue 69 LEU Chi-restraints excluded: chain d residue 81 THR Chi-restraints excluded: chain d residue 89 TYR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain w residue 21 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 30 SER Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 10 ILE Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 37 SER Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 37 PHE Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain m residue 21 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 509 optimal weight: 5.9990 chunk 820 optimal weight: 2.9990 chunk 500 optimal weight: 6.9990 chunk 389 optimal weight: 5.9990 chunk 570 optimal weight: 8.9990 chunk 860 optimal weight: 6.9990 chunk 792 optimal weight: 0.9980 chunk 685 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 529 optimal weight: 1.9990 chunk 420 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 456 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** ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 GLN ** G 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 685 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 116 GLN ** 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 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** ** a 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 95557 Z= 0.192 Angle : 0.744 15.677 136125 Z= 0.334 Chirality : 0.045 0.396 11785 Planarity : 0.005 0.108 18332 Dihedral : 17.077 111.101 13478 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 3.62 % Allowed : 29.57 % Favored : 66.81 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -1.46 (0.09), residues: 8724 helix: 0.39 (0.08), residues: 4280 sheet: -1.04 (0.37), residues: 196 loop : -2.51 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP E 290 HIS 0.021 0.001 HIS b 379 PHE 0.058 0.002 PHE b 284 TYR 0.029 0.001 TYR O 107 ARG 0.009 0.000 ARG w 33 ********************** 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 1131 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 872 time to evaluate : 6.841 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: A 58 ASP cc_start: 0.7091 (p0) cc_final: 0.6557 (p0) REVERT: A 78 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: A 180 HIS cc_start: 0.6706 (OUTLIER) cc_final: 0.5780 (t-90) REVERT: A 298 HIS cc_start: 0.6820 (m-70) cc_final: 0.6500 (m-70) REVERT: A 415 ARG cc_start: 0.7054 (mmt90) cc_final: 0.6752 (mmt-90) REVERT: A 599 MET cc_start: 0.7968 (ppp) cc_final: 0.7714 (ppp) REVERT: A 608 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.5993 (m-10) REVERT: B 49 THR cc_start: 0.8156 (p) cc_final: 0.7948 (p) REVERT: B 294 ASN cc_start: 0.7864 (p0) cc_final: 0.6914 (t0) REVERT: B 435 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7693 (t80) REVERT: B 723 THR cc_start: 0.7920 (p) cc_final: 0.7660 (t) REVERT: C 9 THR cc_start: 0.7784 (p) cc_final: 0.7415 (p) REVERT: C 77 MET cc_start: 0.7460 (mmm) cc_final: 0.7189 (mmm) REVERT: D 51 MET cc_start: 0.7011 (mtp) cc_final: 0.6156 (mtm) REVERT: E 91 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7278 (ptt) REVERT: E 370 HIS cc_start: 0.6280 (OUTLIER) cc_final: 0.5981 (t-170) REVERT: E 462 MET cc_start: 0.7355 (mmm) cc_final: 0.7086 (mmm) REVERT: E 514 VAL cc_start: 0.7504 (OUTLIER) cc_final: 0.7286 (p) REVERT: E 599 MET cc_start: 0.8030 (ppp) cc_final: 0.7284 (ppp) REVERT: E 638 MET cc_start: 0.5293 (tmm) cc_final: 0.3889 (ptt) REVERT: E 646 TRP cc_start: 0.6878 (OUTLIER) cc_final: 0.4035 (m100) REVERT: G 304 MET cc_start: 0.6790 (mmm) cc_final: 0.6027 (mmm) REVERT: G 351 LEU cc_start: 0.8470 (tp) cc_final: 0.8106 (tt) REVERT: G 443 HIS cc_start: 0.5746 (OUTLIER) cc_final: 0.5276 (t-90) REVERT: G 450 PHE cc_start: 0.5452 (t80) cc_final: 0.5228 (t80) REVERT: G 620 MET cc_start: 0.4210 (ttm) cc_final: 0.4000 (ttm) REVERT: G 695 ARG cc_start: 0.6806 (ptt-90) cc_final: 0.5190 (tpt-90) REVERT: H 27 MET cc_start: 0.4975 (tpp) cc_final: 0.4598 (tpp) REVERT: N 77 LYS cc_start: 0.5732 (OUTLIER) cc_final: 0.5394 (mtmm) REVERT: W 55 GLU cc_start: 0.3422 (tp30) cc_final: 0.3046 (tt0) REVERT: R 54 LEU cc_start: 0.3960 (OUTLIER) cc_final: 0.3627 (tt) REVERT: e 58 ASP cc_start: 0.7154 (p0) cc_final: 0.6739 (p0) REVERT: e 298 HIS cc_start: 0.6765 (m90) cc_final: 0.6523 (m-70) REVERT: e 471 MET cc_start: 0.6134 (tmm) cc_final: 0.5315 (tmm) REVERT: e 599 MET cc_start: 0.7901 (ppp) cc_final: 0.7625 (ppp) REVERT: e 608 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.5862 (m-10) REVERT: e 672 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7487 (pp) REVERT: g 294 ASN cc_start: 0.7989 (p0) cc_final: 0.7042 (t0) REVERT: g 414 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6261 (tpp-160) REVERT: g 457 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7299 (tp) REVERT: g 574 SER cc_start: 0.6274 (OUTLIER) cc_final: 0.5850 (t) REVERT: g 652 MET cc_start: 0.7026 (mmt) cc_final: 0.6715 (mtm) REVERT: h 9 THR cc_start: 0.7865 (p) cc_final: 0.7353 (p) REVERT: n 51 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.5296 (mtm) REVERT: n 82 ASP cc_start: 0.4770 (OUTLIER) cc_final: 0.3768 (t0) REVERT: n 89 TYR cc_start: 0.7326 (m-80) cc_final: 0.7063 (m-80) REVERT: p 1 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6436 (tmm) REVERT: a 462 MET cc_start: 0.7644 (mmt) cc_final: 0.7077 (mmm) REVERT: a 514 VAL cc_start: 0.7395 (OUTLIER) cc_final: 0.7181 (p) REVERT: a 599 MET cc_start: 0.7666 (ppp) cc_final: 0.7331 (ppp) REVERT: a 638 MET cc_start: 0.5133 (tmm) cc_final: 0.3790 (ptt) REVERT: a 646 TRP cc_start: 0.6720 (OUTLIER) cc_final: 0.3909 (m100) REVERT: a 654 GLN cc_start: 0.5330 (tp40) cc_final: 0.5077 (mm-40) REVERT: a 723 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: b 304 MET cc_start: 0.6797 (mmm) cc_final: 0.5834 (mmm) REVERT: b 351 LEU cc_start: 0.8481 (tp) cc_final: 0.8098 (tt) REVERT: b 443 HIS cc_start: 0.5971 (OUTLIER) cc_final: 0.5366 (t-90) REVERT: b 695 ARG cc_start: 0.6785 (ptt-90) cc_final: 0.5149 (tpt-90) REVERT: c 27 MET cc_start: 0.4657 (tpp) cc_final: 0.3141 (tpp) REVERT: d 89 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6472 (m-10) REVERT: d 127 ASP cc_start: 0.6029 (OUTLIER) cc_final: 0.5720 (p0) REVERT: w 55 GLU cc_start: 0.2484 (mm-30) cc_final: 0.1400 (tt0) outliers start: 259 outliers final: 215 residues processed: 1058 average time/residue: 0.7711 time to fit residues: 1458.2261 Evaluate side-chains 1091 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 851 time to evaluate : 6.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 651 TRP Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain V residue 40 PHE Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain E residue 28 LYS Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 87 TRP Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 241 HIS Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 450 PHE Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 646 TRP Chi-restraints excluded: chain E residue 702 VAL Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain G residue 327 TYR Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 435 PHE Chi-restraints excluded: chain G residue 443 HIS Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 505 ASN Chi-restraints excluded: chain G residue 562 CYS Chi-restraints excluded: chain G residue 577 ASP Chi-restraints excluded: chain G residue 580 TYR Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 37 PHE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 78 PHE Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain e residue 34 HIS Chi-restraints excluded: chain e residue 128 ASN Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 232 VAL Chi-restraints excluded: chain e residue 266 THR Chi-restraints excluded: chain e residue 274 ASP Chi-restraints excluded: chain e residue 285 VAL Chi-restraints excluded: chain e residue 305 PHE Chi-restraints excluded: chain e residue 342 TYR Chi-restraints excluded: chain e residue 400 PHE Chi-restraints excluded: chain e residue 456 TYR Chi-restraints excluded: chain e residue 534 MET Chi-restraints excluded: chain e residue 608 TYR Chi-restraints excluded: chain e residue 609 HIS Chi-restraints excluded: chain e residue 614 MET Chi-restraints excluded: chain e residue 672 LEU Chi-restraints excluded: chain e residue 683 SER Chi-restraints excluded: chain e residue 684 LEU Chi-restraints excluded: chain e residue 713 THR Chi-restraints excluded: chain e residue 738 VAL Chi-restraints excluded: chain e residue 744 PHE Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 118 SER Chi-restraints excluded: chain g residue 142 LEU Chi-restraints excluded: chain g residue 206 HIS Chi-restraints excluded: chain g residue 349 THR Chi-restraints excluded: chain g residue 365 MET Chi-restraints excluded: chain g residue 376 TYR Chi-restraints excluded: chain g residue 397 PHE Chi-restraints excluded: chain g residue 412 LEU Chi-restraints excluded: chain g residue 414 ARG Chi-restraints excluded: chain g residue 456 GLN Chi-restraints excluded: chain g residue 457 ILE Chi-restraints excluded: chain g residue 552 ASP Chi-restraints excluded: chain g residue 574 SER Chi-restraints excluded: chain g residue 623 LEU Chi-restraints excluded: chain g residue 654 LEU Chi-restraints excluded: chain g residue 680 THR Chi-restraints excluded: chain h residue 44 THR Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain n residue 51 MET Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 108 VAL Chi-restraints excluded: chain v residue 43 VAL Chi-restraints excluded: chain o residue 47 THR Chi-restraints excluded: chain o residue 53 SER Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain q residue 32 LEU Chi-restraints excluded: chain q residue 40 TYR Chi-restraints excluded: chain s residue 88 ASP Chi-restraints excluded: chain s residue 163 ASN Chi-restraints excluded: chain t residue 28 VAL Chi-restraints excluded: chain a residue 60 ASP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 87 TRP Chi-restraints excluded: chain a residue 254 TYR Chi-restraints excluded: chain a residue 274 ASP Chi-restraints excluded: chain a residue 285 VAL Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 400 PHE Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 450 PHE Chi-restraints excluded: chain a residue 514 VAL Chi-restraints excluded: chain a residue 562 LEU Chi-restraints excluded: chain a residue 583 THR Chi-restraints excluded: chain a residue 590 ASP Chi-restraints excluded: chain a residue 646 TRP Chi-restraints excluded: chain a residue 684 LEU Chi-restraints excluded: chain a residue 702 VAL Chi-restraints excluded: chain a residue 723 GLN Chi-restraints excluded: chain a residue 745 GLU Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 141 PHE Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 301 ILE Chi-restraints excluded: chain b residue 315 THR Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 327 TYR Chi-restraints excluded: chain b residue 350 SER Chi-restraints excluded: chain b residue 384 VAL Chi-restraints excluded: chain b residue 440 LEU Chi-restraints excluded: chain b residue 443 HIS Chi-restraints excluded: chain b residue 562 CYS Chi-restraints excluded: chain b residue 570 THR Chi-restraints excluded: chain b residue 574 SER Chi-restraints excluded: chain b residue 580 TYR Chi-restraints excluded: chain b residue 622 TRP Chi-restraints excluded: chain b residue 623 LEU Chi-restraints excluded: chain b residue 648 VAL Chi-restraints excluded: chain c residue 10 CYS Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 53 CYS Chi-restraints excluded: chain c residue 61 PHE Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain d residue 69 LEU Chi-restraints excluded: chain d residue 81 THR Chi-restraints excluded: chain d residue 89 TYR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 30 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 10 ILE Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 37 SER Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 37 PHE Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain m residue 21 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 544 optimal weight: 8.9990 chunk 730 optimal weight: 0.6980 chunk 209 optimal weight: 5.9990 chunk 632 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 686 optimal weight: 9.9990 chunk 287 optimal weight: 3.9990 chunk 704 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS ** 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 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 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 685 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 GLN ** 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 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 613 ASN ** 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 = 0.4224 r_free = 0.4224 target = 0.120335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.105523 restraints weight = 336115.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.106327 restraints weight = 225355.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.106475 restraints weight = 181492.561| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 95557 Z= 0.177 Angle : 0.735 15.167 136125 Z= 0.329 Chirality : 0.044 0.376 11785 Planarity : 0.005 0.108 18332 Dihedral : 16.821 109.444 13477 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.17 % Favored : 90.82 % Rotamer: Outliers : 3.69 % Allowed : 29.51 % Favored : 66.80 % 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: -1.38 (0.09), residues: 8724 helix: 0.44 (0.08), residues: 4304 sheet: -0.96 (0.37), residues: 196 loop : -2.46 (0.09), residues: 4224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP E 290 HIS 0.023 0.001 HIS b 379 PHE 0.065 0.002 PHE E 74 TYR 0.029 0.001 TYR e 160 ARG 0.008 0.000 ARG w 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23813.57 seconds wall clock time: 416 minutes 40.76 seconds (25000.76 seconds total)