Starting phenix.real_space_refine on Thu Mar 14 23:44:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k39_36848/03_2024/8k39_36848.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k39_36848/03_2024/8k39_36848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k39_36848/03_2024/8k39_36848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k39_36848/03_2024/8k39_36848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k39_36848/03_2024/8k39_36848.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k39_36848/03_2024/8k39_36848.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 2.155 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: 4 Type Number sf(0) Gaussians S 672 5.16 5 C 78268 2.51 5 N 21741 2.21 5 O 23937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 120": "OE1" <-> "OE2" Residue "0 GLU 158": "OE1" <-> "OE2" Residue "0 TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 201": "OD1" <-> "OD2" Residue "0 GLU 259": "OE1" <-> "OE2" Residue "0 ASP 292": "OD1" <-> "OD2" Residue "1 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 201": "OD1" <-> "OD2" Residue "1 GLU 216": "OE1" <-> "OE2" Residue "1 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 145": "OE1" <-> "OE2" Residue "2 GLU 185": "OE1" <-> "OE2" Residue "2 GLU 216": "OE1" <-> "OE2" Residue "2 GLU 229": "OE1" <-> "OE2" Residue "2 ASP 313": "OD1" <-> "OD2" Residue "3 ASP 97": "OD1" <-> "OD2" Residue "3 TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 247": "OD1" <-> "OD2" Residue "3 GLU 296": "OE1" <-> "OE2" Residue "3 ASP 331": "OD1" <-> "OD2" Residue "3 GLU 334": "OE1" <-> "OE2" Residue "4 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 61": "OE1" <-> "OE2" Residue "4 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 227": "OE1" <-> "OE2" Residue "4 TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 185": "OE1" <-> "OE2" Residue "5 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 259": "OE1" <-> "OE2" Residue "5 ASP 290": "OD1" <-> "OD2" Residue "5 ASP 292": "OD1" <-> "OD2" Residue "6 PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 97": "OD1" <-> "OD2" Residue "6 GLU 145": "OE1" <-> "OE2" Residue "6 GLU 259": "OE1" <-> "OE2" Residue "6 GLU 296": "OE1" <-> "OE2" Residue "7 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 96": "OE1" <-> "OE2" Residue "7 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 119": "OE1" <-> "OE2" Residue "7 ASP 269": "OD1" <-> "OD2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "A ASP 219": "OD1" <-> "OD2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ASP 313": "OD1" <-> "OD2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C ASP 313": "OD1" <-> "OD2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 118": "OD1" <-> "OD2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E ASP 95": "OD1" <-> "OD2" Residue "E ASP 219": "OD1" <-> "OD2" Residue "E TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "E PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F ASP 201": "OD1" <-> "OD2" Residue "F GLU 296": "OE1" <-> "OE2" Residue "G GLU 159": "OE1" <-> "OE2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 219": "OD1" <-> "OD2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "I PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 145": "OE1" <-> "OE2" Residue "I ASP 201": "OD1" <-> "OD2" Residue "I GLU 229": "OE1" <-> "OE2" Residue "I ASP 313": "OD1" <-> "OD2" Residue "I PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "J ASP 95": "OD1" <-> "OD2" Residue "J ASP 97": "OD1" <-> "OD2" Residue "J TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 247": "OD1" <-> "OD2" Residue "J PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 103": "OD1" <-> "OD2" Residue "K PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 151": "OE1" <-> "OE2" Residue "K PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 14": "OE1" <-> "OE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "L PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 158": "OE1" <-> "OE2" Residue "M GLU 159": "OE1" <-> "OE2" Residue "M TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 216": "OE1" <-> "OE2" Residue "M TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 296": "OE1" <-> "OE2" Residue "M TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 334": "OE1" <-> "OE2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 145": "OE1" <-> "OE2" Residue "N GLU 158": "OE1" <-> "OE2" Residue "O TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 120": "OE1" <-> "OE2" Residue "O TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 182": "OD1" <-> "OD2" Residue "O GLU 227": "OE1" <-> "OE2" Residue "P ASP 97": "OD1" <-> "OD2" Residue "P GLU 158": "OE1" <-> "OE2" Residue "P TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 37": "OE1" <-> "OE2" Residue "Q TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 83": "OE1" <-> "OE2" Residue "Q ASP 153": "OD1" <-> "OD2" Residue "Q GLU 158": "OE1" <-> "OE2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "Q ASP 313": "OD1" <-> "OD2" Residue "R ASP 20": "OD1" <-> "OD2" Residue "R TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 182": "OD1" <-> "OD2" Residue "R ASP 313": "OD1" <-> "OD2" Residue "S TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 95": "OD1" <-> "OD2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S ASP 148": "OD1" <-> "OD2" Residue "S ASP 269": "OD1" <-> "OD2" Residue "T GLU 83": "OE1" <-> "OE2" Residue "T ASP 95": "OD1" <-> "OD2" Residue "T TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 313": "OD1" <-> "OD2" Residue "U TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 120": "OE1" <-> "OE2" Residue "U GLU 140": "OE1" <-> "OE2" Residue "U ASP 242": "OD1" <-> "OD2" Residue "U PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 355": "OE1" <-> "OE2" Residue "U GLU 488": "OE1" <-> "OE2" Residue "V ASP 46": "OD1" <-> "OD2" Residue "V GLU 120": "OE1" <-> "OE2" Residue "V PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 346": "OD1" <-> "OD2" Residue "V ASP 348": "OD1" <-> "OD2" Residue "W TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 121": "OD1" <-> "OD2" Residue "W PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 337": "OD1" <-> "OD2" Residue "W TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 446": "OD1" <-> "OD2" Residue "W GLU 460": "OE1" <-> "OE2" Residue "X ASP 46": "OD1" <-> "OD2" Residue "X GLU 103": "OE1" <-> "OE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X ASP 185": "OD1" <-> "OD2" Residue "X TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 456": "OD1" <-> "OD2" Residue "X GLU 478": "OE1" <-> "OE2" Residue "X ASP 484": "OD1" <-> "OD2" Residue "Y TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 110": "OE1" <-> "OE2" Residue "Y GLU 112": "OE1" <-> "OE2" Residue "Y TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 460": "OE1" <-> "OE2" Residue "Z PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 241": "OE1" <-> "OE2" Residue "Z GLU 478": "OE1" <-> "OE2" Residue "a PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 127": "OD1" <-> "OD2" Residue "a ASP 158": "OD1" <-> "OD2" Residue "a ASP 197": "OD1" <-> "OD2" Residue "a GLU 238": "OE1" <-> "OE2" Residue "a TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 285": "OE1" <-> "OE2" Residue "a TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 120": "OE1" <-> "OE2" Residue "b ASP 158": "OD1" <-> "OD2" Residue "b PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 241": "OE1" <-> "OE2" Residue "b TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 437": "OE1" <-> "OE2" Residue "c PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 127": "OD1" <-> "OD2" Residue "c GLU 208": "OE1" <-> "OE2" Residue "c GLU 238": "OE1" <-> "OE2" Residue "c GLU 355": "OE1" <-> "OE2" Residue "c GLU 437": "OE1" <-> "OE2" Residue "d GLU 43": "OE1" <-> "OE2" Residue "d TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 120": "OE1" <-> "OE2" Residue "d GLU 225": "OE1" <-> "OE2" Residue "d ASP 242": "OD1" <-> "OD2" Residue "d GLU 478": "OE1" <-> "OE2" Residue "e ASP 61": "OD1" <-> "OD2" Residue "e ASP 127": "OD1" <-> "OD2" Residue "e TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 238": "OE1" <-> "OE2" Residue "e GLU 283": "OE1" <-> "OE2" Residue "e ASP 346": "OD1" <-> "OD2" Residue "e GLU 488": "OE1" <-> "OE2" Residue "f GLU 102": "OE1" <-> "OE2" Residue "f GLU 225": "OE1" <-> "OE2" Residue "f GLU 238": "OE1" <-> "OE2" Residue "f ASP 446": "OD1" <-> "OD2" Residue "f ASP 456": "OD1" <-> "OD2" Residue "g TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 103": "OD1" <-> "OD2" Residue "g GLU 145": "OE1" <-> "OE2" Residue "g ASP 182": "OD1" <-> "OD2" Residue "g GLU 227": "OE1" <-> "OE2" Residue "g TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 159": "OE1" <-> "OE2" Residue "h PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 227": "OE1" <-> "OE2" Residue "h GLU 296": "OE1" <-> "OE2" Time to flip residues: 0.27s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 124618 Number of models: 1 Model: "" Number of chains: 42 Chain: "0" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "1" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "2" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "3" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2649 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 18, 'TRANS': 318} Chain: "4" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2649 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 18, 'TRANS': 318} Chain: "5" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2649 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 18, 'TRANS': 318} Chain: "6" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "7" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "A" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "B" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "C" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "D" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "E" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "F" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "G" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "H" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "I" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "J" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "K" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "L" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "M" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "N" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2649 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 18, 'TRANS': 318} Chain: "O" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "P" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "Q" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "R" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "S" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "T" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "U" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3675 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "V" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3708 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 17, 'TRANS': 454} Chain breaks: 1 Chain: "W" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3708 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 17, 'TRANS': 454} Chain breaks: 1 Chain: "X" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3708 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 17, 'TRANS': 454} Chain breaks: 1 Chain: "Y" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3708 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 17, 'TRANS': 454} Chain breaks: 1 Chain: "Z" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3708 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 17, 'TRANS': 454} Chain breaks: 1 Chain: "a" Number of atoms: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3743 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 17, 'TRANS': 458} Chain breaks: 1 Chain: "b" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3708 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 17, 'TRANS': 454} Chain breaks: 1 Chain: "c" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3708 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 17, 'TRANS': 454} Chain breaks: 1 Chain: "d" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3708 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 17, 'TRANS': 454} Chain breaks: 1 Chain: "e" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3708 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 17, 'TRANS': 454} Chain breaks: 1 Chain: "f" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3708 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 17, 'TRANS': 454} Chain breaks: 1 Chain: "g" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "h" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2649 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 18, 'TRANS': 318} Time building chain proxies: 47.45, per 1000 atoms: 0.38 Number of scatterers: 124618 At special positions: 0 Unit cell: (380.8, 378.08, 121.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 672 16.00 O 23937 8.00 N 21741 7.00 C 78268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 33.31 Conformation dependent library (CDL) restraints added in 16.5 seconds 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 29408 Finding SS restraints... Secondary structure from input PDB file: 442 helices and 230 sheets defined 35.1% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.35 Creating SS restraints... Processing helix chain '0' and resid 21 through 27 Processing helix chain '0' and resid 85 through 91 removed outlier: 3.889A pdb=" N THR 0 89 " --> pdb=" O ASN 0 85 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG 0 91 " --> pdb=" O GLN 0 87 " (cutoff:3.500A) Processing helix chain '0' and resid 103 through 137 removed outlier: 3.927A pdb=" N ARG 0 109 " --> pdb=" O ALA 0 105 " (cutoff:3.500A) Processing helix chain '0' and resid 157 through 161 Processing helix chain '0' and resid 180 through 189 Processing helix chain '0' and resid 201 through 210 Processing helix chain '0' and resid 211 through 217 removed outlier: 3.620A pdb=" N LYS 0 215 " --> pdb=" O PHE 0 211 " (cutoff:3.500A) Processing helix chain '0' and resid 290 through 296 removed outlier: 3.777A pdb=" N GLN 0 294 " --> pdb=" O ASP 0 290 " (cutoff:3.500A) Processing helix chain '1' and resid 21 through 27 Processing helix chain '1' and resid 85 through 90 removed outlier: 3.748A pdb=" N THR 1 89 " --> pdb=" O ASN 1 85 " (cutoff:3.500A) Processing helix chain '1' and resid 103 through 137 removed outlier: 3.545A pdb=" N ARG 1 107 " --> pdb=" O ASP 1 103 " (cutoff:3.500A) Processing helix chain '1' and resid 180 through 189 Processing helix chain '1' and resid 201 through 210 Processing helix chain '1' and resid 211 through 220 removed outlier: 3.610A pdb=" N LEU 1 218 " --> pdb=" O VAL 1 214 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP 1 219 " --> pdb=" O LYS 1 215 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR 1 220 " --> pdb=" O GLU 1 216 " (cutoff:3.500A) Processing helix chain '1' and resid 290 through 296 removed outlier: 4.367A pdb=" N GLN 1 294 " --> pdb=" O ASP 1 290 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG 1 295 " --> pdb=" O ALA 1 291 " (cutoff:3.500A) Processing helix chain '2' and resid 21 through 27 Processing helix chain '2' and resid 85 through 90 removed outlier: 3.785A pdb=" N THR 2 89 " --> pdb=" O ASN 2 85 " (cutoff:3.500A) Processing helix chain '2' and resid 103 through 137 removed outlier: 3.550A pdb=" N ARG 2 107 " --> pdb=" O ASP 2 103 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG 2 109 " --> pdb=" O ALA 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 157 through 161 removed outlier: 3.657A pdb=" N ASN 2 161 " --> pdb=" O GLU 2 158 " (cutoff:3.500A) Processing helix chain '2' and resid 180 through 189 Processing helix chain '2' and resid 201 through 209 Processing helix chain '2' and resid 211 through 220 removed outlier: 3.562A pdb=" N LYS 2 215 " --> pdb=" O PHE 2 211 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP 2 219 " --> pdb=" O LYS 2 215 " (cutoff:3.500A) Processing helix chain '2' and resid 290 through 297 removed outlier: 4.093A pdb=" N GLN 2 294 " --> pdb=" O ASP 2 290 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '3' and resid 22 through 27 Processing helix chain '3' and resid 85 through 90 removed outlier: 3.832A pdb=" N THR 3 89 " --> pdb=" O ASN 3 85 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU 3 90 " --> pdb=" O PRO 3 86 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 85 through 90' Processing helix chain '3' and resid 103 through 137 removed outlier: 3.852A pdb=" N ARG 3 109 " --> pdb=" O ALA 3 105 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG 3 110 " --> pdb=" O TYR 3 106 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE 3 111 " --> pdb=" O ARG 3 107 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE 3 112 " --> pdb=" O ARG 3 108 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET 3 113 " --> pdb=" O ARG 3 109 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA 3 134 " --> pdb=" O GLN 3 130 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL 3 135 " --> pdb=" O ALA 3 131 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS 3 137 " --> pdb=" O SER 3 133 " (cutoff:3.500A) Processing helix chain '3' and resid 180 through 189 Processing helix chain '3' and resid 201 through 210 removed outlier: 3.613A pdb=" N SER 3 210 " --> pdb=" O ALA 3 206 " (cutoff:3.500A) Processing helix chain '3' and resid 211 through 217 removed outlier: 3.784A pdb=" N LYS 3 215 " --> pdb=" O PHE 3 211 " (cutoff:3.500A) Processing helix chain '3' and resid 290 through 297 removed outlier: 3.532A pdb=" N GLY 3 297 " --> pdb=" O ALA 3 293 " (cutoff:3.500A) Processing helix chain '4' and resid 21 through 28 Processing helix chain '4' and resid 85 through 91 removed outlier: 3.898A pdb=" N THR 4 89 " --> pdb=" O ASN 4 85 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU 4 90 " --> pdb=" O PRO 4 86 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG 4 91 " --> pdb=" O GLN 4 87 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 85 through 91' Processing helix chain '4' and resid 103 through 137 removed outlier: 3.764A pdb=" N ARG 4 107 " --> pdb=" O ASP 4 103 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG 4 108 " --> pdb=" O PRO 4 104 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET 4 113 " --> pdb=" O ARG 4 109 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS 4 137 " --> pdb=" O SER 4 133 " (cutoff:3.500A) Processing helix chain '4' and resid 180 through 189 Processing helix chain '4' and resid 201 through 210 removed outlier: 3.542A pdb=" N SER 4 210 " --> pdb=" O ALA 4 206 " (cutoff:3.500A) Processing helix chain '4' and resid 211 through 217 removed outlier: 3.511A pdb=" N LYS 4 215 " --> pdb=" O PHE 4 211 " (cutoff:3.500A) Processing helix chain '4' and resid 290 through 297 Processing helix chain '5' and resid 22 through 28 Processing helix chain '5' and resid 85 through 91 removed outlier: 3.936A pdb=" N THR 5 89 " --> pdb=" O ASN 5 85 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU 5 90 " --> pdb=" O PRO 5 86 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG 5 91 " --> pdb=" O GLN 5 87 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 85 through 91' Processing helix chain '5' and resid 103 through 137 removed outlier: 3.641A pdb=" N ARG 5 108 " --> pdb=" O PRO 5 104 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG 5 109 " --> pdb=" O ALA 5 105 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG 5 110 " --> pdb=" O TYR 5 106 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE 5 111 " --> pdb=" O ARG 5 107 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE 5 112 " --> pdb=" O ARG 5 108 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET 5 113 " --> pdb=" O ARG 5 109 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA 5 134 " --> pdb=" O GLN 5 130 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL 5 135 " --> pdb=" O ALA 5 131 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS 5 137 " --> pdb=" O SER 5 133 " (cutoff:3.500A) Processing helix chain '5' and resid 180 through 189 Processing helix chain '5' and resid 201 through 210 removed outlier: 3.536A pdb=" N SER 5 210 " --> pdb=" O ALA 5 206 " (cutoff:3.500A) Processing helix chain '5' and resid 211 through 220 removed outlier: 3.501A pdb=" N LYS 5 215 " --> pdb=" O PHE 5 211 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU 5 218 " --> pdb=" O VAL 5 214 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP 5 219 " --> pdb=" O LYS 5 215 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR 5 220 " --> pdb=" O GLU 5 216 " (cutoff:3.500A) Processing helix chain '5' and resid 290 through 297 Processing helix chain '5' and resid 331 through 335 removed outlier: 3.780A pdb=" N GLU 5 334 " --> pdb=" O ASP 5 331 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE 5 335 " --> pdb=" O PRO 5 332 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 331 through 335' Processing helix chain '6' and resid 21 through 28 Processing helix chain '6' and resid 85 through 91 removed outlier: 3.561A pdb=" N THR 6 89 " --> pdb=" O ASN 6 85 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG 6 91 " --> pdb=" O GLN 6 87 " (cutoff:3.500A) Processing helix chain '6' and resid 103 through 137 removed outlier: 3.538A pdb=" N GLU 6 119 " --> pdb=" O ASN 6 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU 6 120 " --> pdb=" O MET 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 180 through 189 Processing helix chain '6' and resid 201 through 211 removed outlier: 4.171A pdb=" N PHE 6 211 " --> pdb=" O LEU 6 207 " (cutoff:3.500A) Processing helix chain '6' and resid 211 through 220 removed outlier: 3.922A pdb=" N LYS 6 215 " --> pdb=" O PHE 6 211 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU 6 218 " --> pdb=" O VAL 6 214 " (cutoff:3.500A) Processing helix chain '6' and resid 290 through 297 Processing helix chain '6' and resid 331 through 335 removed outlier: 3.734A pdb=" N PHE 6 335 " --> pdb=" O PRO 6 332 " (cutoff:3.500A) Processing helix chain '7' and resid 21 through 27 removed outlier: 3.562A pdb=" N PHE 7 27 " --> pdb=" O PHE 7 23 " (cutoff:3.500A) Processing helix chain '7' and resid 85 through 91 removed outlier: 3.600A pdb=" N THR 7 89 " --> pdb=" O ASN 7 85 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG 7 91 " --> pdb=" O GLN 7 87 " (cutoff:3.500A) Processing helix chain '7' and resid 103 through 137 removed outlier: 3.572A pdb=" N ARG 7 107 " --> pdb=" O ASP 7 103 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU 7 120 " --> pdb=" O MET 7 116 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS 7 137 " --> pdb=" O SER 7 133 " (cutoff:3.500A) Processing helix chain '7' and resid 180 through 189 Processing helix chain '7' and resid 201 through 211 removed outlier: 3.738A pdb=" N ALA 7 206 " --> pdb=" O PRO 7 202 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE 7 211 " --> pdb=" O LEU 7 207 " (cutoff:3.500A) Processing helix chain '7' and resid 212 through 220 removed outlier: 4.019A pdb=" N LEU 7 218 " --> pdb=" O VAL 7 214 " (cutoff:3.500A) Processing helix chain '7' and resid 290 through 296 Processing helix chain '7' and resid 331 through 335 removed outlier: 3.717A pdb=" N GLU 7 334 " --> pdb=" O ASP 7 331 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE 7 335 " --> pdb=" O PRO 7 332 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 331 through 335' Processing helix chain 'A' and resid 21 through 27 Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.837A pdb=" N THR A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 137 removed outlier: 3.563A pdb=" N ARG A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 removed outlier: 4.360A pdb=" N ASP A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 211 through 220 removed outlier: 3.638A pdb=" N LYS A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.552A pdb=" N GLY A 297 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 27 Processing helix chain 'B' and resid 85 through 91 removed outlier: 3.785A pdb=" N THR B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG B 91 " --> pdb=" O GLN B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 137 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 331 through 335 removed outlier: 3.785A pdb=" N PHE B 335 " --> pdb=" O PRO B 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 27 removed outlier: 3.569A pdb=" N ARG C 25 " --> pdb=" O PRO C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 91 removed outlier: 3.734A pdb=" N THR C 89 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ARG C 91 " --> pdb=" O GLN C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 137 removed outlier: 3.526A pdb=" N ARG C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 189 removed outlier: 4.581A pdb=" N ASP C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 210 Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.783A pdb=" N LYS C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 218 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.750A pdb=" N GLU C 296 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 335 removed outlier: 4.187A pdb=" N PHE C 335 " --> pdb=" O PRO C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 27 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.799A pdb=" N THR D 89 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG D 91 " --> pdb=" O GLN D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 137 removed outlier: 3.549A pdb=" N MET D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS D 137 " --> pdb=" O SER D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 189 removed outlier: 4.441A pdb=" N ASP D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 210 Processing helix chain 'D' and resid 211 through 220 removed outlier: 3.888A pdb=" N LYS D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR D 220 " --> pdb=" O GLU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 296 removed outlier: 3.629A pdb=" N GLU D 296 " --> pdb=" O ALA D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 335 removed outlier: 3.965A pdb=" N PHE D 335 " --> pdb=" O PRO D 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 27 Processing helix chain 'E' and resid 85 through 91 removed outlier: 4.389A pdb=" N ARG E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 137 removed outlier: 3.506A pdb=" N ARG E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 189 Processing helix chain 'E' and resid 201 through 210 removed outlier: 3.709A pdb=" N SER E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 217 Processing helix chain 'E' and resid 290 through 297 Processing helix chain 'E' and resid 331 through 335 removed outlier: 4.295A pdb=" N GLU E 334 " --> pdb=" O ASP E 331 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE E 335 " --> pdb=" O PRO E 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 331 through 335' Processing helix chain 'F' and resid 21 through 27 Processing helix chain 'F' and resid 85 through 91 removed outlier: 3.673A pdb=" N THR F 89 " --> pdb=" O ASN F 85 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG F 91 " --> pdb=" O GLN F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 137 removed outlier: 3.518A pdb=" N ARG F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 189 Processing helix chain 'F' and resid 201 through 210 removed outlier: 3.610A pdb=" N SER F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 218 removed outlier: 3.517A pdb=" N LYS F 215 " --> pdb=" O PHE F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 297 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 85 through 91 removed outlier: 4.174A pdb=" N ARG G 91 " --> pdb=" O GLN G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 137 removed outlier: 3.544A pdb=" N ARG G 107 " --> pdb=" O ASP G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 159 No H-bonds generated for 'chain 'G' and resid 157 through 159' Processing helix chain 'G' and resid 180 through 191 removed outlier: 4.087A pdb=" N ASN G 190 " --> pdb=" O ALA G 186 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA G 191 " --> pdb=" O TYR G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 209 Processing helix chain 'G' and resid 211 through 218 Processing helix chain 'G' and resid 290 through 296 Processing helix chain 'H' and resid 21 through 27 Processing helix chain 'H' and resid 85 through 91 removed outlier: 3.684A pdb=" N THR H 89 " --> pdb=" O ASN H 85 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 137 removed outlier: 3.572A pdb=" N ARG H 107 " --> pdb=" O ASP H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 159 No H-bonds generated for 'chain 'H' and resid 157 through 159' Processing helix chain 'H' and resid 180 through 190 removed outlier: 4.494A pdb=" N ASN H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 210 removed outlier: 3.685A pdb=" N SER H 210 " --> pdb=" O ALA H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 218 removed outlier: 3.516A pdb=" N LYS H 215 " --> pdb=" O PHE H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 296 Processing helix chain 'I' and resid 21 through 27 Processing helix chain 'I' and resid 85 through 91 removed outlier: 3.815A pdb=" N THR I 89 " --> pdb=" O ASN I 85 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG I 91 " --> pdb=" O GLN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 137 removed outlier: 3.633A pdb=" N ARG I 107 " --> pdb=" O ASP I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 189 removed outlier: 4.345A pdb=" N ASP I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 210 Processing helix chain 'I' and resid 211 through 220 removed outlier: 3.843A pdb=" N LYS I 215 " --> pdb=" O PHE I 211 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU I 218 " --> pdb=" O VAL I 214 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP I 219 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR I 220 " --> pdb=" O GLU I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 292 through 296 removed outlier: 4.024A pdb=" N GLU I 296 " --> pdb=" O ALA I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 335 removed outlier: 3.715A pdb=" N PHE I 335 " --> pdb=" O PRO I 332 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 27 Processing helix chain 'J' and resid 85 through 91 removed outlier: 3.666A pdb=" N THR J 89 " --> pdb=" O ASN J 85 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG J 91 " --> pdb=" O GLN J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 137 Processing helix chain 'J' and resid 157 through 161 removed outlier: 3.624A pdb=" N ASN J 161 " --> pdb=" O GLU J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 191 removed outlier: 4.028A pdb=" N ASN J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA J 191 " --> pdb=" O TYR J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 209 Processing helix chain 'J' and resid 211 through 217 Processing helix chain 'J' and resid 290 through 296 Processing helix chain 'K' and resid 21 through 27 Processing helix chain 'K' and resid 85 through 91 removed outlier: 3.756A pdb=" N THR K 89 " --> pdb=" O ASN K 85 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG K 91 " --> pdb=" O GLN K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 137 removed outlier: 3.661A pdb=" N GLU K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU K 120 " --> pdb=" O MET K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 190 removed outlier: 4.293A pdb=" N ASN K 190 " --> pdb=" O ALA K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 210 Processing helix chain 'K' and resid 211 through 220 removed outlier: 3.906A pdb=" N LYS K 215 " --> pdb=" O PHE K 211 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU K 218 " --> pdb=" O VAL K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 297 Processing helix chain 'L' and resid 21 through 27 Processing helix chain 'L' and resid 85 through 90 removed outlier: 3.819A pdb=" N THR L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 137 removed outlier: 3.577A pdb=" N ARG L 107 " --> pdb=" O ASP L 103 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG L 117 " --> pdb=" O MET L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 189 removed outlier: 4.500A pdb=" N ASP L 183 " --> pdb=" O ASP L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 201 through 210 removed outlier: 4.001A pdb=" N ALA L 206 " --> pdb=" O PRO L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 217 removed outlier: 3.791A pdb=" N LYS L 215 " --> pdb=" O PHE L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 290 through 297 Processing helix chain 'L' and resid 331 through 333 No H-bonds generated for 'chain 'L' and resid 331 through 333' Processing helix chain 'M' and resid 21 through 27 Processing helix chain 'M' and resid 85 through 91 removed outlier: 3.566A pdb=" N THR M 89 " --> pdb=" O ASN M 85 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG M 91 " --> pdb=" O GLN M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 137 removed outlier: 3.578A pdb=" N ARG M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 189 removed outlier: 3.656A pdb=" N LEU M 189 " --> pdb=" O GLU M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 210 removed outlier: 3.517A pdb=" N SER M 210 " --> pdb=" O ALA M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 220 removed outlier: 3.594A pdb=" N LEU M 218 " --> pdb=" O VAL M 214 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP M 219 " --> pdb=" O LYS M 215 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR M 220 " --> pdb=" O GLU M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 296 removed outlier: 4.173A pdb=" N GLN M 294 " --> pdb=" O ASP M 290 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG M 295 " --> pdb=" O ALA M 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 28 Processing helix chain 'N' and resid 85 through 90 removed outlier: 3.755A pdb=" N THR N 89 " --> pdb=" O ASN N 85 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU N 90 " --> pdb=" O PRO N 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 85 through 90' Processing helix chain 'N' and resid 107 through 137 removed outlier: 3.649A pdb=" N ILE N 111 " --> pdb=" O ARG N 107 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE N 112 " --> pdb=" O ARG N 108 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N MET N 113 " --> pdb=" O ARG N 109 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA N 134 " --> pdb=" O GLN N 130 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL N 135 " --> pdb=" O ALA N 131 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 189 Processing helix chain 'N' and resid 201 through 210 removed outlier: 3.682A pdb=" N SER N 210 " --> pdb=" O ALA N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 217 Processing helix chain 'N' and resid 292 through 297 removed outlier: 4.317A pdb=" N GLU N 296 " --> pdb=" O ASP N 292 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY N 297 " --> pdb=" O ALA N 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 292 through 297' Processing helix chain 'N' and resid 331 through 335 removed outlier: 3.796A pdb=" N GLU N 334 " --> pdb=" O ASP N 331 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE N 335 " --> pdb=" O PRO N 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 331 through 335' Processing helix chain 'O' and resid 21 through 27 Processing helix chain 'O' and resid 85 through 90 removed outlier: 3.722A pdb=" N THR O 89 " --> pdb=" O ASN O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 137 removed outlier: 3.847A pdb=" N GLU O 120 " --> pdb=" O MET O 116 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS O 137 " --> pdb=" O SER O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 188 Processing helix chain 'O' and resid 189 through 191 No H-bonds generated for 'chain 'O' and resid 189 through 191' Processing helix chain 'O' and resid 201 through 210 removed outlier: 3.566A pdb=" N SER O 210 " --> pdb=" O ALA O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 217 removed outlier: 3.561A pdb=" N LYS O 215 " --> pdb=" O PHE O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 297 Processing helix chain 'P' and resid 21 through 28 Processing helix chain 'P' and resid 85 through 91 removed outlier: 4.054A pdb=" N ARG P 91 " --> pdb=" O GLN P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 137 removed outlier: 3.568A pdb=" N ARG P 107 " --> pdb=" O ASP P 103 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU P 119 " --> pdb=" O ASN P 115 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU P 120 " --> pdb=" O MET P 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 189 Processing helix chain 'P' and resid 201 through 210 removed outlier: 3.679A pdb=" N SER P 210 " --> pdb=" O ALA P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 220 removed outlier: 3.697A pdb=" N LYS P 215 " --> pdb=" O PHE P 211 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU P 218 " --> pdb=" O VAL P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 290 through 296 Processing helix chain 'P' and resid 331 through 335 removed outlier: 3.558A pdb=" N GLU P 334 " --> pdb=" O ASP P 331 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE P 335 " --> pdb=" O PRO P 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 331 through 335' Processing helix chain 'Q' and resid 21 through 27 removed outlier: 3.692A pdb=" N ARG Q 25 " --> pdb=" O PRO Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 90 removed outlier: 3.744A pdb=" N THR Q 89 " --> pdb=" O ASN Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 137 removed outlier: 3.720A pdb=" N ARG Q 107 " --> pdb=" O ASP Q 103 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG Q 117 " --> pdb=" O MET Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 159 No H-bonds generated for 'chain 'Q' and resid 157 through 159' Processing helix chain 'Q' and resid 179 through 189 removed outlier: 4.274A pdb=" N ASP Q 183 " --> pdb=" O ASP Q 179 " (cutoff:3.500A) Processing helix chain 'Q' and resid 201 through 210 Processing helix chain 'Q' and resid 212 through 217 removed outlier: 3.547A pdb=" N GLU Q 216 " --> pdb=" O LYS Q 212 " (cutoff:3.500A) Processing helix chain 'Q' and resid 290 through 297 Processing helix chain 'Q' and resid 331 through 335 removed outlier: 3.627A pdb=" N GLU Q 334 " --> pdb=" O ASP Q 331 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE Q 335 " --> pdb=" O PRO Q 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 331 through 335' Processing helix chain 'R' and resid 21 through 27 Processing helix chain 'R' and resid 85 through 90 removed outlier: 3.645A pdb=" N THR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 137 removed outlier: 3.743A pdb=" N ARG R 107 " --> pdb=" O ASP R 103 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG R 117 " --> pdb=" O MET R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 189 removed outlier: 4.527A pdb=" N ASP R 183 " --> pdb=" O ASP R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 210 Processing helix chain 'R' and resid 211 through 220 removed outlier: 3.750A pdb=" N LYS R 215 " --> pdb=" O PHE R 211 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU R 218 " --> pdb=" O VAL R 214 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP R 219 " --> pdb=" O LYS R 215 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR R 220 " --> pdb=" O GLU R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 297 Processing helix chain 'R' and resid 331 through 333 No H-bonds generated for 'chain 'R' and resid 331 through 333' Processing helix chain 'S' and resid 21 through 27 removed outlier: 3.820A pdb=" N ARG S 25 " --> pdb=" O PRO S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 90 Processing helix chain 'S' and resid 103 through 137 removed outlier: 4.111A pdb=" N ARG S 107 " --> pdb=" O ASP S 103 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG S 117 " --> pdb=" O MET S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 179 through 189 removed outlier: 4.205A pdb=" N ASP S 183 " --> pdb=" O ASP S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 201 through 210 Processing helix chain 'S' and resid 211 through 220 removed outlier: 3.632A pdb=" N LYS S 215 " --> pdb=" O PHE S 211 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU S 218 " --> pdb=" O VAL S 214 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP S 219 " --> pdb=" O LYS S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 290 through 297 Processing helix chain 'S' and resid 331 through 333 No H-bonds generated for 'chain 'S' and resid 331 through 333' Processing helix chain 'T' and resid 21 through 27 Processing helix chain 'T' and resid 85 through 90 removed outlier: 3.946A pdb=" N LEU T 90 " --> pdb=" O GLN T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 137 removed outlier: 3.641A pdb=" N ARG T 107 " --> pdb=" O ASP T 103 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG T 117 " --> pdb=" O MET T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 180 through 189 Processing helix chain 'T' and resid 201 through 210 Processing helix chain 'T' and resid 211 through 217 removed outlier: 3.990A pdb=" N LYS T 215 " --> pdb=" O PHE T 211 " (cutoff:3.500A) Processing helix chain 'T' and resid 290 through 297 Processing helix chain 'U' and resid 44 through 50 Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 67 through 82 removed outlier: 3.622A pdb=" N VAL U 82 " --> pdb=" O GLN U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 93 through 98 Processing helix chain 'U' and resid 101 through 120 Processing helix chain 'U' and resid 133 through 148 Processing helix chain 'U' and resid 179 through 183 Processing helix chain 'U' and resid 249 through 253 removed outlier: 3.824A pdb=" N TYR U 252 " --> pdb=" O ASN U 249 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER U 253 " --> pdb=" O VAL U 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 249 through 253' Processing helix chain 'U' and resid 254 through 276 removed outlier: 3.623A pdb=" N MET U 258 " --> pdb=" O VAL U 254 " (cutoff:3.500A) Processing helix chain 'U' and resid 287 through 295 Processing helix chain 'U' and resid 350 through 367 removed outlier: 3.566A pdb=" N PHE U 354 " --> pdb=" O GLY U 350 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 375 Processing helix chain 'U' and resid 381 through 422 removed outlier: 3.515A pdb=" N ALA U 385 " --> pdb=" O SER U 381 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR U 395 " --> pdb=" O GLU U 391 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA U 404 " --> pdb=" O ARG U 400 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER U 405 " --> pdb=" O LYS U 401 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU U 418 " --> pdb=" O CYS U 414 " (cutoff:3.500A) Processing helix chain 'U' and resid 438 through 443 removed outlier: 3.840A pdb=" N TRP U 442 " --> pdb=" O ALA U 438 " (cutoff:3.500A) Processing helix chain 'U' and resid 456 through 470 removed outlier: 3.553A pdb=" N GLU U 460 " --> pdb=" O ASP U 456 " (cutoff:3.500A) Processing helix chain 'U' and resid 474 through 482 removed outlier: 3.892A pdb=" N ARG U 482 " --> pdb=" O GLU U 478 " (cutoff:3.500A) Processing helix chain 'U' and resid 485 through 504 removed outlier: 3.557A pdb=" N MET U 498 " --> pdb=" O VAL U 494 " (cutoff:3.500A) Processing helix chain 'V' and resid 24 through 28 removed outlier: 3.532A pdb=" N GLY V 27 " --> pdb=" O TYR V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 50 Processing helix chain 'V' and resid 52 through 67 Processing helix chain 'V' and resid 67 through 82 Processing helix chain 'V' and resid 93 through 98 Processing helix chain 'V' and resid 100 through 120 removed outlier: 3.787A pdb=" N GLU V 120 " --> pdb=" O LYS V 116 " (cutoff:3.500A) Processing helix chain 'V' and resid 133 through 148 Processing helix chain 'V' and resid 173 through 177 Processing helix chain 'V' and resid 254 through 278 removed outlier: 4.048A pdb=" N TYR V 278 " --> pdb=" O VAL V 274 " (cutoff:3.500A) Processing helix chain 'V' and resid 287 through 295 Processing helix chain 'V' and resid 350 through 367 removed outlier: 3.857A pdb=" N PHE V 354 " --> pdb=" O GLY V 350 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 375 removed outlier: 3.560A pdb=" N LEU V 373 " --> pdb=" O SER V 369 " (cutoff:3.500A) Processing helix chain 'V' and resid 381 through 422 removed outlier: 3.535A pdb=" N ALA V 385 " --> pdb=" O SER V 381 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR V 395 " --> pdb=" O GLU V 391 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA V 404 " --> pdb=" O ARG V 400 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER V 405 " --> pdb=" O LYS V 401 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU V 418 " --> pdb=" O CYS V 414 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 443 removed outlier: 3.502A pdb=" N TRP V 442 " --> pdb=" O ALA V 438 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY V 443 " --> pdb=" O ARG V 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 438 through 443' Processing helix chain 'V' and resid 456 through 470 removed outlier: 3.705A pdb=" N GLU V 460 " --> pdb=" O ASP V 456 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL V 461 " --> pdb=" O GLY V 457 " (cutoff:3.500A) Processing helix chain 'V' and resid 474 through 482 removed outlier: 3.520A pdb=" N GLU V 478 " --> pdb=" O THR V 474 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG V 482 " --> pdb=" O GLU V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 485 through 504 removed outlier: 3.835A pdb=" N MET V 498 " --> pdb=" O VAL V 494 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 50 Processing helix chain 'W' and resid 52 through 67 removed outlier: 3.556A pdb=" N GLY W 56 " --> pdb=" O ASN W 52 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 82 Processing helix chain 'W' and resid 93 through 98 removed outlier: 3.682A pdb=" N LEU W 97 " --> pdb=" O SER W 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 119 Processing helix chain 'W' and resid 133 through 149 Processing helix chain 'W' and resid 179 through 183 Processing helix chain 'W' and resid 249 through 253 removed outlier: 3.670A pdb=" N TYR W 252 " --> pdb=" O ASN W 249 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER W 253 " --> pdb=" O VAL W 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 249 through 253' Processing helix chain 'W' and resid 254 through 278 removed outlier: 3.665A pdb=" N LYS W 259 " --> pdb=" O MET W 255 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR W 278 " --> pdb=" O VAL W 274 " (cutoff:3.500A) Processing helix chain 'W' and resid 287 through 295 Processing helix chain 'W' and resid 350 through 367 removed outlier: 3.698A pdb=" N PHE W 354 " --> pdb=" O GLY W 350 " (cutoff:3.500A) Processing helix chain 'W' and resid 369 through 375 Processing helix chain 'W' and resid 381 through 422 removed outlier: 3.550A pdb=" N ALA W 385 " --> pdb=" O SER W 381 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR W 395 " --> pdb=" O GLU W 391 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA W 404 " --> pdb=" O ARG W 400 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER W 405 " --> pdb=" O LYS W 401 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU W 418 " --> pdb=" O CYS W 414 " (cutoff:3.500A) Processing helix chain 'W' and resid 438 through 444 removed outlier: 3.751A pdb=" N TRP W 442 " --> pdb=" O ALA W 438 " (cutoff:3.500A) Processing helix chain 'W' and resid 456 through 470 removed outlier: 3.978A pdb=" N GLU W 460 " --> pdb=" O ASP W 456 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL W 461 " --> pdb=" O GLY W 457 " (cutoff:3.500A) Processing helix chain 'W' and resid 474 through 481 Processing helix chain 'W' and resid 485 through 504 removed outlier: 3.719A pdb=" N MET W 498 " --> pdb=" O VAL W 494 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 50 Processing helix chain 'X' and resid 52 through 66 Processing helix chain 'X' and resid 67 through 82 removed outlier: 3.657A pdb=" N ALA X 71 " --> pdb=" O ASN X 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 93 through 98 Processing helix chain 'X' and resid 100 through 120 removed outlier: 3.697A pdb=" N GLU X 120 " --> pdb=" O LYS X 116 " (cutoff:3.500A) Processing helix chain 'X' and resid 133 through 148 Processing helix chain 'X' and resid 179 through 183 Processing helix chain 'X' and resid 250 through 253 removed outlier: 4.033A pdb=" N SER X 253 " --> pdb=" O VAL X 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 250 through 253' Processing helix chain 'X' and resid 254 through 278 removed outlier: 4.053A pdb=" N TYR X 278 " --> pdb=" O VAL X 274 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 295 removed outlier: 3.679A pdb=" N MET X 292 " --> pdb=" O THR X 288 " (cutoff:3.500A) Processing helix chain 'X' and resid 350 through 367 Processing helix chain 'X' and resid 369 through 375 Processing helix chain 'X' and resid 381 through 422 removed outlier: 3.901A pdb=" N TYR X 395 " --> pdb=" O GLU X 391 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA X 404 " --> pdb=" O ARG X 400 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER X 405 " --> pdb=" O LYS X 401 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU X 418 " --> pdb=" O CYS X 414 " (cutoff:3.500A) Processing helix chain 'X' and resid 438 through 443 removed outlier: 3.711A pdb=" N TRP X 442 " --> pdb=" O ALA X 438 " (cutoff:3.500A) Processing helix chain 'X' and resid 456 through 470 removed outlier: 3.869A pdb=" N GLU X 460 " --> pdb=" O ASP X 456 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL X 461 " --> pdb=" O GLY X 457 " (cutoff:3.500A) Processing helix chain 'X' and resid 474 through 481 Processing helix chain 'X' and resid 485 through 504 removed outlier: 3.887A pdb=" N MET X 498 " --> pdb=" O VAL X 494 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 50 Processing helix chain 'Y' and resid 52 through 67 Processing helix chain 'Y' and resid 67 through 82 removed outlier: 3.542A pdb=" N VAL Y 82 " --> pdb=" O GLN Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 93 through 98 Processing helix chain 'Y' and resid 100 through 120 removed outlier: 3.756A pdb=" N GLU Y 120 " --> pdb=" O LYS Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 148 Processing helix chain 'Y' and resid 179 through 183 removed outlier: 4.296A pdb=" N ASN Y 182 " --> pdb=" O ASN Y 179 " (cutoff:3.500A) Processing helix chain 'Y' and resid 249 through 253 removed outlier: 3.644A pdb=" N TYR Y 252 " --> pdb=" O ASN Y 249 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER Y 253 " --> pdb=" O VAL Y 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 249 through 253' Processing helix chain 'Y' and resid 254 through 276 removed outlier: 3.547A pdb=" N LYS Y 259 " --> pdb=" O MET Y 255 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 295 Processing helix chain 'Y' and resid 350 through 367 Processing helix chain 'Y' and resid 369 through 375 Processing helix chain 'Y' and resid 381 through 422 removed outlier: 3.652A pdb=" N ALA Y 385 " --> pdb=" O SER Y 381 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR Y 395 " --> pdb=" O GLU Y 391 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA Y 404 " --> pdb=" O ARG Y 400 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER Y 405 " --> pdb=" O LYS Y 401 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU Y 418 " --> pdb=" O CYS Y 414 " (cutoff:3.500A) Processing helix chain 'Y' and resid 438 through 443 removed outlier: 3.688A pdb=" N TRP Y 442 " --> pdb=" O ALA Y 438 " (cutoff:3.500A) Processing helix chain 'Y' and resid 456 through 470 removed outlier: 3.946A pdb=" N GLU Y 460 " --> pdb=" O ASP Y 456 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL Y 461 " --> pdb=" O GLY Y 457 " (cutoff:3.500A) Processing helix chain 'Y' and resid 474 through 481 removed outlier: 3.879A pdb=" N GLU Y 478 " --> pdb=" O THR Y 474 " (cutoff:3.500A) Processing helix chain 'Y' and resid 485 through 504 removed outlier: 3.689A pdb=" N MET Y 498 " --> pdb=" O VAL Y 494 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 50 Processing helix chain 'Z' and resid 52 through 67 Processing helix chain 'Z' and resid 67 through 82 removed outlier: 3.668A pdb=" N ALA Z 71 " --> pdb=" O ASN Z 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 93 through 98 Processing helix chain 'Z' and resid 101 through 120 Processing helix chain 'Z' and resid 133 through 149 Processing helix chain 'Z' and resid 173 through 177 removed outlier: 3.675A pdb=" N ILE Z 177 " --> pdb=" O PRO Z 174 " (cutoff:3.500A) Processing helix chain 'Z' and resid 179 through 183 Processing helix chain 'Z' and resid 250 through 253 removed outlier: 4.241A pdb=" N SER Z 253 " --> pdb=" O VAL Z 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 250 through 253' Processing helix chain 'Z' and resid 254 through 278 removed outlier: 4.061A pdb=" N TYR Z 278 " --> pdb=" O VAL Z 274 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 295 removed outlier: 3.788A pdb=" N MET Z 292 " --> pdb=" O THR Z 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 350 through 367 removed outlier: 3.676A pdb=" N PHE Z 354 " --> pdb=" O GLY Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 369 through 375 Processing helix chain 'Z' and resid 381 through 422 removed outlier: 3.611A pdb=" N ALA Z 385 " --> pdb=" O SER Z 381 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR Z 395 " --> pdb=" O GLU Z 391 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA Z 404 " --> pdb=" O ARG Z 400 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER Z 405 " --> pdb=" O LYS Z 401 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU Z 418 " --> pdb=" O CYS Z 414 " (cutoff:3.500A) Processing helix chain 'Z' and resid 438 through 443 removed outlier: 3.518A pdb=" N TRP Z 442 " --> pdb=" O ALA Z 438 " (cutoff:3.500A) Processing helix chain 'Z' and resid 456 through 470 removed outlier: 3.853A pdb=" N GLU Z 460 " --> pdb=" O ASP Z 456 " (cutoff:3.500A) Processing helix chain 'Z' and resid 474 through 482 removed outlier: 3.564A pdb=" N GLU Z 478 " --> pdb=" O THR Z 474 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG Z 482 " --> pdb=" O GLU Z 478 " (cutoff:3.500A) Processing helix chain 'Z' and resid 485 through 504 Processing helix chain 'a' and resid 24 through 28 removed outlier: 3.649A pdb=" N GLY a 27 " --> pdb=" O TYR a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 50 Processing helix chain 'a' and resid 52 through 66 Processing helix chain 'a' and resid 67 through 82 removed outlier: 3.582A pdb=" N ALA a 71 " --> pdb=" O ASN a 67 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL a 82 " --> pdb=" O GLN a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 98 removed outlier: 3.629A pdb=" N LEU a 97 " --> pdb=" O SER a 93 " (cutoff:3.500A) Processing helix chain 'a' and resid 101 through 120 removed outlier: 3.582A pdb=" N GLU a 120 " --> pdb=" O LYS a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 149 Processing helix chain 'a' and resid 173 through 177 Processing helix chain 'a' and resid 179 through 183 removed outlier: 3.741A pdb=" N ASN a 182 " --> pdb=" O ASN a 179 " (cutoff:3.500A) Processing helix chain 'a' and resid 249 through 253 removed outlier: 3.788A pdb=" N TYR a 252 " --> pdb=" O ASN a 249 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER a 253 " --> pdb=" O VAL a 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 249 through 253' Processing helix chain 'a' and resid 254 through 278 removed outlier: 4.043A pdb=" N TYR a 278 " --> pdb=" O VAL a 274 " (cutoff:3.500A) Processing helix chain 'a' and resid 287 through 295 removed outlier: 3.633A pdb=" N ALA a 291 " --> pdb=" O ASP a 287 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET a 292 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing helix chain 'a' and resid 350 through 367 removed outlier: 3.617A pdb=" N PHE a 354 " --> pdb=" O GLY a 350 " (cutoff:3.500A) Processing helix chain 'a' and resid 369 through 375 Processing helix chain 'a' and resid 381 through 422 removed outlier: 3.732A pdb=" N TYR a 395 " --> pdb=" O GLU a 391 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA a 404 " --> pdb=" O ARG a 400 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER a 405 " --> pdb=" O LYS a 401 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU a 418 " --> pdb=" O CYS a 414 " (cutoff:3.500A) Processing helix chain 'a' and resid 438 through 443 Processing helix chain 'a' and resid 456 through 470 removed outlier: 4.467A pdb=" N GLU a 460 " --> pdb=" O ASP a 456 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL a 461 " --> pdb=" O GLY a 457 " (cutoff:3.500A) Processing helix chain 'a' and resid 474 through 481 Processing helix chain 'a' and resid 485 through 504 removed outlier: 3.662A pdb=" N MET a 498 " --> pdb=" O VAL a 494 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY a 504 " --> pdb=" O ARG a 500 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 28 removed outlier: 3.549A pdb=" N GLY b 27 " --> pdb=" O TYR b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 50 Processing helix chain 'b' and resid 52 through 67 Processing helix chain 'b' and resid 67 through 82 Processing helix chain 'b' and resid 93 through 98 Processing helix chain 'b' and resid 100 through 120 removed outlier: 3.735A pdb=" N GLU b 120 " --> pdb=" O LYS b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 149 Processing helix chain 'b' and resid 179 through 183 Processing helix chain 'b' and resid 254 through 278 removed outlier: 4.078A pdb=" N TYR b 278 " --> pdb=" O VAL b 274 " (cutoff:3.500A) Processing helix chain 'b' and resid 287 through 295 Processing helix chain 'b' and resid 350 through 367 Processing helix chain 'b' and resid 369 through 375 Processing helix chain 'b' and resid 381 through 422 removed outlier: 4.053A pdb=" N TYR b 395 " --> pdb=" O GLU b 391 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA b 404 " --> pdb=" O ARG b 400 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER b 405 " --> pdb=" O LYS b 401 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU b 418 " --> pdb=" O CYS b 414 " (cutoff:3.500A) Processing helix chain 'b' and resid 438 through 443 Processing helix chain 'b' and resid 456 through 470 removed outlier: 3.502A pdb=" N GLU b 460 " --> pdb=" O ASP b 456 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL b 461 " --> pdb=" O GLY b 457 " (cutoff:3.500A) Processing helix chain 'b' and resid 474 through 481 Processing helix chain 'b' and resid 485 through 504 Processing helix chain 'c' and resid 44 through 50 Processing helix chain 'c' and resid 52 through 67 removed outlier: 3.570A pdb=" N GLY c 56 " --> pdb=" O ASN c 52 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 82 Processing helix chain 'c' and resid 93 through 98 removed outlier: 3.784A pdb=" N LEU c 97 " --> pdb=" O SER c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 100 through 120 Processing helix chain 'c' and resid 133 through 148 Processing helix chain 'c' and resid 173 through 177 Processing helix chain 'c' and resid 179 through 183 Processing helix chain 'c' and resid 250 through 253 removed outlier: 3.875A pdb=" N SER c 253 " --> pdb=" O VAL c 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 250 through 253' Processing helix chain 'c' and resid 254 through 278 removed outlier: 4.443A pdb=" N TYR c 278 " --> pdb=" O VAL c 274 " (cutoff:3.500A) Processing helix chain 'c' and resid 287 through 295 removed outlier: 3.712A pdb=" N MET c 292 " --> pdb=" O THR c 288 " (cutoff:3.500A) Processing helix chain 'c' and resid 350 through 367 Processing helix chain 'c' and resid 369 through 375 Processing helix chain 'c' and resid 381 through 422 removed outlier: 3.616A pdb=" N ALA c 385 " --> pdb=" O SER c 381 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR c 395 " --> pdb=" O GLU c 391 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA c 404 " --> pdb=" O ARG c 400 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SER c 405 " --> pdb=" O LYS c 401 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU c 418 " --> pdb=" O CYS c 414 " (cutoff:3.500A) Processing helix chain 'c' and resid 438 through 443 removed outlier: 3.659A pdb=" N TRP c 442 " --> pdb=" O ALA c 438 " (cutoff:3.500A) Processing helix chain 'c' and resid 456 through 470 Processing helix chain 'c' and resid 474 through 482 removed outlier: 3.686A pdb=" N ARG c 482 " --> pdb=" O GLU c 478 " (cutoff:3.500A) Processing helix chain 'c' and resid 485 through 504 Processing helix chain 'd' and resid 33 through 37 removed outlier: 4.577A pdb=" N SER d 37 " --> pdb=" O GLN d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 50 Processing helix chain 'd' and resid 52 through 66 Processing helix chain 'd' and resid 67 through 82 removed outlier: 3.608A pdb=" N VAL d 82 " --> pdb=" O GLN d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 98 removed outlier: 3.577A pdb=" N LEU d 97 " --> pdb=" O SER d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 101 through 120 removed outlier: 3.764A pdb=" N GLU d 120 " --> pdb=" O LYS d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 148 Processing helix chain 'd' and resid 179 through 183 removed outlier: 3.756A pdb=" N ASN d 182 " --> pdb=" O ASN d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 249 through 253 removed outlier: 3.735A pdb=" N TYR d 252 " --> pdb=" O ASN d 249 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER d 253 " --> pdb=" O VAL d 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 249 through 253' Processing helix chain 'd' and resid 254 through 278 removed outlier: 3.538A pdb=" N MET d 258 " --> pdb=" O VAL d 254 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR d 278 " --> pdb=" O VAL d 274 " (cutoff:3.500A) Processing helix chain 'd' and resid 287 through 295 removed outlier: 3.635A pdb=" N MET d 292 " --> pdb=" O THR d 288 " (cutoff:3.500A) Processing helix chain 'd' and resid 350 through 367 removed outlier: 3.576A pdb=" N PHE d 354 " --> pdb=" O GLY d 350 " (cutoff:3.500A) Processing helix chain 'd' and resid 369 through 374 Processing helix chain 'd' and resid 381 through 422 removed outlier: 3.701A pdb=" N ALA d 385 " --> pdb=" O SER d 381 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR d 395 " --> pdb=" O GLU d 391 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA d 404 " --> pdb=" O ARG d 400 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER d 405 " --> pdb=" O LYS d 401 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU d 418 " --> pdb=" O CYS d 414 " (cutoff:3.500A) Processing helix chain 'd' and resid 438 through 443 removed outlier: 3.746A pdb=" N TRP d 442 " --> pdb=" O ALA d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 456 through 470 removed outlier: 3.635A pdb=" N GLU d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) Processing helix chain 'd' and resid 474 through 482 removed outlier: 3.737A pdb=" N GLU d 478 " --> pdb=" O THR d 474 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG d 482 " --> pdb=" O GLU d 478 " (cutoff:3.500A) Processing helix chain 'd' and resid 485 through 503 removed outlier: 3.525A pdb=" N MET d 498 " --> pdb=" O VAL d 494 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 50 Processing helix chain 'e' and resid 52 through 67 Processing helix chain 'e' and resid 67 through 82 Processing helix chain 'e' and resid 93 through 98 Processing helix chain 'e' and resid 100 through 119 Processing helix chain 'e' and resid 133 through 149 removed outlier: 3.538A pdb=" N GLY e 149 " --> pdb=" O HIS e 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 173 through 177 removed outlier: 3.572A pdb=" N ILE e 177 " --> pdb=" O PRO e 174 " (cutoff:3.500A) Processing helix chain 'e' and resid 179 through 183 removed outlier: 3.652A pdb=" N ASN e 182 " --> pdb=" O ASN e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 254 through 278 removed outlier: 4.160A pdb=" N TYR e 278 " --> pdb=" O VAL e 274 " (cutoff:3.500A) Processing helix chain 'e' and resid 287 through 295 Processing helix chain 'e' and resid 350 through 367 removed outlier: 3.542A pdb=" N PHE e 354 " --> pdb=" O GLY e 350 " (cutoff:3.500A) Processing helix chain 'e' and resid 369 through 375 Processing helix chain 'e' and resid 381 through 422 removed outlier: 3.576A pdb=" N ALA e 385 " --> pdb=" O SER e 381 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR e 395 " --> pdb=" O GLU e 391 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA e 404 " --> pdb=" O ARG e 400 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER e 405 " --> pdb=" O LYS e 401 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU e 418 " --> pdb=" O CYS e 414 " (cutoff:3.500A) Processing helix chain 'e' and resid 438 through 443 removed outlier: 3.773A pdb=" N TRP e 442 " --> pdb=" O ALA e 438 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 470 removed outlier: 3.967A pdb=" N GLU e 460 " --> pdb=" O ASP e 456 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL e 461 " --> pdb=" O GLY e 457 " (cutoff:3.500A) Processing helix chain 'e' and resid 474 through 482 removed outlier: 3.697A pdb=" N ARG e 482 " --> pdb=" O GLU e 478 " (cutoff:3.500A) Processing helix chain 'e' and resid 485 through 504 removed outlier: 3.613A pdb=" N MET e 498 " --> pdb=" O VAL e 494 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 50 Processing helix chain 'f' and resid 52 through 67 Processing helix chain 'f' and resid 67 through 82 removed outlier: 3.515A pdb=" N VAL f 82 " --> pdb=" O GLN f 78 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 98 Processing helix chain 'f' and resid 100 through 120 removed outlier: 3.708A pdb=" N GLU f 120 " --> pdb=" O LYS f 116 " (cutoff:3.500A) Processing helix chain 'f' and resid 133 through 148 Processing helix chain 'f' and resid 173 through 177 Processing helix chain 'f' and resid 179 through 183 removed outlier: 3.527A pdb=" N ASN f 182 " --> pdb=" O ASN f 179 " (cutoff:3.500A) Processing helix chain 'f' and resid 250 through 253 removed outlier: 3.671A pdb=" N SER f 253 " --> pdb=" O VAL f 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 250 through 253' Processing helix chain 'f' and resid 254 through 278 removed outlier: 3.934A pdb=" N LYS f 259 " --> pdb=" O MET f 255 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR f 278 " --> pdb=" O VAL f 274 " (cutoff:3.500A) Processing helix chain 'f' and resid 287 through 295 Processing helix chain 'f' and resid 350 through 367 Processing helix chain 'f' and resid 369 through 375 Processing helix chain 'f' and resid 381 through 422 removed outlier: 3.547A pdb=" N ALA f 385 " --> pdb=" O SER f 381 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR f 395 " --> pdb=" O GLU f 391 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA f 404 " --> pdb=" O ARG f 400 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER f 405 " --> pdb=" O LYS f 401 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU f 418 " --> pdb=" O CYS f 414 " (cutoff:3.500A) Processing helix chain 'f' and resid 439 through 444 Processing helix chain 'f' and resid 456 through 470 removed outlier: 3.760A pdb=" N GLU f 460 " --> pdb=" O ASP f 456 " (cutoff:3.500A) Processing helix chain 'f' and resid 474 through 482 removed outlier: 4.051A pdb=" N ARG f 482 " --> pdb=" O GLU f 478 " (cutoff:3.500A) Processing helix chain 'f' and resid 485 through 504 removed outlier: 3.631A pdb=" N MET f 498 " --> pdb=" O VAL f 494 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA f 503 " --> pdb=" O GLU f 499 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 27 Processing helix chain 'g' and resid 85 through 91 removed outlier: 3.827A pdb=" N THR g 89 " --> pdb=" O ASN g 85 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG g 91 " --> pdb=" O GLN g 87 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 137 removed outlier: 3.688A pdb=" N ARG g 109 " --> pdb=" O ALA g 105 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL g 126 " --> pdb=" O ALA g 122 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA g 134 " --> pdb=" O GLN g 130 " (cutoff:3.500A) Processing helix chain 'g' and resid 180 through 189 removed outlier: 3.601A pdb=" N LEU g 189 " --> pdb=" O GLU g 185 " (cutoff:3.500A) Processing helix chain 'g' and resid 201 through 210 Processing helix chain 'g' and resid 211 through 220 removed outlier: 3.539A pdb=" N LYS g 215 " --> pdb=" O PHE g 211 " (cutoff:3.500A) Processing helix chain 'g' and resid 290 through 296 removed outlier: 4.300A pdb=" N GLN g 294 " --> pdb=" O ASP g 290 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG g 295 " --> pdb=" O ALA g 291 " (cutoff:3.500A) Processing helix chain 'h' and resid 21 through 27 Processing helix chain 'h' and resid 85 through 91 removed outlier: 3.844A pdb=" N THR h 89 " --> pdb=" O ASN h 85 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU h 90 " --> pdb=" O PRO h 86 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ARG h 91 " --> pdb=" O GLN h 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 85 through 91' Processing helix chain 'h' and resid 103 through 137 removed outlier: 3.676A pdb=" N ARG h 107 " --> pdb=" O ASP h 103 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG h 108 " --> pdb=" O PRO h 104 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN h 115 " --> pdb=" O ILE h 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET h 116 " --> pdb=" O ILE h 112 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL h 135 " --> pdb=" O ALA h 131 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS h 137 " --> pdb=" O SER h 133 " (cutoff:3.500A) Processing helix chain 'h' and resid 179 through 189 removed outlier: 4.466A pdb=" N ASP h 183 " --> pdb=" O ASP h 179 " (cutoff:3.500A) Processing helix chain 'h' and resid 201 through 210 removed outlier: 3.520A pdb=" N SER h 210 " --> pdb=" O ALA h 206 " (cutoff:3.500A) Processing helix chain 'h' and resid 211 through 219 removed outlier: 3.504A pdb=" N LEU h 218 " --> pdb=" O VAL h 214 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP h 219 " --> pdb=" O LYS h 215 " (cutoff:3.500A) Processing helix chain 'h' and resid 290 through 297 Processing helix chain 'h' and resid 331 through 335 removed outlier: 4.220A pdb=" N PHE h 335 " --> pdb=" O PRO h 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0' and resid 7 through 14 removed outlier: 6.679A pdb=" N GLN 0 8 " --> pdb=" O TYR Q 40 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N SER Q 42 " --> pdb=" O GLN 0 8 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N LEU 0 10 " --> pdb=" O SER Q 42 " (cutoff:3.500A) removed outlier: 12.688A pdb=" N ILE Q 44 " --> pdb=" O LEU 0 10 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N ALA 0 12 " --> pdb=" O ILE Q 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 28 through 33 removed outlier: 4.243A pdb=" N PHE 0 28 " --> pdb=" O GLY 0 281 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ARG 0 283 " --> pdb=" O PHE 0 28 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU 0 30 " --> pdb=" O ARG 0 283 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N TYR 0 285 " --> pdb=" O GLU 0 30 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR 0 32 " --> pdb=" O TYR 0 285 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 69 through 73 removed outlier: 6.451A pdb=" N TYR 0 40 " --> pdb=" O LEU 4 9 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA 4 11 " --> pdb=" O TYR 0 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '0' and resid 81 through 84 removed outlier: 3.506A pdb=" N GLU 0 317 " --> pdb=" O VAL 0 84 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP 0 308 " --> pdb=" O PHE 0 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '0' and resid 140 through 144 removed outlier: 5.838A pdb=" N GLY 0 144 " --> pdb=" O ASP 0 148 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASP 0 148 " --> pdb=" O GLY 0 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '0' and resid 239 through 245 removed outlier: 5.484A pdb=" N ILE 0 250 " --> pdb=" O LYS 0 242 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N MET 0 244 " --> pdb=" O VAL 0 248 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL 0 248 " --> pdb=" O MET 0 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE 0 198 " --> pdb=" O VAL 0 251 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR 0 253 " --> pdb=" O ILE 0 198 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N PHE 0 200 " --> pdb=" O TYR 0 253 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET 0 272 " --> pdb=" O VAL 0 338 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '0' and resid 256 through 257 Processing sheet with id=AA8, first strand: chain '1' and resid 8 through 11 removed outlier: 6.653A pdb=" N GLN 1 8 " --> pdb=" O TYR R 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '1' and resid 28 through 31 removed outlier: 4.679A pdb=" N PHE 1 28 " --> pdb=" O GLY 1 281 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG 1 283 " --> pdb=" O PHE 1 28 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU 1 30 " --> pdb=" O ARG 1 283 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N TYR 1 285 " --> pdb=" O GLU 1 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '1' and resid 69 through 73 removed outlier: 6.545A pdb=" N TYR 1 40 " --> pdb=" O LEU 5 9 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA 5 11 " --> pdb=" O TYR 1 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '1' and resid 81 through 84 removed outlier: 3.681A pdb=" N TRP 1 308 " --> pdb=" O PHE 1 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '1' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain '1' and resid 161 through 162 removed outlier: 6.198A pdb=" N ILE 1 198 " --> pdb=" O VAL 1 251 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N TYR 1 253 " --> pdb=" O ILE 1 198 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N PHE 1 200 " --> pdb=" O TYR 1 253 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE 1 250 " --> pdb=" O GLY 1 243 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY 1 243 " --> pdb=" O ILE 1 250 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL 1 252 " --> pdb=" O TYR 1 241 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR 1 241 " --> pdb=" O VAL 1 252 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '1' and resid 256 through 257 Processing sheet with id=AB6, first strand: chain '2' and resid 8 through 12 removed outlier: 7.024A pdb=" N GLN 2 8 " --> pdb=" O TYR S 40 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N SER S 42 " --> pdb=" O GLN 2 8 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N LEU 2 10 " --> pdb=" O SER S 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '2' and resid 28 through 33 removed outlier: 7.047A pdb=" N GLY 2 281 " --> pdb=" O PHE 2 28 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU 2 30 " --> pdb=" O GLY 2 281 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU 2 282 " --> pdb=" O LEU 2 328 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 69 through 73 removed outlier: 7.870A pdb=" N SER 2 42 " --> pdb=" O LEU 3 10 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ALA 3 12 " --> pdb=" O SER 2 42 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '2' and resid 81 through 84 removed outlier: 3.804A pdb=" N TRP 2 308 " --> pdb=" O PHE 2 318 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '2' and resid 139 through 142 Processing sheet with id=AC2, first strand: chain '2' and resid 239 through 245 removed outlier: 3.501A pdb=" N SER 2 240 " --> pdb=" O VAL 2 252 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL 2 252 " --> pdb=" O SER 2 240 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE 2 250 " --> pdb=" O LYS 2 242 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N MET 2 244 " --> pdb=" O VAL 2 248 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL 2 248 " --> pdb=" O MET 2 244 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET 2 272 " --> pdb=" O VAL 2 338 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '2' and resid 256 through 257 Processing sheet with id=AC4, first strand: chain '3' and resid 31 through 33 removed outlier: 3.679A pdb=" N TYR 3 285 " --> pdb=" O TYR 3 32 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '3' and resid 69 through 73 removed outlier: 8.109A pdb=" N SER 3 42 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA C 12 " --> pdb=" O SER 3 42 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE 3 44 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU C 14 " --> pdb=" O ILE 3 44 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '3' and resid 81 through 82 Processing sheet with id=AC7, first strand: chain '3' and resid 139 through 142 Processing sheet with id=AC8, first strand: chain '3' and resid 239 through 245 removed outlier: 5.483A pdb=" N TYR 3 241 " --> pdb=" O VAL 3 252 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL 3 252 " --> pdb=" O TYR 3 241 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLY 3 243 " --> pdb=" O ILE 3 250 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE 3 250 " --> pdb=" O GLY 3 243 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL 3 248 " --> pdb=" O TYR 3 245 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE 3 198 " --> pdb=" O VAL 3 251 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR 3 253 " --> pdb=" O ILE 3 198 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N PHE 3 200 " --> pdb=" O TYR 3 253 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '3' and resid 256 through 258 Processing sheet with id=AD1, first strand: chain '4' and resid 31 through 33 removed outlier: 4.017A pdb=" N TYR 4 285 " --> pdb=" O TYR 4 32 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '4' and resid 69 through 73 removed outlier: 8.026A pdb=" N SER 4 42 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA A 12 " --> pdb=" O SER 4 42 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '4' and resid 81 through 82 removed outlier: 3.594A pdb=" N THR 4 319 " --> pdb=" O HIS 4 82 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP 4 308 " --> pdb=" O PHE 4 318 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '4' and resid 139 through 142 removed outlier: 3.738A pdb=" N VAL 4 150 " --> pdb=" O MET 4 142 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '4' and resid 239 through 245 removed outlier: 5.610A pdb=" N TYR 4 241 " --> pdb=" O VAL 4 252 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL 4 252 " --> pdb=" O TYR 4 241 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLY 4 243 " --> pdb=" O ILE 4 250 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE 4 250 " --> pdb=" O GLY 4 243 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL 4 248 " --> pdb=" O TYR 4 245 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR 4 253 " --> pdb=" O PHE 4 200 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '4' and resid 256 through 258 Processing sheet with id=AD7, first strand: chain '5' and resid 69 through 73 removed outlier: 6.921A pdb=" N LYS 5 38 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU B 9 " --> pdb=" O LYS 5 38 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR 5 40 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA B 11 " --> pdb=" O TYR 5 40 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '5' and resid 81 through 82 removed outlier: 3.572A pdb=" N GLN 5 322 " --> pdb=" O TYR 5 304 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '5' and resid 139 through 142 Processing sheet with id=AE1, first strand: chain '5' and resid 239 through 245 removed outlier: 3.502A pdb=" N VAL 5 252 " --> pdb=" O SER 5 240 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE 5 250 " --> pdb=" O LYS 5 242 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N MET 5 244 " --> pdb=" O VAL 5 248 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL 5 248 " --> pdb=" O MET 5 244 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE 5 198 " --> pdb=" O VAL 5 251 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR 5 253 " --> pdb=" O ILE 5 198 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE 5 200 " --> pdb=" O TYR 5 253 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '5' and resid 256 through 258 Processing sheet with id=AE3, first strand: chain '5' and resid 281 through 285 Processing sheet with id=AE4, first strand: chain '5' and resid 309 through 312 removed outlier: 7.792A pdb=" N THR 5 310 " --> pdb=" O GLU 5 317 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N GLU 5 317 " --> pdb=" O THR 5 310 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY 5 312 " --> pdb=" O ALA 5 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '6' and resid 7 through 14 removed outlier: 6.199A pdb=" N GLN 6 8 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N SER E 42 " --> pdb=" O GLN 6 8 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N LEU 6 10 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 13.453A pdb=" N ILE E 44 " --> pdb=" O LEU 6 10 " (cutoff:3.500A) removed outlier: 10.740A pdb=" N ALA 6 12 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL E 39 " --> pdb=" O PHE E 73 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '6' and resid 69 through 73 removed outlier: 3.569A pdb=" N VAL 6 39 " --> pdb=" O PHE 6 73 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N SER 6 42 " --> pdb=" O LEU Q 10 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA Q 12 " --> pdb=" O SER 6 42 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE 6 44 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLU Q 14 " --> pdb=" O ILE 6 44 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '6' and resid 139 through 142 Processing sheet with id=AE8, first strand: chain '6' and resid 239 through 244 removed outlier: 5.747A pdb=" N TYR 6 241 " --> pdb=" O VAL 6 252 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL 6 252 " --> pdb=" O TYR 6 241 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY 6 243 " --> pdb=" O ILE 6 250 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILE 6 198 " --> pdb=" O VAL 6 251 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR 6 253 " --> pdb=" O ILE 6 198 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE 6 197 " --> pdb=" O GLY 6 275 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '6' and resid 256 through 259 Processing sheet with id=AF1, first strand: chain '6' and resid 281 through 285 Processing sheet with id=AF2, first strand: chain '6' and resid 304 through 310 removed outlier: 3.543A pdb=" N TYR 6 304 " --> pdb=" O GLN 6 322 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN 6 322 " --> pdb=" O TYR 6 304 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG 6 316 " --> pdb=" O THR 6 310 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '7' and resid 7 through 14 removed outlier: 6.197A pdb=" N GLN 7 8 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N SER F 42 " --> pdb=" O GLN 7 8 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N LEU 7 10 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 13.002A pdb=" N ILE F 44 " --> pdb=" O LEU 7 10 " (cutoff:3.500A) removed outlier: 10.396A pdb=" N ALA 7 12 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL F 39 " --> pdb=" O PHE F 73 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '7' and resid 28 through 33 removed outlier: 6.372A pdb=" N GLY 7 281 " --> pdb=" O PHE 7 28 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU 7 30 " --> pdb=" O GLY 7 281 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '7' and resid 72 through 73 removed outlier: 3.653A pdb=" N LEU R 10 " --> pdb=" O TYR 7 40 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N SER 7 42 " --> pdb=" O LEU R 10 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA R 12 " --> pdb=" O SER 7 42 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE 7 44 " --> pdb=" O ALA R 12 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLU R 14 " --> pdb=" O ILE 7 44 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '7' and resid 81 through 84 removed outlier: 3.861A pdb=" N HIS 7 82 " --> pdb=" O THR 7 319 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR 7 319 " --> pdb=" O HIS 7 82 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL 7 84 " --> pdb=" O GLU 7 317 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU 7 317 " --> pdb=" O VAL 7 84 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG 7 316 " --> pdb=" O THR 7 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE 7 318 " --> pdb=" O TRP 7 308 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '7' and resid 139 through 142 Processing sheet with id=AF8, first strand: chain '7' and resid 239 through 244 removed outlier: 5.520A pdb=" N TYR 7 241 " --> pdb=" O VAL 7 252 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL 7 252 " --> pdb=" O TYR 7 241 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY 7 243 " --> pdb=" O ILE 7 250 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE 7 198 " --> pdb=" O VAL 7 251 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR 7 253 " --> pdb=" O ILE 7 198 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain '7' and resid 256 through 259 Processing sheet with id=AG1, first strand: chain 'A' and resid 30 through 31 removed outlier: 6.961A pdb=" N GLU A 30 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N TYR A 285 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 69 through 73 removed outlier: 3.573A pdb=" N VAL A 39 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N SER A 42 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA E 12 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE A 44 " --> pdb=" O ALA E 12 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU E 14 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY A 46 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS E 16 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 81 through 84 Processing sheet with id=AG4, first strand: chain 'A' and resid 139 through 140 removed outlier: 3.570A pdb=" N TYR A 140 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 152 " --> pdb=" O TYR A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'A' and resid 161 through 162 removed outlier: 3.631A pdb=" N ILE A 197 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE A 250 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 252 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 256 through 259 Processing sheet with id=AG7, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.583A pdb=" N PHE B 28 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG B 283 " --> pdb=" O PHE B 28 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU B 30 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N TYR B 285 " --> pdb=" O GLU B 30 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 72 through 73 removed outlier: 3.878A pdb=" N PHE B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 39 " --> pdb=" O PHE B 73 " (cutoff:3.500A) removed outlier: 10.768A pdb=" N LYS B 38 " --> pdb=" O LEU F 9 " (cutoff:3.500A) removed outlier: 10.352A pdb=" N ALA F 11 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N TYR B 40 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N ASN F 13 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N SER B 42 " --> pdb=" O ASN F 13 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLN F 15 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE B 44 " --> pdb=" O GLN F 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'B' and resid 81 through 84 removed outlier: 3.504A pdb=" N TRP B 308 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.605A pdb=" N TYR B 140 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 161 through 163 removed outlier: 5.063A pdb=" N ILE B 250 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 256 through 259 Processing sheet with id=AH4, first strand: chain 'C' and resid 69 through 73 removed outlier: 3.933A pdb=" N PHE C 73 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL C 39 " --> pdb=" O PHE C 73 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N SER C 42 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA G 12 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE C 44 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLU G 14 " --> pdb=" O ILE C 44 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 81 through 84 Processing sheet with id=AH6, first strand: chain 'C' and resid 139 through 141 removed outlier: 3.854A pdb=" N TYR C 140 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL C 152 " --> pdb=" O TYR C 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'C' and resid 161 through 163 removed outlier: 7.250A pdb=" N ILE C 162 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL C 248 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 250 " --> pdb=" O GLY C 243 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY C 243 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL C 252 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR C 241 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 256 through 259 Processing sheet with id=AH9, first strand: chain 'C' and resid 281 through 285 Processing sheet with id=AI1, first strand: chain 'D' and resid 8 through 14 removed outlier: 6.667A pdb=" N GLN D 8 " --> pdb=" O TYR N 40 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER N 42 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N LEU D 10 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 12.985A pdb=" N ILE N 44 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N ALA D 12 " --> pdb=" O ILE N 44 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 30 through 33 removed outlier: 7.019A pdb=" N GLU D 30 " --> pdb=" O ARG D 283 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N TYR D 285 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR D 32 " --> pdb=" O TYR D 285 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D' and resid 38 through 44 removed outlier: 8.060A pdb=" N SER D 42 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA H 12 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE D 44 " --> pdb=" O ALA H 12 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLU H 14 " --> pdb=" O ILE D 44 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.783A pdb=" N TRP D 308 " --> pdb=" O PHE D 318 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 161 through 162 Processing sheet with id=AI6, first strand: chain 'D' and resid 239 through 244 removed outlier: 3.630A pdb=" N VAL D 252 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE D 250 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'D' and resid 256 through 259 Processing sheet with id=AI8, first strand: chain 'E' and resid 28 through 33 removed outlier: 6.509A pdb=" N GLY E 281 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU E 30 " --> pdb=" O GLY E 281 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR E 285 " --> pdb=" O TYR E 32 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU E 328 " --> pdb=" O LEU E 282 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.602A pdb=" N GLU E 317 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.569A pdb=" N TYR E 140 " --> pdb=" O VAL E 152 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'E' and resid 161 through 163 removed outlier: 3.512A pdb=" N ILE E 162 " --> pdb=" O SER E 337 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL E 248 " --> pdb=" O MET E 244 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N MET E 244 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE E 250 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 256 through 259 Processing sheet with id=AJ4, first strand: chain 'F' and resid 31 through 33 removed outlier: 3.783A pdb=" N TYR F 285 " --> pdb=" O TYR F 32 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.580A pdb=" N GLU F 317 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 140 through 142 removed outlier: 3.803A pdb=" N TYR F 140 " --> pdb=" O VAL F 152 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 161 through 163 removed outlier: 7.563A pdb=" N ILE F 162 " --> pdb=" O GLN F 339 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE F 198 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TYR F 253 " --> pdb=" O ILE F 198 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N PHE F 200 " --> pdb=" O TYR F 253 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL F 252 " --> pdb=" O TYR F 241 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TYR F 241 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'F' and resid 256 through 258 Processing sheet with id=AJ9, first strand: chain 'G' and resid 70 through 73 removed outlier: 3.588A pdb=" N VAL G 39 " --> pdb=" O PHE G 73 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR G 40 " --> pdb=" O LEU O 9 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ALA O 11 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER G 42 " --> pdb=" O ALA O 11 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'G' and resid 81 through 84 removed outlier: 3.886A pdb=" N VAL G 84 " --> pdb=" O GLU G 317 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU G 317 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP G 308 " --> pdb=" O PHE G 318 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'G' and resid 140 through 142 removed outlier: 4.013A pdb=" N TYR G 140 " --> pdb=" O VAL G 152 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'G' and resid 161 through 163 removed outlier: 7.164A pdb=" N ILE G 162 " --> pdb=" O GLN G 339 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE G 198 " --> pdb=" O VAL G 251 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR G 253 " --> pdb=" O ILE G 198 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N PHE G 200 " --> pdb=" O TYR G 253 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY G 243 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL G 252 " --> pdb=" O TYR G 241 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TYR G 241 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'G' and resid 256 through 258 Processing sheet with id=AK5, first strand: chain 'G' and resid 281 through 285 removed outlier: 3.507A pdb=" N LEU G 328 " --> pdb=" O LEU G 282 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'H' and resid 70 through 73 removed outlier: 3.663A pdb=" N VAL H 39 " --> pdb=" O PHE H 73 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU P 10 " --> pdb=" O TYR H 40 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N SER H 42 " --> pdb=" O LEU P 10 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA P 12 " --> pdb=" O SER H 42 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'H' and resid 81 through 84 removed outlier: 3.512A pdb=" N THR H 319 " --> pdb=" O HIS H 82 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU H 317 " --> pdb=" O VAL H 84 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP H 308 " --> pdb=" O PHE H 318 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'H' and resid 140 through 142 Processing sheet with id=AK9, first strand: chain 'H' and resid 161 through 163 removed outlier: 7.364A pdb=" N ILE H 162 " --> pdb=" O GLN H 339 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE H 198 " --> pdb=" O VAL H 251 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR H 253 " --> pdb=" O ILE H 198 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE H 200 " --> pdb=" O TYR H 253 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY H 243 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL H 252 " --> pdb=" O TYR H 241 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N TYR H 241 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'H' and resid 256 through 258 Processing sheet with id=AL2, first strand: chain 'H' and resid 282 through 285 removed outlier: 3.622A pdb=" N LEU H 328 " --> pdb=" O LEU H 282 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'I' and resid 7 through 14 removed outlier: 6.752A pdb=" N GLN I 8 " --> pdb=" O TYR h 40 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N SER h 42 " --> pdb=" O GLN I 8 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N LEU I 10 " --> pdb=" O SER h 42 " (cutoff:3.500A) removed outlier: 12.923A pdb=" N ILE h 44 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N ALA I 12 " --> pdb=" O ILE h 44 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'I' and resid 30 through 31 removed outlier: 6.795A pdb=" N GLU I 30 " --> pdb=" O ARG I 283 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N TYR I 285 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'I' and resid 72 through 73 removed outlier: 3.890A pdb=" N PHE I 73 " --> pdb=" O VAL I 39 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL I 39 " --> pdb=" O PHE I 73 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N LYS I 38 " --> pdb=" O LEU J 9 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N ALA J 11 " --> pdb=" O LYS I 38 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR I 40 " --> pdb=" O ALA J 11 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ASN J 13 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER I 42 " --> pdb=" O ASN J 13 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N GLN J 15 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE I 44 " --> pdb=" O GLN J 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL5 Processing sheet with id=AL6, first strand: chain 'I' and resid 81 through 84 removed outlier: 3.973A pdb=" N ARG I 316 " --> pdb=" O THR I 310 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR I 310 " --> pdb=" O ARG I 316 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'I' and resid 139 through 141 removed outlier: 3.564A pdb=" N TYR I 140 " --> pdb=" O VAL I 152 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL I 152 " --> pdb=" O TYR I 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL7 Processing sheet with id=AL8, first strand: chain 'I' and resid 161 through 163 removed outlier: 4.987A pdb=" N ILE I 250 " --> pdb=" O LYS I 242 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'I' and resid 256 through 259 Processing sheet with id=AM1, first strand: chain 'J' and resid 30 through 33 removed outlier: 4.063A pdb=" N GLU J 30 " --> pdb=" O GLY J 281 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR J 285 " --> pdb=" O TYR J 32 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'J' and resid 70 through 73 removed outlier: 3.538A pdb=" N VAL J 39 " --> pdb=" O PHE J 73 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU K 10 " --> pdb=" O TYR J 40 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N SER J 42 " --> pdb=" O LEU K 10 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALA K 12 " --> pdb=" O SER J 42 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'J' and resid 81 through 82 Processing sheet with id=AM4, first strand: chain 'J' and resid 140 through 142 Processing sheet with id=AM5, first strand: chain 'J' and resid 239 through 244 removed outlier: 5.458A pdb=" N TYR J 241 " --> pdb=" O VAL J 252 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL J 252 " --> pdb=" O TYR J 241 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE J 198 " --> pdb=" O VAL J 251 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TYR J 253 " --> pdb=" O ILE J 198 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N PHE J 200 " --> pdb=" O TYR J 253 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'J' and resid 256 through 258 Processing sheet with id=AM7, first strand: chain 'K' and resid 28 through 33 removed outlier: 6.540A pdb=" N GLY K 281 " --> pdb=" O PHE K 28 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU K 30 " --> pdb=" O GLY K 281 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR K 285 " --> pdb=" O TYR K 32 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'K' and resid 69 through 73 removed outlier: 7.908A pdb=" N SER K 42 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA L 12 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE K 44 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU L 14 " --> pdb=" O ILE K 44 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'K' and resid 81 through 84 removed outlier: 3.633A pdb=" N HIS K 82 " --> pdb=" O THR K 319 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL K 84 " --> pdb=" O GLU K 317 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU K 317 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG K 316 " --> pdb=" O THR K 310 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN K 322 " --> pdb=" O TYR K 304 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'K' and resid 139 through 142 Processing sheet with id=AN2, first strand: chain 'K' and resid 239 through 244 removed outlier: 5.626A pdb=" N TYR K 241 " --> pdb=" O VAL K 252 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL K 252 " --> pdb=" O TYR K 241 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY K 243 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ILE K 198 " --> pdb=" O VAL K 251 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR K 253 " --> pdb=" O ILE K 198 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'K' and resid 256 through 259 removed outlier: 3.606A pdb=" N GLU K 259 " --> pdb=" O VAL K 262 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'L' and resid 28 through 33 removed outlier: 4.222A pdb=" N PHE L 28 " --> pdb=" O GLY L 281 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG L 283 " --> pdb=" O PHE L 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU L 30 " --> pdb=" O ARG L 283 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N TYR L 285 " --> pdb=" O GLU L 30 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR L 32 " --> pdb=" O TYR L 285 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'L' and resid 72 through 73 removed outlier: 3.639A pdb=" N VAL L 39 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N SER L 42 " --> pdb=" O LEU g 10 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA g 12 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE L 44 " --> pdb=" O ALA g 12 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU g 14 " --> pdb=" O ILE L 44 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'L' and resid 82 through 84 removed outlier: 3.796A pdb=" N VAL L 84 " --> pdb=" O GLU L 317 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU L 317 " --> pdb=" O VAL L 84 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP L 308 " --> pdb=" O PHE L 318 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'L' and resid 139 through 142 removed outlier: 3.808A pdb=" N VAL L 152 " --> pdb=" O TYR L 140 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'L' and resid 161 through 162 removed outlier: 6.513A pdb=" N VAL L 248 " --> pdb=" O MET L 244 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N MET L 244 " --> pdb=" O VAL L 248 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE L 250 " --> pdb=" O LYS L 242 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'L' and resid 256 through 258 Processing sheet with id=AO1, first strand: chain 'M' and resid 7 through 14 removed outlier: 6.778A pdb=" N GLN M 8 " --> pdb=" O TYR T 40 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N SER T 42 " --> pdb=" O GLN M 8 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N LEU M 10 " --> pdb=" O SER T 42 " (cutoff:3.500A) removed outlier: 13.106A pdb=" N ILE T 44 " --> pdb=" O LEU M 10 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N ALA M 12 " --> pdb=" O ILE T 44 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'M' and resid 28 through 33 removed outlier: 6.979A pdb=" N GLY M 281 " --> pdb=" O PHE M 28 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU M 30 " --> pdb=" O GLY M 281 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR M 285 " --> pdb=" O TYR M 32 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'M' and resid 70 through 73 removed outlier: 3.511A pdb=" N LEU N 10 " --> pdb=" O TYR M 40 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N SER M 42 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA N 12 " --> pdb=" O SER M 42 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'M' and resid 81 through 84 removed outlier: 3.902A pdb=" N GLU M 317 " --> pdb=" O VAL M 84 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'M' and resid 140 through 144 removed outlier: 5.772A pdb=" N GLY M 144 " --> pdb=" O ASP M 148 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASP M 148 " --> pdb=" O GLY M 144 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'M' and resid 239 through 245 removed outlier: 5.321A pdb=" N TYR M 241 " --> pdb=" O VAL M 252 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL M 252 " --> pdb=" O TYR M 241 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY M 243 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET M 272 " --> pdb=" O VAL M 338 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'M' and resid 256 through 257 Processing sheet with id=AO8, first strand: chain 'N' and resid 32 through 33 Processing sheet with id=AO9, first strand: chain 'N' and resid 81 through 82 Processing sheet with id=AP1, first strand: chain 'N' and resid 139 through 142 Processing sheet with id=AP2, first strand: chain 'N' and resid 239 through 245 removed outlier: 5.606A pdb=" N TYR N 241 " --> pdb=" O VAL N 252 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL N 252 " --> pdb=" O TYR N 241 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY N 243 " --> pdb=" O ILE N 250 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE N 250 " --> pdb=" O GLY N 243 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL N 248 " --> pdb=" O TYR N 245 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL N 336 " --> pdb=" O LEU N 274 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'N' and resid 256 through 259 removed outlier: 3.646A pdb=" N GLU N 259 " --> pdb=" O VAL N 262 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL N 262 " --> pdb=" O GLU N 259 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'O' and resid 30 through 33 removed outlier: 3.971A pdb=" N GLU O 30 " --> pdb=" O GLY O 281 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR O 285 " --> pdb=" O TYR O 32 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'O' and resid 69 through 73 removed outlier: 3.561A pdb=" N LEU S 10 " --> pdb=" O TYR O 40 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N SER O 42 " --> pdb=" O LEU S 10 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA S 12 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE O 44 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLU S 14 " --> pdb=" O ILE O 44 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'O' and resid 81 through 84 removed outlier: 3.921A pdb=" N GLU O 317 " --> pdb=" O VAL O 84 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG O 316 " --> pdb=" O THR O 310 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE O 318 " --> pdb=" O TRP O 308 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP O 308 " --> pdb=" O PHE O 318 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'O' and resid 139 through 142 Processing sheet with id=AP8, first strand: chain 'O' and resid 197 through 199 removed outlier: 5.765A pdb=" N ILE O 198 " --> pdb=" O VAL O 251 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY O 243 " --> pdb=" O ILE O 250 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'O' and resid 256 through 259 Processing sheet with id=AQ1, first strand: chain 'P' and resid 30 through 33 removed outlier: 3.900A pdb=" N GLU P 30 " --> pdb=" O GLY P 281 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR P 285 " --> pdb=" O TYR P 32 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'P' and resid 69 through 73 removed outlier: 7.698A pdb=" N SER P 42 " --> pdb=" O LEU T 10 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA T 12 " --> pdb=" O SER P 42 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE P 44 " --> pdb=" O ALA T 12 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU T 14 " --> pdb=" O ILE P 44 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'P' and resid 81 through 84 removed outlier: 3.775A pdb=" N VAL P 84 " --> pdb=" O GLU P 317 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU P 317 " --> pdb=" O VAL P 84 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG P 316 " --> pdb=" O THR P 310 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP P 308 " --> pdb=" O PHE P 318 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN P 322 " --> pdb=" O TYR P 304 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'P' and resid 139 through 142 Processing sheet with id=AQ5, first strand: chain 'P' and resid 241 through 244 removed outlier: 5.770A pdb=" N ILE P 250 " --> pdb=" O LYS P 242 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE P 198 " --> pdb=" O VAL P 251 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'P' and resid 256 through 259 Processing sheet with id=AQ7, first strand: chain 'Q' and resid 28 through 33 removed outlier: 6.989A pdb=" N GLY Q 281 " --> pdb=" O PHE Q 28 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU Q 30 " --> pdb=" O GLY Q 281 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR Q 285 " --> pdb=" O TYR Q 32 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'Q' and resid 82 through 84 removed outlier: 3.628A pdb=" N VAL Q 84 " --> pdb=" O GLU Q 317 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU Q 317 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TRP Q 308 " --> pdb=" O PHE Q 318 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET Q 320 " --> pdb=" O LYS Q 306 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'Q' and resid 139 through 142 removed outlier: 3.753A pdb=" N VAL Q 152 " --> pdb=" O TYR Q 140 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET Q 142 " --> pdb=" O VAL Q 150 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL Q 150 " --> pdb=" O MET Q 142 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'Q' and resid 161 through 162 removed outlier: 6.239A pdb=" N VAL Q 248 " --> pdb=" O MET Q 244 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N MET Q 244 " --> pdb=" O VAL Q 248 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE Q 250 " --> pdb=" O LYS Q 242 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'Q' and resid 256 through 258 Processing sheet with id=AR3, first strand: chain 'R' and resid 28 through 33 removed outlier: 6.835A pdb=" N GLY R 281 " --> pdb=" O PHE R 28 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR R 285 " --> pdb=" O TYR R 32 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'R' and resid 82 through 84 removed outlier: 3.771A pdb=" N VAL R 84 " --> pdb=" O GLU R 317 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU R 317 " --> pdb=" O VAL R 84 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'R' and resid 139 through 140 removed outlier: 4.107A pdb=" N VAL R 152 " --> pdb=" O TYR R 140 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'R' and resid 239 through 245 removed outlier: 5.495A pdb=" N TYR R 241 " --> pdb=" O VAL R 252 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL R 252 " --> pdb=" O TYR R 241 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY R 243 " --> pdb=" O ILE R 250 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL R 248 " --> pdb=" O TYR R 245 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET R 272 " --> pdb=" O VAL R 338 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'R' and resid 256 through 258 Processing sheet with id=AR8, first strand: chain 'S' and resid 30 through 33 removed outlier: 3.547A pdb=" N GLU S 30 " --> pdb=" O GLY S 281 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'S' and resid 82 through 84 removed outlier: 3.655A pdb=" N VAL S 84 " --> pdb=" O GLU S 317 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU S 317 " --> pdb=" O VAL S 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP S 308 " --> pdb=" O PHE S 318 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'S' and resid 139 through 142 removed outlier: 3.643A pdb=" N VAL S 152 " --> pdb=" O TYR S 140 " (cutoff:3.500A) Processing sheet with id=AS2, first strand: chain 'S' and resid 161 through 162 removed outlier: 5.907A pdb=" N VAL S 248 " --> pdb=" O MET S 244 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N MET S 244 " --> pdb=" O VAL S 248 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE S 250 " --> pdb=" O LYS S 242 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'S' and resid 256 through 258 Processing sheet with id=AS4, first strand: chain 'T' and resid 28 through 33 removed outlier: 4.591A pdb=" N PHE T 28 " --> pdb=" O GLY T 281 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ARG T 283 " --> pdb=" O PHE T 28 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU T 30 " --> pdb=" O ARG T 283 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N TYR T 285 " --> pdb=" O GLU T 30 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TYR T 32 " --> pdb=" O TYR T 285 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'T' and resid 82 through 84 removed outlier: 3.570A pdb=" N VAL T 84 " --> pdb=" O GLU T 317 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU T 317 " --> pdb=" O VAL T 84 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'T' and resid 139 through 142 removed outlier: 3.541A pdb=" N MET T 142 " --> pdb=" O VAL T 150 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'T' and resid 161 through 162 removed outlier: 3.512A pdb=" N VAL T 199 " --> pdb=" O VAL T 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE T 250 " --> pdb=" O GLY T 243 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY T 243 " --> pdb=" O ILE T 250 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL T 252 " --> pdb=" O TYR T 241 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR T 241 " --> pdb=" O VAL T 252 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'T' and resid 256 through 258 Processing sheet with id=AS9, first strand: chain 'U' and resid 86 through 90 Processing sheet with id=AT1, first strand: chain 'U' and resid 167 through 172 removed outlier: 4.110A pdb=" N PHE U 152 " --> pdb=" O VAL U 172 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU U 151 " --> pdb=" O VAL U 236 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL U 236 " --> pdb=" O LEU U 151 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'U' and resid 193 through 195 removed outlier: 4.096A pdb=" N GLY U 203 " --> pdb=" O GLN U 194 " (cutoff:3.500A) Processing sheet with id=AT3, first strand: chain 'U' and resid 338 through 341 removed outlier: 8.333A pdb=" N LEU V 333 " --> pdb=" O ALA U 280 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE U 282 " --> pdb=" O LEU V 333 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'U' and resid 332 through 333 Processing sheet with id=AT5, first strand: chain 'V' and resid 87 through 90 Processing sheet with id=AT6, first strand: chain 'V' and resid 167 through 172 removed outlier: 3.883A pdb=" N PHE V 152 " --> pdb=" O VAL V 172 " (cutoff:3.500A) Processing sheet with id=AT7, first strand: chain 'V' and resid 189 through 190 removed outlier: 3.716A pdb=" N ARG V 190 " --> pdb=" O VAL V 193 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY V 203 " --> pdb=" O GLN V 194 " (cutoff:3.500A) Processing sheet with id=AT8, first strand: chain 'V' and resid 338 through 341 removed outlier: 8.429A pdb=" N LEU W 333 " --> pdb=" O ALA V 280 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE V 282 " --> pdb=" O LEU W 333 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'W' and resid 87 through 90 Processing sheet with id=AU1, first strand: chain 'W' and resid 167 through 172 removed outlier: 4.126A pdb=" N PHE W 152 " --> pdb=" O VAL W 172 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'W' and resid 189 through 190 removed outlier: 4.237A pdb=" N GLY W 203 " --> pdb=" O GLN W 194 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL W 206 " --> pdb=" O THR W 220 " (cutoff:3.500A) Processing sheet with id=AU3, first strand: chain 'W' and resid 338 through 340 removed outlier: 6.417A pdb=" N ILE W 282 " --> pdb=" O LEU X 333 " (cutoff:3.500A) Processing sheet with id=AU4, first strand: chain 'X' and resid 87 through 90 Processing sheet with id=AU5, first strand: chain 'X' and resid 167 through 172 removed outlier: 3.990A pdb=" N PHE X 152 " --> pdb=" O VAL X 172 " (cutoff:3.500A) Processing sheet with id=AU6, first strand: chain 'X' and resid 189 through 190 removed outlier: 4.284A pdb=" N GLY X 203 " --> pdb=" O GLN X 194 " (cutoff:3.500A) Processing sheet with id=AU7, first strand: chain 'X' and resid 338 through 341 removed outlier: 8.515A pdb=" N LEU Y 333 " --> pdb=" O ALA X 280 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE X 282 " --> pdb=" O LEU Y 333 " (cutoff:3.500A) Processing sheet with id=AU8, first strand: chain 'Y' and resid 168 through 172 removed outlier: 3.838A pdb=" N PHE Y 152 " --> pdb=" O VAL Y 172 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU Y 151 " --> pdb=" O VAL Y 236 " (cutoff:3.500A) Processing sheet with id=AU9, first strand: chain 'Y' and resid 189 through 190 removed outlier: 4.409A pdb=" N GLY Y 203 " --> pdb=" O GLN Y 194 " (cutoff:3.500A) Processing sheet with id=AV1, first strand: chain 'Y' and resid 338 through 340 removed outlier: 6.311A pdb=" N ILE Y 282 " --> pdb=" O LEU Z 333 " (cutoff:3.500A) Processing sheet with id=AV2, first strand: chain 'Z' and resid 87 through 90 Processing sheet with id=AV3, first strand: chain 'Z' and resid 167 through 172 removed outlier: 4.029A pdb=" N PHE Z 152 " --> pdb=" O VAL Z 172 " (cutoff:3.500A) Processing sheet with id=AV4, first strand: chain 'Z' and resid 189 through 190 removed outlier: 6.938A pdb=" N GLN Z 194 " --> pdb=" O LEU Z 202 " (cutoff:3.500A) Processing sheet with id=AV5, first strand: chain 'Z' and resid 338 through 341 removed outlier: 8.262A pdb=" N LEU a 333 " --> pdb=" O ALA Z 280 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE Z 282 " --> pdb=" O LEU a 333 " (cutoff:3.500A) Processing sheet with id=AV6, first strand: chain 'a' and resid 87 through 90 Processing sheet with id=AV7, first strand: chain 'a' and resid 168 through 172 removed outlier: 3.983A pdb=" N PHE a 152 " --> pdb=" O VAL a 172 " (cutoff:3.500A) Processing sheet with id=AV8, first strand: chain 'a' and resid 189 through 190 removed outlier: 3.725A pdb=" N ARG a 190 " --> pdb=" O VAL a 193 " (cutoff:3.500A) Processing sheet with id=AV9, first strand: chain 'a' and resid 203 through 206 Processing sheet with id=AW1, first strand: chain 'a' and resid 338 through 340 removed outlier: 6.195A pdb=" N ILE a 282 " --> pdb=" O LEU b 333 " (cutoff:3.500A) Processing sheet with id=AW2, first strand: chain 'b' and resid 87 through 90 Processing sheet with id=AW3, first strand: chain 'b' and resid 167 through 172 removed outlier: 4.112A pdb=" N PHE b 152 " --> pdb=" O VAL b 172 " (cutoff:3.500A) Processing sheet with id=AW4, first strand: chain 'b' and resid 189 through 190 removed outlier: 4.194A pdb=" N GLY b 203 " --> pdb=" O GLN b 194 " (cutoff:3.500A) Processing sheet with id=AW5, first strand: chain 'b' and resid 338 through 340 removed outlier: 6.479A pdb=" N ILE b 282 " --> pdb=" O LEU c 333 " (cutoff:3.500A) Processing sheet with id=AW6, first strand: chain 'c' and resid 87 through 90 Processing sheet with id=AW7, first strand: chain 'c' and resid 168 through 172 removed outlier: 4.070A pdb=" N PHE c 152 " --> pdb=" O VAL c 172 " (cutoff:3.500A) Processing sheet with id=AW8, first strand: chain 'c' and resid 189 through 190 removed outlier: 4.632A pdb=" N GLY c 203 " --> pdb=" O GLN c 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR c 220 " --> pdb=" O VAL c 206 " (cutoff:3.500A) Processing sheet with id=AW9, first strand: chain 'c' and resid 338 through 341 removed outlier: 8.314A pdb=" N LEU d 333 " --> pdb=" O ALA c 280 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE c 282 " --> pdb=" O LEU d 333 " (cutoff:3.500A) Processing sheet with id=AX1, first strand: chain 'd' and resid 87 through 90 Processing sheet with id=AX2, first strand: chain 'd' and resid 167 through 172 removed outlier: 3.791A pdb=" N PHE d 152 " --> pdb=" O VAL d 172 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU d 151 " --> pdb=" O VAL d 236 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL d 236 " --> pdb=" O LEU d 151 " (cutoff:3.500A) Processing sheet with id=AX3, first strand: chain 'd' and resid 189 through 190 removed outlier: 3.953A pdb=" N GLY d 203 " --> pdb=" O GLN d 194 " (cutoff:3.500A) Processing sheet with id=AX4, first strand: chain 'd' and resid 338 through 341 removed outlier: 8.362A pdb=" N LEU e 333 " --> pdb=" O ALA d 280 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE d 282 " --> pdb=" O LEU e 333 " (cutoff:3.500A) Processing sheet with id=AX5, first strand: chain 'e' and resid 87 through 90 Processing sheet with id=AX6, first strand: chain 'e' and resid 167 through 172 removed outlier: 3.961A pdb=" N PHE e 152 " --> pdb=" O VAL e 172 " (cutoff:3.500A) Processing sheet with id=AX7, first strand: chain 'e' and resid 193 through 195 removed outlier: 6.888A pdb=" N GLN e 194 " --> pdb=" O LEU e 202 " (cutoff:3.500A) Processing sheet with id=AX8, first strand: chain 'e' and resid 338 through 341 removed outlier: 8.209A pdb=" N LEU f 333 " --> pdb=" O ALA e 280 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE e 282 " --> pdb=" O LEU f 333 " (cutoff:3.500A) Processing sheet with id=AX9, first strand: chain 'f' and resid 87 through 90 Processing sheet with id=AY1, first strand: chain 'f' and resid 167 through 172 removed outlier: 4.425A pdb=" N PHE f 152 " --> pdb=" O VAL f 172 " (cutoff:3.500A) Processing sheet with id=AY2, first strand: chain 'f' and resid 189 through 190 removed outlier: 6.992A pdb=" N GLN f 194 " --> pdb=" O LEU f 202 " (cutoff:3.500A) Processing sheet with id=AY3, first strand: chain 'g' and resid 28 through 33 removed outlier: 6.928A pdb=" N GLY g 281 " --> pdb=" O PHE g 28 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU g 30 " --> pdb=" O GLY g 281 " (cutoff:3.500A) Processing sheet with id=AY4, first strand: chain 'g' and resid 69 through 73 removed outlier: 8.011A pdb=" N SER g 42 " --> pdb=" O LEU h 10 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA h 12 " --> pdb=" O SER g 42 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE g 44 " --> pdb=" O ALA h 12 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLU h 14 " --> pdb=" O ILE g 44 " (cutoff:3.500A) Processing sheet with id=AY5, first strand: chain 'g' and resid 81 through 84 removed outlier: 3.591A pdb=" N GLU g 317 " --> pdb=" O VAL g 84 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP g 308 " --> pdb=" O PHE g 318 " (cutoff:3.500A) Processing sheet with id=AY6, first strand: chain 'g' and resid 139 through 142 Processing sheet with id=AY7, first strand: chain 'g' and resid 239 through 245 removed outlier: 5.595A pdb=" N TYR g 241 " --> pdb=" O VAL g 252 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL g 252 " --> pdb=" O TYR g 241 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY g 243 " --> pdb=" O ILE g 250 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE g 250 " --> pdb=" O GLY g 243 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET g 272 " --> pdb=" O VAL g 338 " (cutoff:3.500A) Processing sheet with id=AY8, first strand: chain 'g' and resid 256 through 258 Processing sheet with id=AY9, first strand: chain 'h' and resid 31 through 33 removed outlier: 3.646A pdb=" N TYR h 285 " --> pdb=" O TYR h 32 " (cutoff:3.500A) Processing sheet with id=AZ1, first strand: chain 'h' and resid 81 through 84 removed outlier: 3.551A pdb=" N GLN h 322 " --> pdb=" O TYR h 304 " (cutoff:3.500A) Processing sheet with id=AZ2, first strand: chain 'h' and resid 81 through 84 removed outlier: 6.766A pdb=" N ARG h 316 " --> pdb=" O THR h 310 " (cutoff:3.500A) Processing sheet with id=AZ3, first strand: chain 'h' and resid 139 through 142 removed outlier: 3.517A pdb=" N TYR h 140 " --> pdb=" O VAL h 152 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL h 152 " --> pdb=" O TYR h 140 " (cutoff:3.500A) Processing sheet with id=AZ4, first strand: chain 'h' and resid 239 through 245 removed outlier: 5.634A pdb=" N TYR h 241 " --> pdb=" O VAL h 252 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL h 252 " --> pdb=" O TYR h 241 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY h 243 " --> pdb=" O ILE h 250 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE h 250 " --> pdb=" O GLY h 243 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL h 248 " --> pdb=" O TYR h 245 " (cutoff:3.500A) Processing sheet with id=AZ5, first strand: chain 'h' and resid 256 through 258 4766 hydrogen bonds defined for protein. 13410 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: 55.93 Time building geometry restraints manager: 36.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 21428 1.32 - 1.44: 33909 1.44 - 1.57: 70639 1.57 - 1.69: 2 1.69 - 1.82: 1230 Bond restraints: 127208 Sorted by residual: bond pdb=" CA ASN V 179 " pdb=" C ASN V 179 " ideal model delta sigma weight residual 1.524 1.451 0.073 1.26e-02 6.30e+03 3.38e+01 bond pdb=" CA GLU c 208 " pdb=" C GLU c 208 " ideal model delta sigma weight residual 1.522 1.457 0.066 1.19e-02 7.06e+03 3.04e+01 bond pdb=" CA ALA X 419 " pdb=" C ALA X 419 " ideal model delta sigma weight residual 1.524 1.456 0.068 1.24e-02 6.50e+03 3.00e+01 bond pdb=" CA LEU c 416 " pdb=" C LEU c 416 " ideal model delta sigma weight residual 1.523 1.453 0.071 1.30e-02 5.92e+03 2.96e+01 bond pdb=" CA SER V 178 " pdb=" C SER V 178 " ideal model delta sigma weight residual 1.528 1.460 0.069 1.38e-02 5.25e+03 2.49e+01 ... (remaining 127203 not shown) Histogram of bond angle deviations from ideal: 97.50 - 105.44: 2828 105.44 - 113.38: 67480 113.38 - 121.32: 68334 121.32 - 129.26: 32819 129.26 - 137.20: 645 Bond angle restraints: 172106 Sorted by residual: angle pdb=" N ARG T 91 " pdb=" CA ARG T 91 " pdb=" C ARG T 91 " ideal model delta sigma weight residual 109.54 122.69 -13.15 1.37e+00 5.33e-01 9.22e+01 angle pdb=" N ARG L 91 " pdb=" CA ARG L 91 " pdb=" C ARG L 91 " ideal model delta sigma weight residual 108.49 123.64 -15.15 1.65e+00 3.67e-01 8.43e+01 angle pdb=" N GLU 0 37 " pdb=" CA GLU 0 37 " pdb=" C GLU 0 37 " ideal model delta sigma weight residual 111.28 120.85 -9.57 1.09e+00 8.42e-01 7.71e+01 angle pdb=" N ASP T 95 " pdb=" CA ASP T 95 " pdb=" C ASP T 95 " ideal model delta sigma weight residual 113.17 124.12 -10.95 1.26e+00 6.30e-01 7.55e+01 angle pdb=" N LYS O 175 " pdb=" CA LYS O 175 " pdb=" C LYS O 175 " ideal model delta sigma weight residual 110.17 97.50 12.67 1.51e+00 4.39e-01 7.04e+01 ... (remaining 172101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 69239 18.11 - 36.21: 6318 36.21 - 54.32: 1021 54.32 - 72.43: 217 72.43 - 90.53: 113 Dihedral angle restraints: 76908 sinusoidal: 31068 harmonic: 45840 Sorted by residual: dihedral pdb=" CA LEU S 93 " pdb=" C LEU S 93 " pdb=" N PRO S 94 " pdb=" CA PRO S 94 " ideal model delta harmonic sigma weight residual 180.00 -151.16 -28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ARG R 91 " pdb=" C ARG R 91 " pdb=" N ARG R 92 " pdb=" CA ARG R 92 " ideal model delta harmonic sigma weight residual 180.00 153.50 26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA ARG S 91 " pdb=" C ARG S 91 " pdb=" N ARG S 92 " pdb=" CA ARG S 92 " ideal model delta harmonic sigma weight residual 180.00 154.28 25.72 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 76905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 17848 0.110 - 0.219: 530 0.219 - 0.329: 42 0.329 - 0.438: 17 0.438 - 0.548: 5 Chirality restraints: 18442 Sorted by residual: chirality pdb=" CA ASP A 313 " pdb=" N ASP A 313 " pdb=" C ASP A 313 " pdb=" CB ASP A 313 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" CA ASP h 182 " pdb=" N ASP h 182 " pdb=" C ASP h 182 " pdb=" CB ASP h 182 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" CA ALA C 315 " pdb=" N ALA C 315 " pdb=" C ALA C 315 " pdb=" CB ALA C 315 " both_signs ideal model delta sigma weight residual False 2.48 1.97 0.51 2.00e-01 2.50e+01 6.52e+00 ... (remaining 18439 not shown) Planarity restraints: 22762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR Q 89 " -0.022 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C THR Q 89 " 0.075 2.00e-02 2.50e+03 pdb=" O THR Q 89 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU Q 90 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA 7 324 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO 7 325 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO 7 325 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO 7 325 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO h 104 " 0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C PRO h 104 " -0.069 2.00e-02 2.50e+03 pdb=" O PRO h 104 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA h 105 " 0.024 2.00e-02 2.50e+03 ... (remaining 22759 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 10528 2.74 - 3.28: 121727 3.28 - 3.82: 190729 3.82 - 4.36: 219562 4.36 - 4.90: 396405 Nonbonded interactions: 938951 Sorted by model distance: nonbonded pdb=" OD2 ASP N 290 " pdb=" NE2 GLN N 322 " model vdw 2.196 2.520 nonbonded pdb=" OH TYR I 178 " pdb=" OD2 ASP I 183 " model vdw 2.198 2.440 nonbonded pdb=" OH TYR M 178 " pdb=" OD2 ASP M 183 " model vdw 2.200 2.440 nonbonded pdb=" OD2 ASP 3 290 " pdb=" NE2 GLN 3 322 " model vdw 2.211 2.520 nonbonded pdb=" OH TYR 0 77 " pdb=" O CYS 0 287 " model vdw 2.215 2.440 ... (remaining 938946 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 '0' and resid 5 through 341) selection = (chain '1' and resid 5 through 341) selection = (chain '2' and resid 5 through 341) selection = chain '3' selection = chain '4' selection = chain '5' selection = (chain '6' and resid 5 through 341) selection = (chain '7' and resid 5 through 341) selection = (chain 'A' and resid 5 through 341) selection = (chain 'B' and resid 5 through 341) selection = (chain 'C' and resid 5 through 341) selection = (chain 'D' and resid 5 through 341) selection = (chain 'E' and resid 5 through 341) selection = (chain 'F' and resid 5 through 341) selection = (chain 'G' and resid 5 through 341) selection = (chain 'H' and resid 5 through 341) selection = (chain 'I' and resid 5 through 341) selection = (chain 'J' and resid 5 through 341) selection = (chain 'K' and resid 5 through 341) selection = (chain 'L' and resid 5 through 341) selection = (chain 'M' and resid 5 through 341) selection = chain 'N' selection = (chain 'O' and resid 5 through 341) selection = (chain 'P' and resid 5 through 341) selection = (chain 'Q' and resid 5 through 341) selection = (chain 'R' and resid 5 through 341) selection = (chain 'S' and resid 5 through 341) selection = (chain 'T' and resid 5 through 341) selection = (chain 'g' and resid 5 through 341) selection = chain 'h' } ncs_group { reference = chain 'U' selection = (chain 'V' and (resid 24 through 212 or resid 217 through 513)) selection = (chain 'W' and (resid 24 through 212 or resid 217 through 513)) selection = (chain 'X' and (resid 24 through 212 or resid 217 through 513)) selection = (chain 'Y' and (resid 24 through 212 or resid 217 through 513)) selection = (chain 'Z' and (resid 24 through 212 or resid 217 through 513)) selection = (chain 'a' and (resid 24 through 212 or resid 217 through 301 or resid 320 throu \ gh 513)) selection = (chain 'b' and (resid 24 through 212 or resid 217 through 513)) selection = (chain 'c' and (resid 24 through 212 or resid 217 through 513)) selection = (chain 'd' and (resid 24 through 212 or resid 217 through 513)) selection = (chain 'e' and (resid 24 through 212 or resid 217 through 513)) selection = (chain 'f' and (resid 24 through 212 or resid 217 through 513)) } 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: 2.300 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: 0.070 Extract box with map and model: 18.210 Check model and map are aligned: 1.360 Set scattering table: 0.870 Process input model: 247.740 Find NCS groups from input model: 7.370 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 281.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.005 0.104 127208 Z= 0.307 Angle : 0.688 15.148 172106 Z= 0.392 Chirality : 0.048 0.548 18442 Planarity : 0.005 0.104 22762 Dihedral : 14.313 90.535 47500 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.69 % Favored : 94.03 % Rotamer: Outliers : 0.24 % Allowed : 0.63 % Favored : 99.13 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.06), residues: 15739 helix: 1.27 (0.08), residues: 4596 sheet: -0.51 (0.09), residues: 3041 loop : -1.64 (0.06), residues: 8102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP Y 442 HIS 0.009 0.001 HIS 6 82 PHE 0.036 0.002 PHE F 200 TYR 0.030 0.002 TYR 0 77 ARG 0.009 0.000 ARG e 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1885 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1853 time to evaluate : 10.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 323 SER cc_start: 0.9341 (t) cc_final: 0.9131 (t) REVERT: 2 100 ASN cc_start: 0.8116 (m110) cc_final: 0.7417 (t0) REVERT: 2 333 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7557 (p0) REVERT: 3 247 ASP cc_start: 0.7677 (m-30) cc_final: 0.7269 (m-30) REVERT: 6 129 MET cc_start: 0.7681 (tpt) cc_final: 0.7394 (tpt) REVERT: A 95 ASP cc_start: 0.7891 (p0) cc_final: 0.7654 (p0) REVERT: A 327 MET cc_start: 0.8559 (mmp) cc_final: 0.8252 (mmp) REVERT: B 20 ASP cc_start: 0.8865 (t0) cc_final: 0.8545 (t0) REVERT: B 216 GLU cc_start: 0.7811 (tp30) cc_final: 0.7556 (tp30) REVERT: C 95 ASP cc_start: 0.8132 (p0) cc_final: 0.7914 (p0) REVERT: C 331 ASP cc_start: 0.8455 (t0) cc_final: 0.7738 (t0) REVERT: E 247 ASP cc_start: 0.8076 (t0) cc_final: 0.7828 (t0) REVERT: F 277 THR cc_start: 0.8455 (t) cc_final: 0.8120 (m) REVERT: F 333 ASP cc_start: 0.7864 (p0) cc_final: 0.7597 (p0) REVERT: G 32 TYR cc_start: 0.8476 (m-80) cc_final: 0.8260 (m-80) REVERT: G 97 ASP cc_start: 0.8253 (p0) cc_final: 0.7958 (p0) REVERT: H 259 GLU cc_start: 0.8623 (pp20) cc_final: 0.8353 (pp20) REVERT: H 290 ASP cc_start: 0.7590 (t70) cc_final: 0.7350 (t0) REVERT: K 234 ASP cc_start: 0.8156 (m-30) cc_final: 0.7826 (m-30) REVERT: K 264 LYS cc_start: 0.8164 (mttt) cc_final: 0.7642 (mttp) REVERT: K 317 GLU cc_start: 0.9073 (pp20) cc_final: 0.8862 (pp20) REVERT: L 88 MET cc_start: 0.8093 (ptt) cc_final: 0.7755 (ptt) REVERT: L 93 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7515 (mt) REVERT: M 216 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7864 (tp30) REVERT: O 50 MET cc_start: 0.8162 (ttp) cc_final: 0.7833 (ttm) REVERT: O 128 GLU cc_start: 0.8092 (tp30) cc_final: 0.7381 (tp30) REVERT: O 182 ASP cc_start: 0.8124 (t0) cc_final: 0.7750 (t0) REVERT: O 296 GLU cc_start: 0.7288 (tm-30) cc_final: 0.7024 (tm-30) REVERT: P 4 TYR cc_start: 0.7261 (m-80) cc_final: 0.6968 (m-80) REVERT: P 139 LYS cc_start: 0.9123 (ptpp) cc_final: 0.8906 (ptpp) REVERT: P 197 ILE cc_start: 0.9251 (tt) cc_final: 0.8967 (tt) REVERT: Q 91 ARG cc_start: 0.7448 (ttp80) cc_final: 0.6391 (tpt170) REVERT: T 91 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.5597 (tpt170) REVERT: U 436 GLN cc_start: 0.7634 (pm20) cc_final: 0.7324 (pm20) REVERT: W 171 MET cc_start: 0.8912 (mmm) cc_final: 0.8648 (mmm) REVERT: W 182 ASN cc_start: 0.7893 (m110) cc_final: 0.7637 (m110) REVERT: W 397 MET cc_start: 0.8918 (mmm) cc_final: 0.8696 (mmm) REVERT: X 105 ARG cc_start: 0.7866 (mpt-90) cc_final: 0.7557 (mmt-90) REVERT: X 125 CYS cc_start: 0.7307 (m) cc_final: 0.6664 (m) REVERT: Y 120 GLU cc_start: 0.8100 (tp30) cc_final: 0.7493 (pp20) REVERT: Y 195 ILE cc_start: 0.9346 (mt) cc_final: 0.9114 (mt) REVERT: a 96 TYR cc_start: 0.7866 (t80) cc_final: 0.6035 (t80) REVERT: b 161 SER cc_start: 0.7969 (OUTLIER) cc_final: 0.7372 (m) REVERT: c 120 GLU cc_start: 0.7741 (mt-10) cc_final: 0.6759 (mp0) REVERT: c 165 PHE cc_start: 0.8461 (m-80) cc_final: 0.8203 (m-80) REVERT: c 206 VAL cc_start: 0.9465 (t) cc_final: 0.9233 (m) REVERT: c 498 MET cc_start: 0.6554 (tpt) cc_final: 0.5886 (tpp) REVERT: d 187 ARG cc_start: 0.6993 (mtp180) cc_final: 0.6728 (mtt180) REVERT: d 397 MET cc_start: 0.8036 (mmm) cc_final: 0.7021 (tpt) REVERT: d 453 MET cc_start: 0.7884 (mtp) cc_final: 0.7644 (mtp) REVERT: e 101 GLU cc_start: 0.6682 (tm-30) cc_final: 0.6273 (tm-30) REVERT: h 32 TYR cc_start: 0.7193 (m-10) cc_final: 0.6945 (m-10) REVERT: h 72 GLU cc_start: 0.8493 (pt0) cc_final: 0.7753 (pm20) outliers start: 32 outliers final: 15 residues processed: 1877 average time/residue: 0.9886 time to fit residues: 3264.6654 Evaluate side-chains 1508 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1489 time to evaluate : 10.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 2 residue 333 ASP Chi-restraints excluded: chain 7 residue 201 ASP Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain M residue 333 ASP Chi-restraints excluded: chain M residue 334 GLU Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 183 THR Chi-restraints excluded: chain b residue 156 THR Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain g residue 258 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1578 random chunks: chunk 1332 optimal weight: 8.9990 chunk 1196 optimal weight: 3.9990 chunk 663 optimal weight: 8.9990 chunk 408 optimal weight: 10.0000 chunk 806 optimal weight: 10.0000 chunk 638 optimal weight: 30.0000 chunk 1236 optimal weight: 0.0170 chunk 478 optimal weight: 7.9990 chunk 752 optimal weight: 10.0000 chunk 920 optimal weight: 9.9990 chunk 1433 optimal weight: 9.9990 overall best weight: 6.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 GLN 1 115 ASN 1 225 ASN ** 3 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 225 ASN 5 8 GLN ** 5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 99 GLN ** 5 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 43 GLN 6 130 GLN 7 130 GLN 7 164 GLN B 100 ASN C 82 HIS C 100 ASN D 100 ASN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN E 130 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN J 161 ASN ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 GLN L 115 ASN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 299 ASN O 82 HIS O 115 ASN O 161 ASN R 8 GLN ** R 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 299 ASN S 164 GLN T 130 GLN T 260 ASN U 39 ASN U 257 GLN U 332 HIS V 340 ASN W 148 ASN W 376 ASN X 72 ASN X 148 ASN X 265 GLN X 340 ASN ** X 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 376 ASN Z 265 GLN Z 436 GLN b 145 HIS ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 265 GLN b 299 ASN ** c 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 181 ASN d 265 GLN d 356 GLN ** e 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 379 GLN e 444 ASN ** f 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 376 ASN g 161 ASN ** h 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN ** h 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 127208 Z= 0.458 Angle : 0.700 9.905 172106 Z= 0.373 Chirality : 0.047 0.227 18442 Planarity : 0.006 0.069 22762 Dihedral : 5.267 59.187 17540 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.47 % Favored : 93.34 % Rotamer: Outliers : 1.69 % Allowed : 9.94 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.06), residues: 15739 helix: 1.19 (0.08), residues: 4717 sheet: -0.61 (0.09), residues: 2901 loop : -1.85 (0.06), residues: 8121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP X 221 HIS 0.010 0.002 HIS Z 235 PHE 0.034 0.002 PHE b 147 TYR 0.031 0.002 TYR E 40 ARG 0.006 0.001 ARG 7 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1746 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1523 time to evaluate : 10.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 50 MET cc_start: 0.9018 (ttp) cc_final: 0.8597 (ttt) REVERT: 0 337 SER cc_start: 0.9229 (m) cc_final: 0.9012 (p) REVERT: 2 100 ASN cc_start: 0.8168 (m110) cc_final: 0.7480 (t0) REVERT: 3 119 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: 3 334 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7916 (mt-10) REVERT: 4 32 TYR cc_start: 0.7143 (m-10) cc_final: 0.6610 (m-80) REVERT: 6 61 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7796 (tm-30) REVERT: 6 129 MET cc_start: 0.8024 (tpt) cc_final: 0.7436 (tpt) REVERT: A 95 ASP cc_start: 0.8025 (p0) cc_final: 0.7772 (p0) REVERT: B 20 ASP cc_start: 0.8806 (t0) cc_final: 0.8529 (t0) REVERT: B 100 ASN cc_start: 0.7489 (OUTLIER) cc_final: 0.6946 (m-40) REVERT: B 216 GLU cc_start: 0.7904 (tp30) cc_final: 0.7584 (tp30) REVERT: B 327 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.9049 (mmm) REVERT: C 331 ASP cc_start: 0.8366 (t0) cc_final: 0.7769 (t0) REVERT: D 100 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8296 (p0) REVERT: D 212 LYS cc_start: 0.8358 (tptp) cc_final: 0.8120 (tptp) REVERT: F 128 GLU cc_start: 0.8476 (tp30) cc_final: 0.8216 (tm-30) REVERT: F 129 MET cc_start: 0.8650 (tpp) cc_final: 0.8166 (tpt) REVERT: F 333 ASP cc_start: 0.7981 (p0) cc_final: 0.7645 (p0) REVERT: G 97 ASP cc_start: 0.8197 (p0) cc_final: 0.7978 (p0) REVERT: H 290 ASP cc_start: 0.7653 (t70) cc_final: 0.7227 (t0) REVERT: I 119 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: J 278 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7191 (tt0) REVERT: K 234 ASP cc_start: 0.8236 (m-30) cc_final: 0.7738 (m-30) REVERT: L 88 MET cc_start: 0.8156 (ptt) cc_final: 0.7808 (ptt) REVERT: L 90 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8425 (tt) REVERT: L 92 ARG cc_start: 0.8088 (mmm160) cc_final: 0.3984 (ptt90) REVERT: L 318 PHE cc_start: 0.8668 (m-80) cc_final: 0.8410 (m-10) REVERT: O 182 ASP cc_start: 0.7770 (t0) cc_final: 0.7482 (t0) REVERT: P 4 TYR cc_start: 0.7317 (m-80) cc_final: 0.7062 (m-80) REVERT: P 139 LYS cc_start: 0.9040 (ptpp) cc_final: 0.8822 (ptpp) REVERT: P 285 TYR cc_start: 0.8858 (m-80) cc_final: 0.8436 (m-80) REVERT: P 303 ARG cc_start: 0.7585 (mmt90) cc_final: 0.7182 (mtt90) REVERT: Q 4 TYR cc_start: 0.8074 (m-80) cc_final: 0.7628 (m-80) REVERT: Q 91 ARG cc_start: 0.7350 (ttp80) cc_final: 0.5976 (tpt170) REVERT: R 212 LYS cc_start: 0.8865 (tttt) cc_final: 0.8589 (tttt) REVERT: S 226 SER cc_start: 0.9057 (m) cc_final: 0.8672 (p) REVERT: T 91 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8382 (ttp-110) REVERT: T 316 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7927 (mtm-85) REVERT: U 258 MET cc_start: 0.8736 (mtp) cc_final: 0.8504 (mtm) REVERT: W 195 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8569 (tt) REVERT: X 125 CYS cc_start: 0.7253 (m) cc_final: 0.6670 (m) REVERT: X 179 ASN cc_start: 0.9311 (m-40) cc_final: 0.8813 (m-40) REVERT: Y 120 GLU cc_start: 0.8012 (tp30) cc_final: 0.7476 (pp20) REVERT: Y 195 ILE cc_start: 0.9408 (mt) cc_final: 0.9188 (mt) REVERT: Y 397 MET cc_start: 0.7898 (mmm) cc_final: 0.7609 (mmp) REVERT: Z 66 ASN cc_start: 0.8621 (m110) cc_final: 0.8407 (m110) REVERT: Z 127 ASP cc_start: 0.8332 (p0) cc_final: 0.8129 (p0) REVERT: Z 215 MET cc_start: 0.6989 (ttm) cc_final: 0.6497 (ttt) REVERT: a 96 TYR cc_start: 0.8039 (t80) cc_final: 0.6480 (t80) REVERT: b 168 GLN cc_start: 0.8479 (mt0) cc_final: 0.8198 (mt0) REVERT: c 211 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8051 (t80) REVERT: c 498 MET cc_start: 0.6359 (tpt) cc_final: 0.5806 (tpp) REVERT: e 125 CYS cc_start: 0.8477 (m) cc_final: 0.7973 (m) REVERT: e 144 MET cc_start: 0.8116 (tpp) cc_final: 0.7753 (tpp) REVERT: h 32 TYR cc_start: 0.7180 (m-10) cc_final: 0.6812 (m-10) REVERT: h 72 GLU cc_start: 0.8432 (pt0) cc_final: 0.7612 (pm20) outliers start: 223 outliers final: 175 residues processed: 1671 average time/residue: 0.9886 time to fit residues: 2899.0124 Evaluate side-chains 1595 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1410 time to evaluate : 10.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 90 LEU Chi-restraints excluded: chain 0 residue 185 GLU Chi-restraints excluded: chain 0 residue 251 VAL Chi-restraints excluded: chain 1 residue 16 LYS Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 201 ASP Chi-restraints excluded: chain 1 residue 251 VAL Chi-restraints excluded: chain 1 residue 301 SER Chi-restraints excluded: chain 1 residue 320 MET Chi-restraints excluded: chain 1 residue 323 SER Chi-restraints excluded: chain 2 residue 48 VAL Chi-restraints excluded: chain 2 residue 201 ASP Chi-restraints excluded: chain 2 residue 311 THR Chi-restraints excluded: chain 3 residue 16 LYS Chi-restraints excluded: chain 3 residue 119 GLU Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 3 residue 194 VAL Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 262 VAL Chi-restraints excluded: chain 3 residue 323 SER Chi-restraints excluded: chain 4 residue 323 SER Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 35 THR Chi-restraints excluded: chain 5 residue 36 THR Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 116 MET Chi-restraints excluded: chain 5 residue 161 ASN Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 282 LEU Chi-restraints excluded: chain 6 residue 290 ASP Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain 7 residue 48 VAL Chi-restraints excluded: chain 7 residue 201 ASP Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 310 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 130 GLN Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 161 ASN Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain M residue 36 THR Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 321 ILE Chi-restraints excluded: chain M residue 334 GLU Chi-restraints excluded: chain M residue 338 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 182 ASP Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 287 CYS Chi-restraints excluded: chain N residue 298 ILE Chi-restraints excluded: chain N residue 323 SER Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 119 GLU Chi-restraints excluded: chain Q residue 287 CYS Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 260 ASN Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain T residue 113 MET Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 174 ASP Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain T residue 232 VAL Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain T residue 316 ARG Chi-restraints excluded: chain U residue 126 ILE Chi-restraints excluded: chain U residue 127 ASP Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 300 SER Chi-restraints excluded: chain U residue 425 VAL Chi-restraints excluded: chain V residue 99 ILE Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 183 THR Chi-restraints excluded: chain V residue 274 VAL Chi-restraints excluded: chain V residue 288 THR Chi-restraints excluded: chain V residue 374 SER Chi-restraints excluded: chain W residue 64 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 195 ILE Chi-restraints excluded: chain W residue 445 CYS Chi-restraints excluded: chain X residue 290 SER Chi-restraints excluded: chain X residue 292 MET Chi-restraints excluded: chain X residue 359 LEU Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Z residue 45 VAL Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 99 ILE Chi-restraints excluded: chain Z residue 123 CYS Chi-restraints excluded: chain Z residue 186 SER Chi-restraints excluded: chain Z residue 220 THR Chi-restraints excluded: chain Z residue 338 SER Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 159 THR Chi-restraints excluded: chain a residue 274 VAL Chi-restraints excluded: chain b residue 43 GLU Chi-restraints excluded: chain b residue 52 ASN Chi-restraints excluded: chain b residue 61 ASP Chi-restraints excluded: chain b residue 156 THR Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 347 THR Chi-restraints excluded: chain c residue 34 GLN Chi-restraints excluded: chain c residue 160 SER Chi-restraints excluded: chain c residue 211 TYR Chi-restraints excluded: chain c residue 220 THR Chi-restraints excluded: chain c residue 453 MET Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 256 GLU Chi-restraints excluded: chain d residue 474 THR Chi-restraints excluded: chain d residue 481 LYS Chi-restraints excluded: chain e residue 137 MET Chi-restraints excluded: chain e residue 271 SER Chi-restraints excluded: chain e residue 340 ASN Chi-restraints excluded: chain e residue 426 THR Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 240 VAL Chi-restraints excluded: chain f residue 368 VAL Chi-restraints excluded: chain f residue 498 MET Chi-restraints excluded: chain g residue 177 THR Chi-restraints excluded: chain g residue 258 VAL Chi-restraints excluded: chain g residue 290 ASP Chi-restraints excluded: chain g residue 313 ASP Chi-restraints excluded: chain g residue 340 LEU Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain h residue 333 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1578 random chunks: chunk 796 optimal weight: 1.9990 chunk 444 optimal weight: 9.9990 chunk 1192 optimal weight: 0.9980 chunk 975 optimal weight: 8.9990 chunk 395 optimal weight: 10.0000 chunk 1435 optimal weight: 5.9990 chunk 1550 optimal weight: 2.9990 chunk 1278 optimal weight: 3.9990 chunk 1423 optimal weight: 0.1980 chunk 489 optimal weight: 9.9990 chunk 1151 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 GLN 0 196 ASN 0 276 ASN 1 225 ASN ** 3 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 13 ASN ** 5 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 260 ASN ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 GLN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 130 GLN ** U 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 72 ASN ** X 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 ASN b 299 ASN b 372 GLN ** c 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 181 ASN ** e 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 257 GLN e 379 GLN ** f 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 376 ASN ** h 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN ** h 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 127208 Z= 0.202 Angle : 0.546 10.309 172106 Z= 0.289 Chirality : 0.042 0.199 18442 Planarity : 0.004 0.061 22762 Dihedral : 4.789 59.043 17533 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 2.01 % Allowed : 13.10 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.06), residues: 15739 helix: 1.50 (0.08), residues: 4852 sheet: -0.51 (0.09), residues: 3041 loop : -1.82 (0.06), residues: 7846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP d 94 HIS 0.005 0.001 HIS 7 82 PHE 0.037 0.001 PHE h 34 TYR 0.019 0.001 TYR W 361 ARG 0.006 0.000 ARG R 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1879 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1613 time to evaluate : 10.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 50 MET cc_start: 0.8866 (ttp) cc_final: 0.8427 (ttt) REVERT: 0 282 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8732 (pp) REVERT: 1 119 GLU cc_start: 0.8229 (mt-10) cc_final: 0.8013 (mt-10) REVERT: 2 100 ASN cc_start: 0.8137 (m110) cc_final: 0.7500 (t0) REVERT: 2 189 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8233 (tp) REVERT: 2 333 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7023 (p0) REVERT: 3 119 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: 3 219 ASP cc_start: 0.8293 (p0) cc_final: 0.8035 (p0) REVERT: 3 334 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7949 (mt-10) REVERT: 4 219 ASP cc_start: 0.7165 (t0) cc_final: 0.6841 (t0) REVERT: 5 313 ASP cc_start: 0.4196 (OUTLIER) cc_final: 0.3892 (p0) REVERT: 6 129 MET cc_start: 0.7922 (tpt) cc_final: 0.7364 (tpt) REVERT: 6 269 ASP cc_start: 0.6309 (p0) cc_final: 0.6094 (p0) REVERT: 7 151 GLU cc_start: 0.8326 (pm20) cc_final: 0.8041 (tt0) REVERT: A 95 ASP cc_start: 0.8042 (p0) cc_final: 0.7789 (p0) REVERT: B 103 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8017 (p0) REVERT: B 128 GLU cc_start: 0.8561 (tp30) cc_final: 0.8082 (tp30) REVERT: B 216 GLU cc_start: 0.7807 (tp30) cc_final: 0.7541 (tp30) REVERT: B 327 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8939 (mmm) REVERT: C 119 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: C 331 ASP cc_start: 0.8346 (t0) cc_final: 0.7656 (t0) REVERT: D 212 LYS cc_start: 0.8241 (tptp) cc_final: 0.7999 (tptp) REVERT: E 50 MET cc_start: 0.8898 (ttp) cc_final: 0.8542 (ttp) REVERT: E 116 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7120 (pmm) REVERT: E 247 ASP cc_start: 0.8083 (t0) cc_final: 0.7773 (t0) REVERT: E 258 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8239 (p) REVERT: E 295 ARG cc_start: 0.5486 (mmp-170) cc_final: 0.4769 (mmm160) REVERT: F 129 MET cc_start: 0.8521 (tpp) cc_final: 0.8262 (tpt) REVERT: F 185 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6024 (mt-10) REVERT: G 97 ASP cc_start: 0.8114 (p0) cc_final: 0.7897 (p0) REVERT: G 327 MET cc_start: 0.8623 (mmm) cc_final: 0.8394 (mmm) REVERT: H 127 GLU cc_start: 0.6019 (tp30) cc_final: 0.5709 (tp30) REVERT: H 290 ASP cc_start: 0.7603 (t70) cc_final: 0.6937 (t0) REVERT: I 50 MET cc_start: 0.7595 (mmm) cc_final: 0.6697 (tpt) REVERT: I 119 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6845 (pm20) REVERT: I 334 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7908 (tp30) REVERT: J 278 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7205 (tt0) REVERT: K 264 LYS cc_start: 0.8168 (mttt) cc_final: 0.7849 (mttp) REVERT: L 88 MET cc_start: 0.8029 (ptt) cc_final: 0.7792 (ptt) REVERT: L 90 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8481 (tt) REVERT: L 92 ARG cc_start: 0.7924 (mmm160) cc_final: 0.3879 (ptt90) REVERT: M 37 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7101 (tm-30) REVERT: M 38 LYS cc_start: 0.8512 (mttm) cc_final: 0.7824 (mttm) REVERT: M 119 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: O 182 ASP cc_start: 0.7757 (t0) cc_final: 0.7492 (t0) REVERT: O 320 MET cc_start: 0.7510 (ttt) cc_final: 0.7180 (ttm) REVERT: Q 4 TYR cc_start: 0.8037 (m-80) cc_final: 0.7673 (m-80) REVERT: Q 91 ARG cc_start: 0.7103 (ttp80) cc_final: 0.6088 (tpt170) REVERT: Q 296 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: R 285 TYR cc_start: 0.8729 (m-80) cc_final: 0.8334 (m-80) REVERT: S 272 MET cc_start: 0.9002 (ptp) cc_final: 0.8783 (ttp) REVERT: T 32 TYR cc_start: 0.7640 (m-10) cc_final: 0.7395 (m-10) REVERT: T 316 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7905 (mtm-85) REVERT: U 258 MET cc_start: 0.8710 (mtp) cc_final: 0.8408 (mtm) REVERT: V 418 GLU cc_start: 0.8258 (tp30) cc_final: 0.8043 (tp30) REVERT: W 411 MET cc_start: 0.8235 (mtp) cc_final: 0.7811 (mtp) REVERT: X 125 CYS cc_start: 0.7208 (m) cc_final: 0.6610 (m) REVERT: X 179 ASN cc_start: 0.9267 (m-40) cc_final: 0.8944 (m-40) REVERT: Y 120 GLU cc_start: 0.7938 (tp30) cc_final: 0.7427 (pp20) REVERT: Y 195 ILE cc_start: 0.9360 (mt) cc_final: 0.9135 (mt) REVERT: Y 397 MET cc_start: 0.7680 (mmm) cc_final: 0.7031 (mmp) REVERT: Z 66 ASN cc_start: 0.8535 (m110) cc_final: 0.8325 (m110) REVERT: Z 127 ASP cc_start: 0.8227 (p0) cc_final: 0.8009 (p0) REVERT: Z 157 TRP cc_start: 0.7902 (m-10) cc_final: 0.7630 (m-10) REVERT: Z 215 MET cc_start: 0.7108 (ttm) cc_final: 0.6659 (ttt) REVERT: Z 461 VAL cc_start: 0.9030 (t) cc_final: 0.8672 (m) REVERT: Z 463 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7711 (tp30) REVERT: a 380 MET cc_start: 0.7779 (ptt) cc_final: 0.7417 (ptp) REVERT: b 168 GLN cc_start: 0.8417 (mt0) cc_final: 0.8132 (mt0) REVERT: b 348 ASP cc_start: 0.8319 (t0) cc_final: 0.7691 (p0) REVERT: c 197 ASP cc_start: 0.7127 (p0) cc_final: 0.6865 (p0) REVERT: c 211 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7777 (t80) REVERT: c 238 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7548 (tm-30) REVERT: d 397 MET cc_start: 0.7959 (mmm) cc_final: 0.6979 (tpt) REVERT: d 439 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7762 (mtt-85) REVERT: e 101 GLU cc_start: 0.6735 (tm-30) cc_final: 0.6452 (tm-30) REVERT: f 150 GLU cc_start: 0.8444 (mp0) cc_final: 0.8199 (mp0) REVERT: f 273 ILE cc_start: 0.8908 (mt) cc_final: 0.8696 (mp) REVERT: f 282 ILE cc_start: 0.9322 (mm) cc_final: 0.9087 (tt) REVERT: g 77 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: g 109 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7610 (ttm-80) REVERT: g 292 ASP cc_start: 0.6743 (t0) cc_final: 0.6383 (t0) REVERT: h 32 TYR cc_start: 0.7109 (m-10) cc_final: 0.6680 (m-10) REVERT: h 72 GLU cc_start: 0.8386 (pt0) cc_final: 0.7686 (pm20) outliers start: 266 outliers final: 168 residues processed: 1784 average time/residue: 0.9727 time to fit residues: 3056.6105 Evaluate side-chains 1663 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1477 time to evaluate : 10.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 77 TYR Chi-restraints excluded: chain 0 residue 185 GLU Chi-restraints excluded: chain 0 residue 262 VAL Chi-restraints excluded: chain 0 residue 282 LEU Chi-restraints excluded: chain 0 residue 323 SER Chi-restraints excluded: chain 1 residue 16 LYS Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 158 GLU Chi-restraints excluded: chain 1 residue 168 THR Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 251 VAL Chi-restraints excluded: chain 1 residue 320 MET Chi-restraints excluded: chain 2 residue 48 VAL Chi-restraints excluded: chain 2 residue 189 LEU Chi-restraints excluded: chain 2 residue 319 THR Chi-restraints excluded: chain 2 residue 333 ASP Chi-restraints excluded: chain 3 residue 16 LYS Chi-restraints excluded: chain 3 residue 74 THR Chi-restraints excluded: chain 3 residue 95 ASP Chi-restraints excluded: chain 3 residue 119 GLU Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 3 residue 194 VAL Chi-restraints excluded: chain 3 residue 323 SER Chi-restraints excluded: chain 4 residue 258 VAL Chi-restraints excluded: chain 5 residue 13 ASN Chi-restraints excluded: chain 5 residue 35 THR Chi-restraints excluded: chain 5 residue 36 THR Chi-restraints excluded: chain 5 residue 42 SER Chi-restraints excluded: chain 5 residue 48 VAL Chi-restraints excluded: chain 5 residue 49 ASN Chi-restraints excluded: chain 5 residue 74 THR Chi-restraints excluded: chain 5 residue 116 MET Chi-restraints excluded: chain 5 residue 150 VAL Chi-restraints excluded: chain 5 residue 161 ASN Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 313 ASP Chi-restraints excluded: chain 6 residue 282 LEU Chi-restraints excluded: chain 6 residue 290 ASP Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain 7 residue 139 LYS Chi-restraints excluded: chain 7 residue 201 ASP Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 327 MET Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 334 GLU Chi-restraints excluded: chain M residue 338 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 182 ASP Chi-restraints excluded: chain N residue 287 CYS Chi-restraints excluded: chain N residue 298 ILE Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 287 CYS Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain Q residue 296 GLU Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 260 ASN Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 174 ASP Chi-restraints excluded: chain T residue 232 VAL Chi-restraints excluded: chain T residue 260 ASN Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain T residue 316 ARG Chi-restraints excluded: chain U residue 126 ILE Chi-restraints excluded: chain U residue 334 MET Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 99 ILE Chi-restraints excluded: chain V residue 183 THR Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 374 SER Chi-restraints excluded: chain W residue 64 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain X residue 359 LEU Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 144 MET Chi-restraints excluded: chain Y residue 287 ASP Chi-restraints excluded: chain Y residue 474 THR Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 99 ILE Chi-restraints excluded: chain Z residue 186 SER Chi-restraints excluded: chain Z residue 220 THR Chi-restraints excluded: chain b residue 43 GLU Chi-restraints excluded: chain b residue 52 ASN Chi-restraints excluded: chain b residue 61 ASP Chi-restraints excluded: chain b residue 156 THR Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain c residue 34 GLN Chi-restraints excluded: chain c residue 160 SER Chi-restraints excluded: chain c residue 211 TYR Chi-restraints excluded: chain c residue 220 THR Chi-restraints excluded: chain c residue 287 ASP Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 256 GLU Chi-restraints excluded: chain d residue 258 MET Chi-restraints excluded: chain d residue 287 ASP Chi-restraints excluded: chain d residue 474 THR Chi-restraints excluded: chain d residue 481 LYS Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 287 ASP Chi-restraints excluded: chain f residue 338 SER Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 48 VAL Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 77 TYR Chi-restraints excluded: chain g residue 119 GLU Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 319 THR Chi-restraints excluded: chain g residue 340 LEU Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 74 THR Chi-restraints excluded: chain h residue 113 MET Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain h residue 333 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1578 random chunks: chunk 1418 optimal weight: 0.0070 chunk 1079 optimal weight: 0.0040 chunk 745 optimal weight: 6.9990 chunk 158 optimal weight: 0.3980 chunk 685 optimal weight: 7.9990 chunk 963 optimal weight: 4.9990 chunk 1440 optimal weight: 6.9990 chunk 1525 optimal weight: 4.9990 chunk 752 optimal weight: 9.9990 chunk 1365 optimal weight: 5.9990 chunk 411 optimal weight: 20.0000 overall best weight: 2.0814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 GLN 1 115 ASN 1 225 ASN ** 3 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 GLN M 164 GLN N 15 GLN ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 ASN ** O 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 72 ASN ** X 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 ASN ** Y 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 299 ASN ** c 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 181 ASN e 57 ASN e 148 ASN e 244 GLN e 257 GLN e 379 GLN ** f 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 376 ASN ** h 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN ** h 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 127208 Z= 0.201 Angle : 0.532 11.276 172106 Z= 0.280 Chirality : 0.042 0.197 18442 Planarity : 0.004 0.059 22762 Dihedral : 4.595 59.300 17524 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.34 % Favored : 94.49 % Rotamer: Outliers : 2.53 % Allowed : 14.60 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.07), residues: 15739 helix: 1.64 (0.08), residues: 4836 sheet: -0.47 (0.09), residues: 3041 loop : -1.74 (0.06), residues: 7862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP d 94 HIS 0.004 0.001 HIS 7 82 PHE 0.025 0.001 PHE c 147 TYR 0.034 0.001 TYR M 187 ARG 0.007 0.000 ARG g 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1886 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 1552 time to evaluate : 10.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 50 MET cc_start: 0.8836 (ttp) cc_final: 0.8403 (ttt) REVERT: 0 282 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8712 (pp) REVERT: 1 119 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7916 (mt-10) REVERT: 1 331 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7202 (m-30) REVERT: 2 41 LEU cc_start: 0.9177 (mt) cc_final: 0.8682 (mt) REVERT: 2 100 ASN cc_start: 0.7872 (m110) cc_final: 0.7238 (t0) REVERT: 3 116 MET cc_start: 0.6715 (mtp) cc_final: 0.6431 (mtm) REVERT: 3 119 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: 3 219 ASP cc_start: 0.8279 (p0) cc_final: 0.7953 (p0) REVERT: 3 334 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8028 (mt-10) REVERT: 4 219 ASP cc_start: 0.7144 (t0) cc_final: 0.6817 (t0) REVERT: 5 43 GLN cc_start: 0.7646 (pt0) cc_final: 0.7375 (mt0) REVERT: 5 313 ASP cc_start: 0.4185 (OUTLIER) cc_final: 0.3769 (p0) REVERT: 6 113 MET cc_start: 0.7559 (mmp) cc_final: 0.7170 (mmm) REVERT: 6 129 MET cc_start: 0.7861 (tpt) cc_final: 0.7327 (tpt) REVERT: 6 265 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7612 (p0) REVERT: 6 269 ASP cc_start: 0.6319 (p0) cc_final: 0.6058 (p0) REVERT: 7 3 MET cc_start: 0.7371 (tpp) cc_final: 0.7066 (mmm) REVERT: 7 232 VAL cc_start: 0.7047 (OUTLIER) cc_final: 0.6810 (p) REVERT: A 95 ASP cc_start: 0.7983 (p0) cc_final: 0.7756 (p0) REVERT: B 103 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7904 (p0) REVERT: B 128 GLU cc_start: 0.8639 (tp30) cc_final: 0.8008 (tp30) REVERT: B 216 GLU cc_start: 0.7808 (tp30) cc_final: 0.7503 (tp30) REVERT: C 119 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8222 (pm20) REVERT: C 331 ASP cc_start: 0.8336 (t0) cc_final: 0.7976 (t70) REVERT: D 114 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: D 212 LYS cc_start: 0.8228 (tptp) cc_final: 0.7979 (tptp) REVERT: E 50 MET cc_start: 0.8839 (ttp) cc_final: 0.8507 (ttp) REVERT: E 116 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6978 (pmm) REVERT: E 247 ASP cc_start: 0.8086 (t0) cc_final: 0.7780 (t0) REVERT: E 258 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8268 (p) REVERT: E 295 ARG cc_start: 0.5438 (mmp-170) cc_final: 0.4783 (mmm160) REVERT: F 129 MET cc_start: 0.8571 (tpp) cc_final: 0.8264 (tpt) REVERT: F 185 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.5981 (mt-10) REVERT: F 258 VAL cc_start: 0.8033 (OUTLIER) cc_final: 0.7745 (m) REVERT: G 97 ASP cc_start: 0.8076 (p0) cc_final: 0.7829 (p0) REVERT: H 127 GLU cc_start: 0.6222 (tp30) cc_final: 0.5906 (tp30) REVERT: H 259 GLU cc_start: 0.8767 (pp20) cc_final: 0.8461 (pt0) REVERT: H 290 ASP cc_start: 0.7548 (t70) cc_final: 0.7104 (t0) REVERT: I 52 LEU cc_start: 0.7988 (tt) cc_final: 0.7768 (tt) REVERT: I 73 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7361 (p90) REVERT: I 119 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6789 (pm20) REVERT: I 334 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7945 (tp30) REVERT: J 278 GLN cc_start: 0.7501 (mm-40) cc_final: 0.7206 (tt0) REVERT: K 264 LYS cc_start: 0.8163 (mttt) cc_final: 0.7600 (mtpt) REVERT: L 32 TYR cc_start: 0.7705 (m-80) cc_final: 0.7500 (m-80) REVERT: L 88 MET cc_start: 0.8023 (ptt) cc_final: 0.7817 (ptt) REVERT: L 90 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8634 (tt) REVERT: L 92 ARG cc_start: 0.7856 (mmm160) cc_final: 0.3795 (ptt90) REVERT: M 37 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7349 (tm-30) REVERT: M 38 LYS cc_start: 0.8481 (mttm) cc_final: 0.7881 (mttm) REVERT: M 100 ASN cc_start: 0.8641 (t0) cc_final: 0.8439 (t0) REVERT: M 113 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.6810 (mpp) REVERT: M 119 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: O 182 ASP cc_start: 0.7713 (t0) cc_final: 0.7476 (t0) REVERT: O 320 MET cc_start: 0.7547 (ttt) cc_final: 0.7209 (ttm) REVERT: Q 4 TYR cc_start: 0.7772 (m-80) cc_final: 0.7504 (m-80) REVERT: Q 89 THR cc_start: 0.7256 (OUTLIER) cc_final: 0.6843 (t) REVERT: Q 91 ARG cc_start: 0.7088 (ttp80) cc_final: 0.5673 (tpt170) REVERT: Q 296 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: R 285 TYR cc_start: 0.8690 (m-80) cc_final: 0.8374 (m-80) REVERT: T 32 TYR cc_start: 0.7652 (m-10) cc_final: 0.7387 (m-10) REVERT: T 316 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7893 (mtm-85) REVERT: U 258 MET cc_start: 0.8688 (mtp) cc_final: 0.8394 (mtm) REVERT: V 418 GLU cc_start: 0.8279 (tp30) cc_final: 0.8016 (tp30) REVERT: W 411 MET cc_start: 0.8245 (mtp) cc_final: 0.7834 (mtp) REVERT: X 125 CYS cc_start: 0.7237 (m) cc_final: 0.6597 (m) REVERT: X 179 ASN cc_start: 0.9218 (m-40) cc_final: 0.8937 (m-40) REVERT: Y 120 GLU cc_start: 0.7939 (tp30) cc_final: 0.7421 (pp20) REVERT: Y 123 CYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7579 (p) REVERT: Y 195 ILE cc_start: 0.9354 (mt) cc_final: 0.9137 (mt) REVERT: Z 66 ASN cc_start: 0.8559 (m110) cc_final: 0.8328 (m110) REVERT: Z 157 TRP cc_start: 0.7901 (m-10) cc_final: 0.7615 (m-10) REVERT: Z 215 MET cc_start: 0.7096 (ttm) cc_final: 0.6617 (ttt) REVERT: Z 461 VAL cc_start: 0.9023 (t) cc_final: 0.8664 (m) REVERT: a 380 MET cc_start: 0.7797 (ptt) cc_final: 0.7432 (ptp) REVERT: a 463 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7939 (tm-30) REVERT: b 127 ASP cc_start: 0.7790 (p0) cc_final: 0.7539 (p0) REVERT: b 168 GLN cc_start: 0.8405 (mt0) cc_final: 0.8151 (mt0) REVERT: b 348 ASP cc_start: 0.8329 (t0) cc_final: 0.7719 (p0) REVERT: c 197 ASP cc_start: 0.7137 (p0) cc_final: 0.6880 (p0) REVERT: c 211 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7809 (t80) REVERT: c 238 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7511 (tm-30) REVERT: c 493 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8322 (mm-40) REVERT: d 397 MET cc_start: 0.7953 (mmm) cc_final: 0.6954 (tpt) REVERT: d 439 ARG cc_start: 0.7979 (mtt90) cc_final: 0.7752 (mtt-85) REVERT: d 462 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7717 (mt0) REVERT: e 101 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6434 (tm-30) REVERT: g 77 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7134 (m-80) REVERT: g 88 MET cc_start: 0.9279 (mtp) cc_final: 0.8958 (mtt) REVERT: h 32 TYR cc_start: 0.7167 (m-10) cc_final: 0.6757 (m-10) REVERT: h 72 GLU cc_start: 0.8276 (pt0) cc_final: 0.7588 (pm20) REVERT: h 282 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7930 (mm) outliers start: 334 outliers final: 230 residues processed: 1782 average time/residue: 1.0341 time to fit residues: 3262.5507 Evaluate side-chains 1726 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1469 time to evaluate : 10.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 77 TYR Chi-restraints excluded: chain 0 residue 185 GLU Chi-restraints excluded: chain 0 residue 251 VAL Chi-restraints excluded: chain 0 residue 262 VAL Chi-restraints excluded: chain 0 residue 282 LEU Chi-restraints excluded: chain 0 residue 323 SER Chi-restraints excluded: chain 0 residue 338 VAL Chi-restraints excluded: chain 1 residue 16 LYS Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 158 GLU Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 251 VAL Chi-restraints excluded: chain 1 residue 301 SER Chi-restraints excluded: chain 1 residue 320 MET Chi-restraints excluded: chain 1 residue 323 SER Chi-restraints excluded: chain 1 residue 331 ASP Chi-restraints excluded: chain 2 residue 48 VAL Chi-restraints excluded: chain 2 residue 63 ILE Chi-restraints excluded: chain 2 residue 294 GLN Chi-restraints excluded: chain 2 residue 319 THR Chi-restraints excluded: chain 2 residue 337 SER Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 16 LYS Chi-restraints excluded: chain 3 residue 62 VAL Chi-restraints excluded: chain 3 residue 74 THR Chi-restraints excluded: chain 3 residue 95 ASP Chi-restraints excluded: chain 3 residue 119 GLU Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 3 residue 194 VAL Chi-restraints excluded: chain 3 residue 323 SER Chi-restraints excluded: chain 4 residue 36 THR Chi-restraints excluded: chain 4 residue 84 VAL Chi-restraints excluded: chain 4 residue 258 VAL Chi-restraints excluded: chain 5 residue 35 THR Chi-restraints excluded: chain 5 residue 36 THR Chi-restraints excluded: chain 5 residue 48 VAL Chi-restraints excluded: chain 5 residue 49 ASN Chi-restraints excluded: chain 5 residue 52 LEU Chi-restraints excluded: chain 5 residue 74 THR Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 116 MET Chi-restraints excluded: chain 5 residue 150 VAL Chi-restraints excluded: chain 5 residue 161 ASN Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 313 ASP Chi-restraints excluded: chain 6 residue 154 MET Chi-restraints excluded: chain 6 residue 201 ASP Chi-restraints excluded: chain 6 residue 265 ASN Chi-restraints excluded: chain 6 residue 290 ASP Chi-restraints excluded: chain 6 residue 319 THR Chi-restraints excluded: chain 6 residue 338 VAL Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain 7 residue 48 VAL Chi-restraints excluded: chain 7 residue 101 LEU Chi-restraints excluded: chain 7 residue 139 LYS Chi-restraints excluded: chain 7 residue 201 ASP Chi-restraints excluded: chain 7 residue 232 VAL Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 310 THR Chi-restraints excluded: chain 7 residue 327 MET Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 148 ASP Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 334 GLU Chi-restraints excluded: chain M residue 338 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 182 ASP Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 287 CYS Chi-restraints excluded: chain N residue 298 ILE Chi-restraints excluded: chain N residue 323 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 232 VAL Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 287 CYS Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain Q residue 296 GLU Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 234 ASP Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 260 ASN Chi-restraints excluded: chain S residue 272 MET Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 95 ASP Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 174 ASP Chi-restraints excluded: chain T residue 260 ASN Chi-restraints excluded: chain T residue 316 ARG Chi-restraints excluded: chain T residue 320 MET Chi-restraints excluded: chain U residue 126 ILE Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 334 MET Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 99 ILE Chi-restraints excluded: chain V residue 215 MET Chi-restraints excluded: chain V residue 288 THR Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 374 SER Chi-restraints excluded: chain W residue 64 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 282 ILE Chi-restraints excluded: chain X residue 64 VAL Chi-restraints excluded: chain X residue 252 TYR Chi-restraints excluded: chain X residue 258 MET Chi-restraints excluded: chain X residue 359 LEU Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 123 CYS Chi-restraints excluded: chain Y residue 144 MET Chi-restraints excluded: chain Y residue 206 VAL Chi-restraints excluded: chain Y residue 287 ASP Chi-restraints excluded: chain Y residue 474 THR Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 99 ILE Chi-restraints excluded: chain Z residue 186 SER Chi-restraints excluded: chain Z residue 220 THR Chi-restraints excluded: chain Z residue 338 SER Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 349 ASN Chi-restraints excluded: chain b residue 43 GLU Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 52 ASN Chi-restraints excluded: chain b residue 61 ASP Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain b residue 296 LEU Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 325 LEU Chi-restraints excluded: chain c residue 160 SER Chi-restraints excluded: chain c residue 211 TYR Chi-restraints excluded: chain c residue 220 THR Chi-restraints excluded: chain c residue 287 ASP Chi-restraints excluded: chain c residue 453 MET Chi-restraints excluded: chain c residue 493 GLN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 256 GLU Chi-restraints excluded: chain d residue 258 MET Chi-restraints excluded: chain d residue 287 ASP Chi-restraints excluded: chain d residue 462 GLN Chi-restraints excluded: chain d residue 474 THR Chi-restraints excluded: chain e residue 340 ASN Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 287 ASP Chi-restraints excluded: chain f residue 338 SER Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 48 VAL Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 77 TYR Chi-restraints excluded: chain g residue 119 GLU Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 258 VAL Chi-restraints excluded: chain g residue 313 ASP Chi-restraints excluded: chain g residue 319 THR Chi-restraints excluded: chain g residue 340 LEU Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 113 MET Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain h residue 269 ASP Chi-restraints excluded: chain h residue 282 LEU Chi-restraints excluded: chain h residue 319 THR Chi-restraints excluded: chain h residue 333 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1578 random chunks: chunk 1270 optimal weight: 1.9990 chunk 865 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 1135 optimal weight: 6.9990 chunk 629 optimal weight: 0.9990 chunk 1301 optimal weight: 3.9990 chunk 1054 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 778 optimal weight: 30.0000 chunk 1369 optimal weight: 1.9990 chunk 384 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 GLN 0 307 ASN 1 225 ASN ** 3 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 GLN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 ASN O 161 ASN ** V 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 257 GLN W 407 GLN X 72 ASN X 407 GLN a 332 HIS ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 299 ASN ** c 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 332 HIS d 181 ASN e 57 ASN e 379 GLN ** f 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 376 ASN ** h 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN ** h 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 127208 Z= 0.191 Angle : 0.519 11.268 172106 Z= 0.273 Chirality : 0.041 0.197 18442 Planarity : 0.004 0.057 22762 Dihedral : 4.432 56.994 17517 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.22 % Favored : 94.62 % Rotamer: Outliers : 2.83 % Allowed : 15.43 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.07), residues: 15739 helix: 1.73 (0.08), residues: 4837 sheet: -0.42 (0.09), residues: 3096 loop : -1.69 (0.06), residues: 7806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP W 221 HIS 0.005 0.001 HIS 7 82 PHE 0.025 0.001 PHE c 147 TYR 0.021 0.001 TYR W 361 ARG 0.007 0.000 ARG R 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1957 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 374 poor density : 1583 time to evaluate : 10.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 282 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8685 (pp) REVERT: 1 119 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7867 (mt-10) REVERT: 2 41 LEU cc_start: 0.9180 (mt) cc_final: 0.8699 (mt) REVERT: 2 100 ASN cc_start: 0.7867 (m110) cc_final: 0.7213 (t0) REVERT: 2 333 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7063 (p0) REVERT: 3 116 MET cc_start: 0.6703 (mtp) cc_final: 0.6495 (mtm) REVERT: 3 119 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7358 (pm20) REVERT: 3 129 MET cc_start: 0.9150 (tpp) cc_final: 0.8878 (tpp) REVERT: 3 219 ASP cc_start: 0.8246 (p0) cc_final: 0.8003 (p0) REVERT: 3 334 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8017 (mt-10) REVERT: 4 219 ASP cc_start: 0.7124 (t0) cc_final: 0.6812 (t0) REVERT: 5 43 GLN cc_start: 0.7653 (pt0) cc_final: 0.7432 (mt0) REVERT: 5 313 ASP cc_start: 0.4532 (OUTLIER) cc_final: 0.3953 (p0) REVERT: 5 340 LEU cc_start: 0.8235 (mt) cc_final: 0.8035 (mt) REVERT: 6 113 MET cc_start: 0.7479 (mmp) cc_final: 0.7240 (mmm) REVERT: 6 129 MET cc_start: 0.7807 (tpt) cc_final: 0.7280 (tpt) REVERT: 6 265 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7651 (p0) REVERT: 6 269 ASP cc_start: 0.6290 (p0) cc_final: 0.6000 (p0) REVERT: 7 3 MET cc_start: 0.7409 (tpp) cc_final: 0.7070 (mmm) REVERT: 7 128 GLU cc_start: 0.8500 (tm-30) cc_final: 0.7988 (tm-30) REVERT: 7 151 GLU cc_start: 0.8283 (pm20) cc_final: 0.8013 (tt0) REVERT: 7 232 VAL cc_start: 0.7023 (OUTLIER) cc_final: 0.6811 (p) REVERT: A 95 ASP cc_start: 0.7959 (p0) cc_final: 0.7719 (p0) REVERT: B 103 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7797 (p0) REVERT: B 216 GLU cc_start: 0.7805 (tp30) cc_final: 0.7524 (tp30) REVERT: C 73 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6557 (p90) REVERT: C 119 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: C 331 ASP cc_start: 0.8332 (t0) cc_final: 0.7978 (t70) REVERT: D 114 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: E 50 MET cc_start: 0.8767 (ttp) cc_final: 0.8431 (ttp) REVERT: E 116 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6934 (pmm) REVERT: E 247 ASP cc_start: 0.8041 (t0) cc_final: 0.7799 (t0) REVERT: E 258 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8204 (p) REVERT: E 270 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7549 (p0) REVERT: E 295 ARG cc_start: 0.5332 (mmp-170) cc_final: 0.4715 (mmm160) REVERT: F 30 GLU cc_start: 0.7078 (pm20) cc_final: 0.6865 (pt0) REVERT: F 129 MET cc_start: 0.8547 (tpp) cc_final: 0.8199 (tpt) REVERT: F 185 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5835 (mt-10) REVERT: F 258 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7775 (m) REVERT: F 295 ARG cc_start: 0.7052 (mmp80) cc_final: 0.6791 (mmp80) REVERT: G 97 ASP cc_start: 0.8096 (p0) cc_final: 0.7802 (p0) REVERT: G 327 MET cc_start: 0.8517 (mmm) cc_final: 0.8314 (mmm) REVERT: H 259 GLU cc_start: 0.8789 (pp20) cc_final: 0.8488 (pt0) REVERT: H 270 ASN cc_start: 0.6165 (OUTLIER) cc_final: 0.5618 (p0) REVERT: H 290 ASP cc_start: 0.7538 (t70) cc_final: 0.6999 (t0) REVERT: I 50 MET cc_start: 0.7502 (tpt) cc_final: 0.7242 (tpt) REVERT: I 52 LEU cc_start: 0.8063 (tt) cc_final: 0.7783 (tt) REVERT: I 73 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7670 (p90) REVERT: I 119 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6754 (pm20) REVERT: I 334 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7938 (tp30) REVERT: J 278 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7225 (tt0) REVERT: J 296 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7053 (tp30) REVERT: K 264 LYS cc_start: 0.8155 (mttt) cc_final: 0.7541 (mtpt) REVERT: L 92 ARG cc_start: 0.7789 (mmm160) cc_final: 0.3761 (ptt90) REVERT: M 37 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7468 (tm-30) REVERT: M 38 LYS cc_start: 0.8491 (mttm) cc_final: 0.7931 (mttm) REVERT: M 113 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.6808 (mpp) REVERT: M 119 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: N 22 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8812 (tt) REVERT: O 320 MET cc_start: 0.7555 (ttt) cc_final: 0.7230 (ttm) REVERT: Q 4 TYR cc_start: 0.7790 (m-80) cc_final: 0.7536 (m-80) REVERT: Q 89 THR cc_start: 0.7068 (OUTLIER) cc_final: 0.6675 (t) REVERT: Q 91 ARG cc_start: 0.7042 (ttp80) cc_final: 0.5603 (tpt170) REVERT: Q 296 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: R 285 TYR cc_start: 0.8631 (m-80) cc_final: 0.8329 (m-80) REVERT: T 32 TYR cc_start: 0.7652 (m-10) cc_final: 0.7407 (m-10) REVERT: T 316 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7871 (mtm-85) REVERT: U 258 MET cc_start: 0.8690 (mtp) cc_final: 0.8408 (mtm) REVERT: V 178 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8487 (p) REVERT: V 418 GLU cc_start: 0.8261 (tp30) cc_final: 0.8005 (tp30) REVERT: W 241 GLU cc_start: 0.7232 (mt-10) cc_final: 0.7032 (mt-10) REVERT: W 418 GLU cc_start: 0.8326 (tt0) cc_final: 0.8107 (tt0) REVERT: X 125 CYS cc_start: 0.7151 (m) cc_final: 0.6558 (m) REVERT: X 179 ASN cc_start: 0.9221 (m-40) cc_final: 0.9014 (m-40) REVERT: X 493 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8626 (mt0) REVERT: Y 120 GLU cc_start: 0.7945 (tp30) cc_final: 0.7394 (pp20) REVERT: Y 123 CYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7588 (p) REVERT: Y 195 ILE cc_start: 0.9342 (mt) cc_final: 0.9130 (mt) REVERT: Z 66 ASN cc_start: 0.8475 (m110) cc_final: 0.8272 (m110) REVERT: Z 215 MET cc_start: 0.7086 (ttm) cc_final: 0.6603 (ttt) REVERT: Z 461 VAL cc_start: 0.8974 (t) cc_final: 0.8640 (m) REVERT: a 96 TYR cc_start: 0.8126 (t80) cc_final: 0.6954 (t80) REVERT: a 380 MET cc_start: 0.7817 (ptt) cc_final: 0.7457 (ptp) REVERT: a 463 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7893 (tm-30) REVERT: b 348 ASP cc_start: 0.8308 (t0) cc_final: 0.7713 (p0) REVERT: b 478 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7321 (mm-30) REVERT: c 197 ASP cc_start: 0.7177 (p0) cc_final: 0.6925 (p0) REVERT: c 238 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7495 (tm-30) REVERT: c 493 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8267 (mm-40) REVERT: d 397 MET cc_start: 0.7967 (mmm) cc_final: 0.6909 (tpt) REVERT: d 439 ARG cc_start: 0.7968 (mtt90) cc_final: 0.7728 (mtt-85) REVERT: d 462 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7757 (mt0) REVERT: e 101 GLU cc_start: 0.6753 (tm-30) cc_final: 0.6448 (tm-30) REVERT: e 334 MET cc_start: 0.8226 (tpp) cc_final: 0.7946 (tpp) REVERT: f 411 MET cc_start: 0.8155 (mtm) cc_final: 0.7931 (mtp) REVERT: g 77 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7210 (m-80) REVERT: g 88 MET cc_start: 0.9280 (mtp) cc_final: 0.8974 (mtt) REVERT: h 32 TYR cc_start: 0.7161 (m-10) cc_final: 0.6763 (m-10) REVERT: h 72 GLU cc_start: 0.8237 (pt0) cc_final: 0.7578 (pm20) REVERT: h 136 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8390 (mm) REVERT: h 282 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7936 (mm) outliers start: 374 outliers final: 267 residues processed: 1843 average time/residue: 1.0852 time to fit residues: 3575.7527 Evaluate side-chains 1794 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1494 time to evaluate : 10.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 77 TYR Chi-restraints excluded: chain 0 residue 185 GLU Chi-restraints excluded: chain 0 residue 262 VAL Chi-restraints excluded: chain 0 residue 282 LEU Chi-restraints excluded: chain 0 residue 323 SER Chi-restraints excluded: chain 0 residue 338 VAL Chi-restraints excluded: chain 1 residue 16 LYS Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 103 ASP Chi-restraints excluded: chain 1 residue 158 GLU Chi-restraints excluded: chain 1 residue 168 THR Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 251 VAL Chi-restraints excluded: chain 1 residue 301 SER Chi-restraints excluded: chain 1 residue 320 MET Chi-restraints excluded: chain 1 residue 323 SER Chi-restraints excluded: chain 2 residue 48 VAL Chi-restraints excluded: chain 2 residue 63 ILE Chi-restraints excluded: chain 2 residue 72 GLU Chi-restraints excluded: chain 2 residue 132 VAL Chi-restraints excluded: chain 2 residue 294 GLN Chi-restraints excluded: chain 2 residue 319 THR Chi-restraints excluded: chain 2 residue 333 ASP Chi-restraints excluded: chain 2 residue 337 SER Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 16 LYS Chi-restraints excluded: chain 3 residue 62 VAL Chi-restraints excluded: chain 3 residue 74 THR Chi-restraints excluded: chain 3 residue 95 ASP Chi-restraints excluded: chain 3 residue 119 GLU Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 3 residue 194 VAL Chi-restraints excluded: chain 3 residue 247 ASP Chi-restraints excluded: chain 3 residue 323 SER Chi-restraints excluded: chain 4 residue 36 THR Chi-restraints excluded: chain 4 residue 84 VAL Chi-restraints excluded: chain 4 residue 258 VAL Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 35 THR Chi-restraints excluded: chain 5 residue 36 THR Chi-restraints excluded: chain 5 residue 48 VAL Chi-restraints excluded: chain 5 residue 49 ASN Chi-restraints excluded: chain 5 residue 74 THR Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 116 MET Chi-restraints excluded: chain 5 residue 150 VAL Chi-restraints excluded: chain 5 residue 161 ASN Chi-restraints excluded: chain 5 residue 235 LEU Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 313 ASP Chi-restraints excluded: chain 6 residue 154 MET Chi-restraints excluded: chain 6 residue 201 ASP Chi-restraints excluded: chain 6 residue 265 ASN Chi-restraints excluded: chain 6 residue 290 ASP Chi-restraints excluded: chain 6 residue 338 VAL Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain 7 residue 48 VAL Chi-restraints excluded: chain 7 residue 101 LEU Chi-restraints excluded: chain 7 residue 139 LYS Chi-restraints excluded: chain 7 residue 201 ASP Chi-restraints excluded: chain 7 residue 232 VAL Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 274 LEU Chi-restraints excluded: chain 7 residue 310 THR Chi-restraints excluded: chain 7 residue 327 MET Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 148 ASP Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 334 GLU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 182 ASP Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 287 CYS Chi-restraints excluded: chain N residue 298 ILE Chi-restraints excluded: chain N residue 322 GLN Chi-restraints excluded: chain N residue 323 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 201 ASP Chi-restraints excluded: chain O residue 232 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 287 CYS Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain Q residue 296 GLU Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 234 ASP Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain S residue 118 ASP Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 260 ASN Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 95 ASP Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 174 ASP Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain T residue 260 ASN Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain T residue 316 ARG Chi-restraints excluded: chain T residue 320 MET Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 175 LYS Chi-restraints excluded: chain U residue 300 SER Chi-restraints excluded: chain U residue 334 MET Chi-restraints excluded: chain U residue 453 MET Chi-restraints excluded: chain V residue 43 GLU Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 99 ILE Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 215 MET Chi-restraints excluded: chain V residue 274 VAL Chi-restraints excluded: chain V residue 288 THR Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 374 SER Chi-restraints excluded: chain W residue 64 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain X residue 64 VAL Chi-restraints excluded: chain X residue 252 TYR Chi-restraints excluded: chain X residue 258 MET Chi-restraints excluded: chain X residue 359 LEU Chi-restraints excluded: chain X residue 485 ASP Chi-restraints excluded: chain X residue 493 GLN Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 123 CYS Chi-restraints excluded: chain Y residue 144 MET Chi-restraints excluded: chain Y residue 206 VAL Chi-restraints excluded: chain Y residue 222 ILE Chi-restraints excluded: chain Y residue 255 MET Chi-restraints excluded: chain Y residue 287 ASP Chi-restraints excluded: chain Y residue 474 THR Chi-restraints excluded: chain Z residue 45 VAL Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 99 ILE Chi-restraints excluded: chain Z residue 186 SER Chi-restraints excluded: chain Z residue 220 THR Chi-restraints excluded: chain Z residue 338 SER Chi-restraints excluded: chain a residue 91 ARG Chi-restraints excluded: chain a residue 159 THR Chi-restraints excluded: chain a residue 349 ASN Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain b residue 43 GLU Chi-restraints excluded: chain b residue 52 ASN Chi-restraints excluded: chain b residue 61 ASP Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain b residue 296 LEU Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 325 LEU Chi-restraints excluded: chain b residue 450 SER Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 160 SER Chi-restraints excluded: chain c residue 220 THR Chi-restraints excluded: chain c residue 287 ASP Chi-restraints excluded: chain c residue 453 MET Chi-restraints excluded: chain c residue 493 GLN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 256 GLU Chi-restraints excluded: chain d residue 258 MET Chi-restraints excluded: chain d residue 287 ASP Chi-restraints excluded: chain d residue 462 GLN Chi-restraints excluded: chain d residue 474 THR Chi-restraints excluded: chain d residue 481 LYS Chi-restraints excluded: chain e residue 287 ASP Chi-restraints excluded: chain e residue 340 ASN Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 287 ASP Chi-restraints excluded: chain f residue 338 SER Chi-restraints excluded: chain f residue 340 ASN Chi-restraints excluded: chain f residue 376 ASN Chi-restraints excluded: chain g residue 48 VAL Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 77 TYR Chi-restraints excluded: chain g residue 119 GLU Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 258 VAL Chi-restraints excluded: chain g residue 319 THR Chi-restraints excluded: chain g residue 340 LEU Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain h residue 103 ASP Chi-restraints excluded: chain h residue 113 MET Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain h residue 136 LEU Chi-restraints excluded: chain h residue 269 ASP Chi-restraints excluded: chain h residue 282 LEU Chi-restraints excluded: chain h residue 319 THR Chi-restraints excluded: chain h residue 333 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1578 random chunks: chunk 513 optimal weight: 9.9990 chunk 1373 optimal weight: 9.9990 chunk 301 optimal weight: 7.9990 chunk 895 optimal weight: 3.9990 chunk 376 optimal weight: 20.0000 chunk 1526 optimal weight: 5.9990 chunk 1267 optimal weight: 5.9990 chunk 706 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 505 optimal weight: 20.0000 chunk 801 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 225 ASN ** 3 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 225 ASN 5 13 ASN 7 130 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 GLN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 HIS N 115 ASN N 225 ASN W 407 GLN X 72 ASN ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 299 ASN ** c 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 181 ASN e 57 ASN e 379 GLN ** f 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN ** h 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 127208 Z= 0.357 Angle : 0.609 10.908 172106 Z= 0.320 Chirality : 0.044 0.209 18442 Planarity : 0.005 0.057 22762 Dihedral : 4.737 56.048 17517 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.61 % Favored : 93.24 % Rotamer: Outliers : 3.44 % Allowed : 16.23 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.07), residues: 15739 helix: 1.43 (0.08), residues: 4897 sheet: -0.53 (0.09), residues: 3046 loop : -1.83 (0.06), residues: 7796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Y 221 HIS 0.009 0.001 HIS b 332 PHE 0.028 0.002 PHE b 147 TYR 0.021 0.002 TYR M 187 ARG 0.010 0.000 ARG Z 439 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1944 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 454 poor density : 1490 time to evaluate : 10.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 282 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8800 (pp) REVERT: 1 88 MET cc_start: 0.4705 (OUTLIER) cc_final: 0.3437 (mtp) REVERT: 2 100 ASN cc_start: 0.8153 (m110) cc_final: 0.7495 (t0) REVERT: 2 119 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: 2 333 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7224 (p0) REVERT: 3 110 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.8024 (mtt-85) REVERT: 3 119 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: 3 219 ASP cc_start: 0.8278 (p0) cc_final: 0.8033 (p0) REVERT: 3 334 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8053 (mt-10) REVERT: 5 43 GLN cc_start: 0.7755 (pt0) cc_final: 0.7527 (mt0) REVERT: 5 313 ASP cc_start: 0.4632 (OUTLIER) cc_final: 0.4005 (p0) REVERT: 6 3 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7862 (mtm) REVERT: 6 129 MET cc_start: 0.7935 (tpt) cc_final: 0.7329 (tpt) REVERT: 6 265 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7644 (p0) REVERT: 6 269 ASP cc_start: 0.6421 (p0) cc_final: 0.6110 (p0) REVERT: 7 3 MET cc_start: 0.7444 (tpp) cc_final: 0.7112 (mmm) REVERT: 7 128 GLU cc_start: 0.8543 (tm-30) cc_final: 0.7972 (tm-30) REVERT: 7 232 VAL cc_start: 0.7129 (OUTLIER) cc_final: 0.6875 (p) REVERT: A 95 ASP cc_start: 0.8069 (p0) cc_final: 0.7816 (p0) REVERT: B 103 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7991 (p0) REVERT: B 142 MET cc_start: 0.7510 (mtp) cc_final: 0.7308 (mtp) REVERT: B 259 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7035 (mt-10) REVERT: C 38 LYS cc_start: 0.8096 (mtmm) cc_final: 0.7812 (mtmt) REVERT: C 73 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6781 (p90) REVERT: C 331 ASP cc_start: 0.8371 (t0) cc_final: 0.7720 (t0) REVERT: E 50 MET cc_start: 0.8819 (ttp) cc_final: 0.8452 (ttp) REVERT: E 116 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6940 (pmm) REVERT: E 258 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8306 (p) REVERT: E 270 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7735 (p0) REVERT: F 129 MET cc_start: 0.8603 (tpp) cc_final: 0.8260 (tpt) REVERT: F 185 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.5869 (mt-10) REVERT: F 258 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7838 (m) REVERT: F 333 ASP cc_start: 0.7716 (p0) cc_final: 0.7386 (p0) REVERT: G 97 ASP cc_start: 0.8253 (p0) cc_final: 0.8001 (p0) REVERT: H 270 ASN cc_start: 0.5937 (OUTLIER) cc_final: 0.5313 (p0) REVERT: H 290 ASP cc_start: 0.7565 (t70) cc_final: 0.7046 (t0) REVERT: I 50 MET cc_start: 0.7607 (tpt) cc_final: 0.7273 (tpt) REVERT: I 52 LEU cc_start: 0.8073 (tt) cc_final: 0.7737 (tt) REVERT: I 73 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7870 (p90) REVERT: I 119 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6907 (pm20) REVERT: I 334 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7944 (tp30) REVERT: J 278 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7221 (tt0) REVERT: J 296 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7065 (tp30) REVERT: K 234 ASP cc_start: 0.8032 (m-30) cc_final: 0.7595 (m-30) REVERT: L 88 MET cc_start: 0.7573 (ptt) cc_final: 0.7342 (ptt) REVERT: L 92 ARG cc_start: 0.7958 (mmm160) cc_final: 0.3704 (ptt90) REVERT: M 59 SER cc_start: 0.8375 (t) cc_final: 0.8131 (p) REVERT: M 113 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7153 (mpp) REVERT: M 119 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: N 22 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8818 (tt) REVERT: O 239 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8722 (t) REVERT: O 320 MET cc_start: 0.7396 (ttt) cc_final: 0.7098 (ttm) REVERT: P 201 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7931 (p0) REVERT: Q 4 TYR cc_start: 0.7829 (m-80) cc_final: 0.7585 (m-80) REVERT: Q 91 ARG cc_start: 0.7100 (ttp80) cc_final: 0.5547 (tpt170) REVERT: Q 296 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: R 32 TYR cc_start: 0.8158 (m-80) cc_final: 0.7905 (m-80) REVERT: S 135 VAL cc_start: 0.9156 (t) cc_final: 0.8924 (t) REVERT: S 226 SER cc_start: 0.9076 (m) cc_final: 0.8715 (p) REVERT: T 172 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7548 (mmmm) REVERT: T 316 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7892 (mtm-85) REVERT: U 258 MET cc_start: 0.8669 (mtp) cc_final: 0.8392 (mtm) REVERT: V 418 GLU cc_start: 0.8370 (tp30) cc_final: 0.8098 (tp30) REVERT: W 195 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8555 (tt) REVERT: X 125 CYS cc_start: 0.7192 (m) cc_final: 0.6614 (m) REVERT: X 179 ASN cc_start: 0.9317 (m-40) cc_final: 0.8985 (m-40) REVERT: X 493 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8720 (mt0) REVERT: Y 120 GLU cc_start: 0.7999 (tp30) cc_final: 0.7414 (pp20) REVERT: Y 123 CYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7633 (p) REVERT: Y 498 MET cc_start: 0.8280 (ppp) cc_final: 0.7815 (tmm) REVERT: Z 157 TRP cc_start: 0.7697 (m-10) cc_final: 0.7386 (m-10) REVERT: Z 215 MET cc_start: 0.7093 (ttm) cc_final: 0.6589 (ttt) REVERT: Z 349 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.7704 (p0) REVERT: a 96 TYR cc_start: 0.8137 (t80) cc_final: 0.6985 (t80) REVERT: a 380 MET cc_start: 0.7865 (ptt) cc_final: 0.7485 (ptp) REVERT: a 463 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7896 (tm-30) REVERT: b 348 ASP cc_start: 0.8362 (t0) cc_final: 0.7743 (p0) REVERT: c 197 ASP cc_start: 0.7133 (p0) cc_final: 0.6861 (p0) REVERT: c 211 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7938 (t80) REVERT: c 214 TRP cc_start: 0.7138 (m100) cc_final: 0.6938 (m100) REVERT: c 238 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7501 (tm-30) REVERT: c 493 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8281 (mm-40) REVERT: d 439 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7880 (mtt-85) REVERT: d 462 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: e 101 GLU cc_start: 0.6803 (tm-30) cc_final: 0.6028 (tm-30) REVERT: e 125 CYS cc_start: 0.8465 (m) cc_final: 0.7931 (m) REVERT: e 144 MET cc_start: 0.7960 (tpp) cc_final: 0.7559 (tpp) REVERT: e 334 MET cc_start: 0.8294 (tpp) cc_final: 0.8032 (tpp) REVERT: g 77 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: h 32 TYR cc_start: 0.7279 (m-10) cc_final: 0.6931 (m-10) REVERT: h 72 GLU cc_start: 0.8340 (pt0) cc_final: 0.7677 (pm20) REVERT: h 136 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8365 (mm) REVERT: h 282 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7892 (mm) outliers start: 454 outliers final: 349 residues processed: 1814 average time/residue: 0.9942 time to fit residues: 3183.1431 Evaluate side-chains 1822 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 387 poor density : 1435 time to evaluate : 10.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 77 TYR Chi-restraints excluded: chain 0 residue 185 GLU Chi-restraints excluded: chain 0 residue 251 VAL Chi-restraints excluded: chain 0 residue 262 VAL Chi-restraints excluded: chain 0 residue 282 LEU Chi-restraints excluded: chain 0 residue 323 SER Chi-restraints excluded: chain 0 residue 337 SER Chi-restraints excluded: chain 0 residue 338 VAL Chi-restraints excluded: chain 1 residue 16 LYS Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 88 MET Chi-restraints excluded: chain 1 residue 103 ASP Chi-restraints excluded: chain 1 residue 158 GLU Chi-restraints excluded: chain 1 residue 168 THR Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 195 VAL Chi-restraints excluded: chain 1 residue 251 VAL Chi-restraints excluded: chain 1 residue 292 ASP Chi-restraints excluded: chain 1 residue 301 SER Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 1 residue 320 MET Chi-restraints excluded: chain 1 residue 323 SER Chi-restraints excluded: chain 2 residue 48 VAL Chi-restraints excluded: chain 2 residue 63 ILE Chi-restraints excluded: chain 2 residue 72 GLU Chi-restraints excluded: chain 2 residue 119 GLU Chi-restraints excluded: chain 2 residue 126 VAL Chi-restraints excluded: chain 2 residue 132 VAL Chi-restraints excluded: chain 2 residue 294 GLN Chi-restraints excluded: chain 2 residue 311 THR Chi-restraints excluded: chain 2 residue 319 THR Chi-restraints excluded: chain 2 residue 333 ASP Chi-restraints excluded: chain 2 residue 337 SER Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 16 LYS Chi-restraints excluded: chain 3 residue 62 VAL Chi-restraints excluded: chain 3 residue 74 THR Chi-restraints excluded: chain 3 residue 84 VAL Chi-restraints excluded: chain 3 residue 95 ASP Chi-restraints excluded: chain 3 residue 119 GLU Chi-restraints excluded: chain 3 residue 136 LEU Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 3 residue 247 ASP Chi-restraints excluded: chain 3 residue 323 SER Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 36 THR Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 84 VAL Chi-restraints excluded: chain 4 residue 114 GLN Chi-restraints excluded: chain 4 residue 258 VAL Chi-restraints excluded: chain 4 residue 328 LEU Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 35 THR Chi-restraints excluded: chain 5 residue 36 THR Chi-restraints excluded: chain 5 residue 47 LEU Chi-restraints excluded: chain 5 residue 48 VAL Chi-restraints excluded: chain 5 residue 49 ASN Chi-restraints excluded: chain 5 residue 50 MET Chi-restraints excluded: chain 5 residue 74 THR Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 136 LEU Chi-restraints excluded: chain 5 residue 150 VAL Chi-restraints excluded: chain 5 residue 161 ASN Chi-restraints excluded: chain 5 residue 235 LEU Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 313 ASP Chi-restraints excluded: chain 6 residue 3 MET Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 154 MET Chi-restraints excluded: chain 6 residue 201 ASP Chi-restraints excluded: chain 6 residue 248 VAL Chi-restraints excluded: chain 6 residue 265 ASN Chi-restraints excluded: chain 6 residue 290 ASP Chi-restraints excluded: chain 6 residue 319 THR Chi-restraints excluded: chain 6 residue 338 VAL Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain 7 residue 48 VAL Chi-restraints excluded: chain 7 residue 95 ASP Chi-restraints excluded: chain 7 residue 101 LEU Chi-restraints excluded: chain 7 residue 139 LYS Chi-restraints excluded: chain 7 residue 201 ASP Chi-restraints excluded: chain 7 residue 232 VAL Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 274 LEU Chi-restraints excluded: chain 7 residue 310 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 148 ASP Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 36 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 114 GLN Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 321 ILE Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 334 GLU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 182 ASP Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 195 VAL Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 287 CYS Chi-restraints excluded: chain N residue 298 ILE Chi-restraints excluded: chain N residue 322 GLN Chi-restraints excluded: chain N residue 323 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 201 ASP Chi-restraints excluded: chain O residue 232 VAL Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 318 PHE Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain P residue 201 ASP Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 77 TYR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 265 ASN Chi-restraints excluded: chain Q residue 287 CYS Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain Q residue 296 GLU Chi-restraints excluded: chain Q residue 309 VAL Chi-restraints excluded: chain Q residue 321 ILE Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 234 ASP Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain S residue 118 ASP Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 260 ASN Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 95 ASP Chi-restraints excluded: chain T residue 113 MET Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 174 ASP Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain T residue 260 ASN Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain T residue 316 ARG Chi-restraints excluded: chain T residue 320 MET Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 126 ILE Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 175 LYS Chi-restraints excluded: chain U residue 287 ASP Chi-restraints excluded: chain U residue 300 SER Chi-restraints excluded: chain U residue 334 MET Chi-restraints excluded: chain U residue 498 MET Chi-restraints excluded: chain V residue 43 GLU Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 99 ILE Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 183 THR Chi-restraints excluded: chain V residue 215 MET Chi-restraints excluded: chain V residue 274 VAL Chi-restraints excluded: chain V residue 288 THR Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 374 SER Chi-restraints excluded: chain W residue 64 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 195 ILE Chi-restraints excluded: chain W residue 445 CYS Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 64 VAL Chi-restraints excluded: chain X residue 252 TYR Chi-restraints excluded: chain X residue 258 MET Chi-restraints excluded: chain X residue 359 LEU Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 485 ASP Chi-restraints excluded: chain X residue 493 GLN Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 123 CYS Chi-restraints excluded: chain Y residue 144 MET Chi-restraints excluded: chain Y residue 206 VAL Chi-restraints excluded: chain Y residue 222 ILE Chi-restraints excluded: chain Y residue 255 MET Chi-restraints excluded: chain Y residue 287 ASP Chi-restraints excluded: chain Y residue 474 THR Chi-restraints excluded: chain Z residue 45 VAL Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 99 ILE Chi-restraints excluded: chain Z residue 186 SER Chi-restraints excluded: chain Z residue 220 THR Chi-restraints excluded: chain Z residue 338 SER Chi-restraints excluded: chain Z residue 349 ASN Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 91 ARG Chi-restraints excluded: chain a residue 159 THR Chi-restraints excluded: chain a residue 274 VAL Chi-restraints excluded: chain a residue 325 LEU Chi-restraints excluded: chain a residue 349 ASN Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 465 VAL Chi-restraints excluded: chain b residue 43 GLU Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 52 ASN Chi-restraints excluded: chain b residue 61 ASP Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 296 LEU Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 325 LEU Chi-restraints excluded: chain b residue 347 THR Chi-restraints excluded: chain b residue 427 LEU Chi-restraints excluded: chain b residue 450 SER Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 160 SER Chi-restraints excluded: chain c residue 211 TYR Chi-restraints excluded: chain c residue 220 THR Chi-restraints excluded: chain c residue 287 ASP Chi-restraints excluded: chain c residue 453 MET Chi-restraints excluded: chain c residue 493 GLN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 137 MET Chi-restraints excluded: chain d residue 242 ASP Chi-restraints excluded: chain d residue 256 GLU Chi-restraints excluded: chain d residue 258 MET Chi-restraints excluded: chain d residue 287 ASP Chi-restraints excluded: chain d residue 462 GLN Chi-restraints excluded: chain d residue 474 THR Chi-restraints excluded: chain d residue 481 LYS Chi-restraints excluded: chain e residue 183 THR Chi-restraints excluded: chain e residue 287 ASP Chi-restraints excluded: chain e residue 340 ASN Chi-restraints excluded: chain e residue 466 MET Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 74 ILE Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 287 ASP Chi-restraints excluded: chain f residue 288 THR Chi-restraints excluded: chain f residue 338 SER Chi-restraints excluded: chain f residue 340 ASN Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 48 VAL Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 77 TYR Chi-restraints excluded: chain g residue 103 ASP Chi-restraints excluded: chain g residue 119 GLU Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 258 VAL Chi-restraints excluded: chain g residue 290 ASP Chi-restraints excluded: chain g residue 301 SER Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain g residue 319 THR Chi-restraints excluded: chain g residue 321 ILE Chi-restraints excluded: chain g residue 340 LEU Chi-restraints excluded: chain h residue 18 LYS Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain h residue 88 MET Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain h residue 103 ASP Chi-restraints excluded: chain h residue 113 MET Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain h residue 136 LEU Chi-restraints excluded: chain h residue 282 LEU Chi-restraints excluded: chain h residue 319 THR Chi-restraints excluded: chain h residue 333 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1578 random chunks: chunk 1472 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 869 optimal weight: 8.9990 chunk 1114 optimal weight: 9.9990 chunk 863 optimal weight: 6.9990 chunk 1285 optimal weight: 10.0000 chunk 852 optimal weight: 2.9990 chunk 1520 optimal weight: 6.9990 chunk 951 optimal weight: 6.9990 chunk 927 optimal weight: 3.9990 chunk 702 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 125 GLN 1 225 ASN 3 100 ASN ** 3 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 190 ASN 4 225 ASN 5 115 ASN ** 6 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 130 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 ASN P 260 ASN W 257 GLN X 72 ASN X 266 ASN Y 39 ASN ** Y 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 299 ASN ** c 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 181 ASN e 57 ASN e 379 GLN ** f 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN ** h 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 127208 Z= 0.337 Angle : 0.600 11.473 172106 Z= 0.316 Chirality : 0.044 0.208 18442 Planarity : 0.005 0.057 22762 Dihedral : 4.796 58.054 17514 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.28 % Favored : 93.57 % Rotamer: Outliers : 3.60 % Allowed : 16.87 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.06), residues: 15739 helix: 1.37 (0.07), residues: 4897 sheet: -0.62 (0.09), residues: 3026 loop : -1.87 (0.06), residues: 7816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Y 221 HIS 0.008 0.001 HIS b 332 PHE 0.027 0.002 PHE c 147 TYR 0.020 0.002 TYR G 253 ARG 0.007 0.000 ARG Z 439 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1953 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 476 poor density : 1477 time to evaluate : 10.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 88 MET cc_start: 0.4638 (OUTLIER) cc_final: 0.3443 (mtp) REVERT: 2 100 ASN cc_start: 0.8178 (m110) cc_final: 0.7512 (t0) REVERT: 2 119 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: 2 333 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7222 (p0) REVERT: 3 43 GLN cc_start: 0.7670 (pt0) cc_final: 0.7273 (mt0) REVERT: 3 110 ARG cc_start: 0.8282 (mmm-85) cc_final: 0.7916 (mtt-85) REVERT: 3 119 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: 3 129 MET cc_start: 0.9156 (tpp) cc_final: 0.8857 (tpp) REVERT: 3 219 ASP cc_start: 0.8272 (p0) cc_final: 0.8022 (p0) REVERT: 3 334 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8039 (mt-10) REVERT: 5 43 GLN cc_start: 0.7769 (pt0) cc_final: 0.7559 (mt0) REVERT: 5 313 ASP cc_start: 0.4654 (OUTLIER) cc_final: 0.4109 (p0) REVERT: 6 3 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7876 (mtm) REVERT: 6 129 MET cc_start: 0.7953 (tpt) cc_final: 0.7256 (tpt) REVERT: 6 265 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7632 (p0) REVERT: 6 269 ASP cc_start: 0.6448 (p0) cc_final: 0.6148 (p0) REVERT: 7 3 MET cc_start: 0.7472 (tpp) cc_final: 0.7138 (mmm) REVERT: 7 128 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8109 (tm-30) REVERT: 7 232 VAL cc_start: 0.7148 (OUTLIER) cc_final: 0.6912 (p) REVERT: A 95 ASP cc_start: 0.8172 (p0) cc_final: 0.7907 (p0) REVERT: B 103 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8029 (p0) REVERT: B 142 MET cc_start: 0.7591 (mtp) cc_final: 0.7350 (mtp) REVERT: B 259 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7036 (mt-10) REVERT: C 331 ASP cc_start: 0.8361 (t0) cc_final: 0.7712 (t0) REVERT: E 50 MET cc_start: 0.8822 (ttp) cc_final: 0.8464 (ttp) REVERT: E 116 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6934 (pmm) REVERT: E 270 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7768 (p0) REVERT: F 30 GLU cc_start: 0.7047 (pm20) cc_final: 0.6814 (pt0) REVERT: F 129 MET cc_start: 0.8621 (tpp) cc_final: 0.8182 (tpt) REVERT: F 185 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.5856 (mt-10) REVERT: F 333 ASP cc_start: 0.7788 (p0) cc_final: 0.7423 (p0) REVERT: G 97 ASP cc_start: 0.8300 (p0) cc_final: 0.7960 (p0) REVERT: G 327 MET cc_start: 0.8463 (mmm) cc_final: 0.8030 (mmt) REVERT: H 83 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8111 (tm-30) REVERT: H 270 ASN cc_start: 0.6288 (OUTLIER) cc_final: 0.5697 (p0) REVERT: H 290 ASP cc_start: 0.7629 (t70) cc_final: 0.7184 (t0) REVERT: I 50 MET cc_start: 0.7619 (tpt) cc_final: 0.7047 (tpt) REVERT: I 52 LEU cc_start: 0.8084 (tt) cc_final: 0.7752 (tt) REVERT: I 73 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8156 (p90) REVERT: I 119 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: I 334 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7969 (tp30) REVERT: J 278 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7218 (tt0) REVERT: J 296 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7058 (tp30) REVERT: K 234 ASP cc_start: 0.8041 (m-30) cc_final: 0.7644 (m-30) REVERT: L 92 ARG cc_start: 0.7998 (mmm160) cc_final: 0.3768 (ptt90) REVERT: L 205 TRP cc_start: 0.9339 (t-100) cc_final: 0.9066 (t-100) REVERT: M 59 SER cc_start: 0.8372 (t) cc_final: 0.8109 (p) REVERT: M 113 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7149 (mpp) REVERT: M 119 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7665 (mt-10) REVERT: N 22 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8830 (tt) REVERT: O 320 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.7089 (ttm) REVERT: P 201 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7921 (p0) REVERT: Q 4 TYR cc_start: 0.7824 (m-80) cc_final: 0.7587 (m-80) REVERT: Q 89 THR cc_start: 0.7468 (OUTLIER) cc_final: 0.6998 (t) REVERT: Q 91 ARG cc_start: 0.7147 (ttp80) cc_final: 0.5671 (tpt170) REVERT: Q 296 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: S 135 VAL cc_start: 0.9154 (t) cc_final: 0.8912 (t) REVERT: S 226 SER cc_start: 0.9096 (m) cc_final: 0.8717 (p) REVERT: T 172 LYS cc_start: 0.8001 (mmmm) cc_final: 0.7566 (mmmm) REVERT: T 316 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7901 (mtm-85) REVERT: U 258 MET cc_start: 0.8653 (mtp) cc_final: 0.8380 (mtm) REVERT: V 418 GLU cc_start: 0.8344 (tp30) cc_final: 0.8112 (tp30) REVERT: W 195 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8566 (tt) REVERT: X 125 CYS cc_start: 0.7138 (m) cc_final: 0.6601 (m) REVERT: X 179 ASN cc_start: 0.9319 (m-40) cc_final: 0.8859 (m-40) REVERT: X 493 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8717 (mt0) REVERT: Y 120 GLU cc_start: 0.7996 (tp30) cc_final: 0.7394 (pp20) REVERT: Y 123 CYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7631 (p) REVERT: Y 436 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6946 (mm-40) REVERT: Z 215 MET cc_start: 0.7122 (ttm) cc_final: 0.6602 (ttt) REVERT: Z 349 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.7676 (p0) REVERT: a 96 TYR cc_start: 0.8177 (t80) cc_final: 0.7036 (t80) REVERT: a 380 MET cc_start: 0.7869 (ptt) cc_final: 0.7471 (ptp) REVERT: a 463 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7966 (tm-30) REVERT: c 197 ASP cc_start: 0.7141 (p0) cc_final: 0.6877 (p0) REVERT: c 211 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7978 (t80) REVERT: c 238 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7353 (tm-30) REVERT: c 493 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8357 (tp-100) REVERT: d 221 TRP cc_start: 0.8945 (OUTLIER) cc_final: 0.8512 (t-100) REVERT: d 397 MET cc_start: 0.8061 (mmm) cc_final: 0.6931 (tpt) REVERT: d 439 ARG cc_start: 0.8114 (mtt90) cc_final: 0.7811 (mtt-85) REVERT: d 462 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: e 101 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6144 (tm-30) REVERT: e 125 CYS cc_start: 0.8502 (m) cc_final: 0.7998 (m) REVERT: e 334 MET cc_start: 0.8314 (tpp) cc_final: 0.7810 (tpp) REVERT: e 430 LYS cc_start: 0.7404 (mmtm) cc_final: 0.7117 (tppt) REVERT: f 282 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9134 (tt) REVERT: f 377 TYR cc_start: 0.8181 (m-80) cc_final: 0.7967 (m-80) REVERT: g 40 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.7449 (m-80) REVERT: g 77 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: g 340 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8857 (mm) REVERT: h 32 TYR cc_start: 0.7253 (m-10) cc_final: 0.6717 (m-10) REVERT: h 72 GLU cc_start: 0.8321 (pt0) cc_final: 0.7655 (pm20) REVERT: h 136 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8368 (mm) REVERT: h 282 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7885 (mm) outliers start: 476 outliers final: 385 residues processed: 1831 average time/residue: 0.9797 time to fit residues: 3178.1163 Evaluate side-chains 1858 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 424 poor density : 1434 time to evaluate : 10.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 77 TYR Chi-restraints excluded: chain 0 residue 114 GLN Chi-restraints excluded: chain 0 residue 185 GLU Chi-restraints excluded: chain 0 residue 248 VAL Chi-restraints excluded: chain 0 residue 251 VAL Chi-restraints excluded: chain 0 residue 262 VAL Chi-restraints excluded: chain 0 residue 282 LEU Chi-restraints excluded: chain 0 residue 323 SER Chi-restraints excluded: chain 0 residue 337 SER Chi-restraints excluded: chain 0 residue 338 VAL Chi-restraints excluded: chain 1 residue 16 LYS Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 88 MET Chi-restraints excluded: chain 1 residue 103 ASP Chi-restraints excluded: chain 1 residue 158 GLU Chi-restraints excluded: chain 1 residue 168 THR Chi-restraints excluded: chain 1 residue 177 THR Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 195 VAL Chi-restraints excluded: chain 1 residue 251 VAL Chi-restraints excluded: chain 1 residue 282 LEU Chi-restraints excluded: chain 1 residue 292 ASP Chi-restraints excluded: chain 1 residue 301 SER Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 1 residue 320 MET Chi-restraints excluded: chain 1 residue 323 SER Chi-restraints excluded: chain 1 residue 340 LEU Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 2 residue 48 VAL Chi-restraints excluded: chain 2 residue 63 ILE Chi-restraints excluded: chain 2 residue 72 GLU Chi-restraints excluded: chain 2 residue 119 GLU Chi-restraints excluded: chain 2 residue 126 VAL Chi-restraints excluded: chain 2 residue 132 VAL Chi-restraints excluded: chain 2 residue 189 LEU Chi-restraints excluded: chain 2 residue 294 GLN Chi-restraints excluded: chain 2 residue 311 THR Chi-restraints excluded: chain 2 residue 319 THR Chi-restraints excluded: chain 2 residue 333 ASP Chi-restraints excluded: chain 2 residue 337 SER Chi-restraints excluded: chain 2 residue 340 LEU Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 16 LYS Chi-restraints excluded: chain 3 residue 62 VAL Chi-restraints excluded: chain 3 residue 74 THR Chi-restraints excluded: chain 3 residue 84 VAL Chi-restraints excluded: chain 3 residue 95 ASP Chi-restraints excluded: chain 3 residue 119 GLU Chi-restraints excluded: chain 3 residue 136 LEU Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 3 residue 247 ASP Chi-restraints excluded: chain 3 residue 323 SER Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 36 THR Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 84 VAL Chi-restraints excluded: chain 4 residue 114 GLN Chi-restraints excluded: chain 4 residue 258 VAL Chi-restraints excluded: chain 4 residue 328 LEU Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 35 THR Chi-restraints excluded: chain 5 residue 36 THR Chi-restraints excluded: chain 5 residue 48 VAL Chi-restraints excluded: chain 5 residue 49 ASN Chi-restraints excluded: chain 5 residue 50 MET Chi-restraints excluded: chain 5 residue 52 LEU Chi-restraints excluded: chain 5 residue 74 THR Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 136 LEU Chi-restraints excluded: chain 5 residue 150 VAL Chi-restraints excluded: chain 5 residue 161 ASN Chi-restraints excluded: chain 5 residue 235 LEU Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 313 ASP Chi-restraints excluded: chain 6 residue 3 MET Chi-restraints excluded: chain 6 residue 121 LEU Chi-restraints excluded: chain 6 residue 154 MET Chi-restraints excluded: chain 6 residue 201 ASP Chi-restraints excluded: chain 6 residue 248 VAL Chi-restraints excluded: chain 6 residue 265 ASN Chi-restraints excluded: chain 6 residue 290 ASP Chi-restraints excluded: chain 6 residue 319 THR Chi-restraints excluded: chain 6 residue 338 VAL Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain 7 residue 44 ILE Chi-restraints excluded: chain 7 residue 48 VAL Chi-restraints excluded: chain 7 residue 95 ASP Chi-restraints excluded: chain 7 residue 101 LEU Chi-restraints excluded: chain 7 residue 139 LYS Chi-restraints excluded: chain 7 residue 201 ASP Chi-restraints excluded: chain 7 residue 232 VAL Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 274 LEU Chi-restraints excluded: chain 7 residue 310 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 148 ASP Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 36 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 114 GLN Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 334 GLU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 182 ASP Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 195 VAL Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 287 CYS Chi-restraints excluded: chain N residue 298 ILE Chi-restraints excluded: chain N residue 322 GLN Chi-restraints excluded: chain N residue 323 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 201 ASP Chi-restraints excluded: chain O residue 232 VAL Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 320 MET Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain P residue 201 ASP Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain P residue 318 PHE Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 77 TYR Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 119 GLU Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 265 ASN Chi-restraints excluded: chain Q residue 287 CYS Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain Q residue 296 GLU Chi-restraints excluded: chain Q residue 309 VAL Chi-restraints excluded: chain Q residue 321 ILE Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 234 ASP Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 290 ASP Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 197 ILE Chi-restraints excluded: chain S residue 260 ASN Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 95 ASP Chi-restraints excluded: chain T residue 113 MET Chi-restraints excluded: chain T residue 142 MET Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 174 ASP Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain T residue 260 ASN Chi-restraints excluded: chain T residue 309 VAL Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain T residue 316 ARG Chi-restraints excluded: chain T residue 320 MET Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 126 ILE Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 175 LYS Chi-restraints excluded: chain U residue 300 SER Chi-restraints excluded: chain U residue 334 MET Chi-restraints excluded: chain U residue 498 MET Chi-restraints excluded: chain V residue 43 GLU Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 99 ILE Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 183 THR Chi-restraints excluded: chain V residue 215 MET Chi-restraints excluded: chain V residue 274 VAL Chi-restraints excluded: chain V residue 288 THR Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 347 THR Chi-restraints excluded: chain V residue 374 SER Chi-restraints excluded: chain W residue 64 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 195 ILE Chi-restraints excluded: chain W residue 445 CYS Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 64 VAL Chi-restraints excluded: chain X residue 252 TYR Chi-restraints excluded: chain X residue 258 MET Chi-restraints excluded: chain X residue 359 LEU Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 485 ASP Chi-restraints excluded: chain X residue 493 GLN Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 123 CYS Chi-restraints excluded: chain Y residue 144 MET Chi-restraints excluded: chain Y residue 206 VAL Chi-restraints excluded: chain Y residue 222 ILE Chi-restraints excluded: chain Y residue 255 MET Chi-restraints excluded: chain Y residue 287 ASP Chi-restraints excluded: chain Y residue 474 THR Chi-restraints excluded: chain Y residue 494 VAL Chi-restraints excluded: chain Z residue 45 VAL Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 99 ILE Chi-restraints excluded: chain Z residue 186 SER Chi-restraints excluded: chain Z residue 220 THR Chi-restraints excluded: chain Z residue 252 TYR Chi-restraints excluded: chain Z residue 258 MET Chi-restraints excluded: chain Z residue 338 SER Chi-restraints excluded: chain Z residue 349 ASN Chi-restraints excluded: chain Z residue 455 ILE Chi-restraints excluded: chain Z residue 498 MET Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 91 ARG Chi-restraints excluded: chain a residue 159 THR Chi-restraints excluded: chain a residue 274 VAL Chi-restraints excluded: chain a residue 325 LEU Chi-restraints excluded: chain a residue 349 ASN Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 465 VAL Chi-restraints excluded: chain b residue 43 GLU Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 52 ASN Chi-restraints excluded: chain b residue 61 ASP Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 296 LEU Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 325 LEU Chi-restraints excluded: chain b residue 347 THR Chi-restraints excluded: chain b residue 427 LEU Chi-restraints excluded: chain b residue 450 SER Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 160 SER Chi-restraints excluded: chain c residue 211 TYR Chi-restraints excluded: chain c residue 220 THR Chi-restraints excluded: chain c residue 287 ASP Chi-restraints excluded: chain c residue 442 TRP Chi-restraints excluded: chain c residue 453 MET Chi-restraints excluded: chain c residue 493 GLN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 221 TRP Chi-restraints excluded: chain d residue 242 ASP Chi-restraints excluded: chain d residue 256 GLU Chi-restraints excluded: chain d residue 258 MET Chi-restraints excluded: chain d residue 287 ASP Chi-restraints excluded: chain d residue 462 GLN Chi-restraints excluded: chain d residue 474 THR Chi-restraints excluded: chain d residue 481 LYS Chi-restraints excluded: chain e residue 183 THR Chi-restraints excluded: chain e residue 287 ASP Chi-restraints excluded: chain e residue 340 ASN Chi-restraints excluded: chain e residue 426 THR Chi-restraints excluded: chain e residue 466 MET Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 74 ILE Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 282 ILE Chi-restraints excluded: chain f residue 287 ASP Chi-restraints excluded: chain f residue 288 THR Chi-restraints excluded: chain f residue 338 SER Chi-restraints excluded: chain f residue 340 ASN Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 40 TYR Chi-restraints excluded: chain g residue 48 VAL Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 77 TYR Chi-restraints excluded: chain g residue 103 ASP Chi-restraints excluded: chain g residue 119 GLU Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 258 VAL Chi-restraints excluded: chain g residue 290 ASP Chi-restraints excluded: chain g residue 301 SER Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain g residue 319 THR Chi-restraints excluded: chain g residue 321 ILE Chi-restraints excluded: chain g residue 340 LEU Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain h residue 88 MET Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain h residue 103 ASP Chi-restraints excluded: chain h residue 113 MET Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain h residue 136 LEU Chi-restraints excluded: chain h residue 282 LEU Chi-restraints excluded: chain h residue 319 THR Chi-restraints excluded: chain h residue 322 GLN Chi-restraints excluded: chain h residue 333 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1578 random chunks: chunk 940 optimal weight: 4.9990 chunk 607 optimal weight: 20.0000 chunk 908 optimal weight: 6.9990 chunk 458 optimal weight: 8.9990 chunk 298 optimal weight: 6.9990 chunk 294 optimal weight: 8.9990 chunk 966 optimal weight: 9.9990 chunk 1036 optimal weight: 8.9990 chunk 751 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 1195 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 115 ASN 1 225 ASN 2 43 GLN 3 100 ASN ** 3 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 225 ASN ** 5 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 130 GLN 7 164 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN J 190 ASN ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 ASN N 125 GLN N 225 ASN ** S 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 72 ASN Y 39 ASN ** Y 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 299 ASN b 332 HIS ** c 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 181 ASN d 345 GLN e 57 ASN ** e 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 379 GLN ** f 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 125 GLN ** h 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN ** h 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 127208 Z= 0.544 Angle : 0.741 11.778 172106 Z= 0.393 Chirality : 0.049 0.229 18442 Planarity : 0.006 0.064 22762 Dihedral : 5.354 59.043 17514 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.16 % Favored : 91.71 % Rotamer: Outliers : 4.00 % Allowed : 17.15 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.06), residues: 15739 helix: 0.97 (0.07), residues: 4802 sheet: -0.81 (0.09), residues: 2936 loop : -2.06 (0.06), residues: 8001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Z 442 HIS 0.014 0.002 HIS b 332 PHE 0.034 0.003 PHE b 147 TYR 0.025 0.002 TYR 0 77 ARG 0.008 0.001 ARG V 495 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1970 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 529 poor density : 1441 time to evaluate : 10.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 88 MET cc_start: 0.4663 (OUTLIER) cc_final: 0.3536 (mtp) REVERT: 2 119 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: 2 178 TYR cc_start: 0.8955 (t80) cc_final: 0.8666 (t80) REVERT: 2 333 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7340 (p0) REVERT: 3 110 ARG cc_start: 0.8388 (mmm-85) cc_final: 0.8010 (mtt-85) REVERT: 3 119 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: 3 219 ASP cc_start: 0.8319 (p0) cc_final: 0.8061 (p0) REVERT: 3 334 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8084 (mt-10) REVERT: 4 130 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8390 (mm-40) REVERT: 5 43 GLN cc_start: 0.7774 (pt0) cc_final: 0.7519 (mt0) REVERT: 5 313 ASP cc_start: 0.4644 (OUTLIER) cc_final: 0.4045 (p0) REVERT: 6 129 MET cc_start: 0.8079 (tpt) cc_final: 0.7483 (tpt) REVERT: 6 159 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7980 (mm-30) REVERT: 6 265 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7636 (p0) REVERT: 6 269 ASP cc_start: 0.6647 (p0) cc_final: 0.6376 (p0) REVERT: 7 3 MET cc_start: 0.7463 (tpp) cc_final: 0.7116 (mmm) REVERT: 7 128 GLU cc_start: 0.8521 (tm-30) cc_final: 0.7988 (tm-30) REVERT: 7 232 VAL cc_start: 0.7275 (OUTLIER) cc_final: 0.7019 (p) REVERT: A 95 ASP cc_start: 0.8378 (p0) cc_final: 0.8052 (p0) REVERT: A 129 MET cc_start: 0.8922 (tpt) cc_final: 0.8593 (tpt) REVERT: B 103 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8261 (p0) REVERT: B 259 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7163 (mt-10) REVERT: D 209 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8288 (tmm-80) REVERT: E 116 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6794 (pmm) REVERT: E 270 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.7993 (p0) REVERT: F 9 LEU cc_start: 0.8330 (tp) cc_final: 0.8100 (tp) REVERT: F 129 MET cc_start: 0.8693 (tpp) cc_final: 0.7940 (tpt) REVERT: F 185 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6421 (mt-10) REVERT: F 295 ARG cc_start: 0.7155 (mmp80) cc_final: 0.6860 (mmp80) REVERT: F 333 ASP cc_start: 0.7958 (p0) cc_final: 0.7624 (p0) REVERT: G 97 ASP cc_start: 0.8325 (p0) cc_final: 0.7820 (p0) REVERT: H 83 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8165 (tm-30) REVERT: H 270 ASN cc_start: 0.5875 (OUTLIER) cc_final: 0.5358 (p0) REVERT: H 290 ASP cc_start: 0.7704 (t70) cc_final: 0.7404 (t0) REVERT: I 50 MET cc_start: 0.7600 (tpt) cc_final: 0.7031 (tpt) REVERT: I 73 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8440 (p90) REVERT: I 244 MET cc_start: 0.8348 (mmm) cc_final: 0.8145 (mtp) REVERT: J 40 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.7696 (p90) REVERT: J 278 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7221 (tt0) REVERT: J 296 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7054 (tp30) REVERT: K 3 MET cc_start: 0.7067 (tpp) cc_final: 0.6722 (ttm) REVERT: K 88 MET cc_start: 0.3656 (tpt) cc_final: 0.2883 (tpt) REVERT: K 234 ASP cc_start: 0.8054 (m-30) cc_final: 0.7678 (m-30) REVERT: L 92 ARG cc_start: 0.8178 (mmm160) cc_final: 0.7918 (tpt-90) REVERT: L 205 TRP cc_start: 0.9367 (t-100) cc_final: 0.9104 (t-100) REVERT: M 59 SER cc_start: 0.8462 (t) cc_final: 0.8140 (p) REVERT: M 113 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7346 (mpp) REVERT: M 119 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: M 339 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7483 (tp40) REVERT: N 22 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8894 (tt) REVERT: O 320 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7460 (ttm) REVERT: P 165 SER cc_start: 0.8736 (p) cc_final: 0.8511 (p) REVERT: P 201 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7990 (p0) REVERT: Q 4 TYR cc_start: 0.7980 (m-80) cc_final: 0.7653 (m-80) REVERT: Q 91 ARG cc_start: 0.7170 (ttp80) cc_final: 0.5617 (tpt170) REVERT: Q 184 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8642 (tt) REVERT: R 32 TYR cc_start: 0.8131 (m-80) cc_final: 0.7879 (m-80) REVERT: T 316 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8308 (ptt90) REVERT: U 258 MET cc_start: 0.8760 (mtp) cc_final: 0.8515 (mtm) REVERT: V 383 SER cc_start: 0.8888 (m) cc_final: 0.8674 (t) REVERT: W 195 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8562 (tt) REVERT: X 125 CYS cc_start: 0.7089 (m) cc_final: 0.6625 (m) REVERT: X 170 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8116 (mtp180) REVERT: X 493 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8672 (mt0) REVERT: Y 120 GLU cc_start: 0.8003 (tp30) cc_final: 0.7433 (pp20) REVERT: Y 123 CYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7640 (p) REVERT: Y 442 TRP cc_start: 0.7905 (m100) cc_final: 0.7651 (m100) REVERT: Z 215 MET cc_start: 0.7270 (ttm) cc_final: 0.6752 (ttt) REVERT: Z 324 ARG cc_start: 0.7832 (ttt180) cc_final: 0.7022 (mmp-170) REVERT: Z 349 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.7805 (p0) REVERT: a 170 ARG cc_start: 0.8890 (ttt90) cc_final: 0.8659 (ttt180) REVERT: a 346 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8268 (m-30) REVERT: a 390 ASN cc_start: 0.8084 (t0) cc_final: 0.6239 (t0) REVERT: a 463 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7897 (tm-30) REVERT: c 211 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.8167 (t80) REVERT: c 238 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7310 (tm-30) REVERT: c 493 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8419 (tp-100) REVERT: d 221 TRP cc_start: 0.8988 (OUTLIER) cc_final: 0.8742 (t-100) REVERT: d 422 ARG cc_start: 0.6859 (mtt-85) cc_final: 0.6454 (mtt-85) REVERT: d 439 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7937 (mtt-85) REVERT: d 462 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: e 125 CYS cc_start: 0.8682 (m) cc_final: 0.8000 (m) REVERT: e 144 MET cc_start: 0.7964 (tpp) cc_final: 0.7693 (tpp) REVERT: e 334 MET cc_start: 0.8204 (tpp) cc_final: 0.7732 (tpp) REVERT: f 89 SER cc_start: 0.8528 (t) cc_final: 0.7961 (m) REVERT: f 110 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6537 (mt-10) REVERT: f 377 TYR cc_start: 0.8374 (m-80) cc_final: 0.8096 (m-80) REVERT: g 40 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: g 47 LEU cc_start: 0.9051 (mm) cc_final: 0.8607 (mp) REVERT: g 77 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: g 340 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8896 (mm) REVERT: h 32 TYR cc_start: 0.7468 (m-10) cc_final: 0.6912 (m-10) REVERT: h 57 ILE cc_start: 0.8874 (mm) cc_final: 0.8629 (mt) REVERT: h 72 GLU cc_start: 0.8444 (pt0) cc_final: 0.7713 (pm20) REVERT: h 136 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8432 (mm) outliers start: 529 outliers final: 426 residues processed: 1839 average time/residue: 0.9604 time to fit residues: 3129.2859 Evaluate side-chains 1857 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 467 poor density : 1390 time to evaluate : 10.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 77 TYR Chi-restraints excluded: chain 0 residue 114 GLN Chi-restraints excluded: chain 0 residue 185 GLU Chi-restraints excluded: chain 0 residue 248 VAL Chi-restraints excluded: chain 0 residue 251 VAL Chi-restraints excluded: chain 0 residue 282 LEU Chi-restraints excluded: chain 0 residue 323 SER Chi-restraints excluded: chain 0 residue 337 SER Chi-restraints excluded: chain 0 residue 338 VAL Chi-restraints excluded: chain 1 residue 16 LYS Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 74 THR Chi-restraints excluded: chain 1 residue 88 MET Chi-restraints excluded: chain 1 residue 103 ASP Chi-restraints excluded: chain 1 residue 158 GLU Chi-restraints excluded: chain 1 residue 168 THR Chi-restraints excluded: chain 1 residue 177 THR Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 195 VAL Chi-restraints excluded: chain 1 residue 251 VAL Chi-restraints excluded: chain 1 residue 282 LEU Chi-restraints excluded: chain 1 residue 292 ASP Chi-restraints excluded: chain 1 residue 301 SER Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 1 residue 320 MET Chi-restraints excluded: chain 1 residue 323 SER Chi-restraints excluded: chain 1 residue 326 LEU Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 2 residue 48 VAL Chi-restraints excluded: chain 2 residue 63 ILE Chi-restraints excluded: chain 2 residue 72 GLU Chi-restraints excluded: chain 2 residue 119 GLU Chi-restraints excluded: chain 2 residue 132 VAL Chi-restraints excluded: chain 2 residue 189 LEU Chi-restraints excluded: chain 2 residue 294 GLN Chi-restraints excluded: chain 2 residue 311 THR Chi-restraints excluded: chain 2 residue 319 THR Chi-restraints excluded: chain 2 residue 333 ASP Chi-restraints excluded: chain 2 residue 337 SER Chi-restraints excluded: chain 2 residue 340 LEU Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 62 VAL Chi-restraints excluded: chain 3 residue 74 THR Chi-restraints excluded: chain 3 residue 84 VAL Chi-restraints excluded: chain 3 residue 95 ASP Chi-restraints excluded: chain 3 residue 119 GLU Chi-restraints excluded: chain 3 residue 136 LEU Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 3 residue 194 VAL Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 247 ASP Chi-restraints excluded: chain 3 residue 262 VAL Chi-restraints excluded: chain 3 residue 323 SER Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 36 THR Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 54 VAL Chi-restraints excluded: chain 4 residue 84 VAL Chi-restraints excluded: chain 4 residue 114 GLN Chi-restraints excluded: chain 4 residue 126 VAL Chi-restraints excluded: chain 4 residue 130 GLN Chi-restraints excluded: chain 4 residue 150 VAL Chi-restraints excluded: chain 4 residue 258 VAL Chi-restraints excluded: chain 4 residue 311 THR Chi-restraints excluded: chain 4 residue 328 LEU Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 35 THR Chi-restraints excluded: chain 5 residue 36 THR Chi-restraints excluded: chain 5 residue 48 VAL Chi-restraints excluded: chain 5 residue 49 ASN Chi-restraints excluded: chain 5 residue 50 MET Chi-restraints excluded: chain 5 residue 52 LEU Chi-restraints excluded: chain 5 residue 74 THR Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 136 LEU Chi-restraints excluded: chain 5 residue 150 VAL Chi-restraints excluded: chain 5 residue 161 ASN Chi-restraints excluded: chain 5 residue 235 LEU Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 313 ASP Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 63 ILE Chi-restraints excluded: chain 6 residue 121 LEU Chi-restraints excluded: chain 6 residue 154 MET Chi-restraints excluded: chain 6 residue 201 ASP Chi-restraints excluded: chain 6 residue 248 VAL Chi-restraints excluded: chain 6 residue 265 ASN Chi-restraints excluded: chain 6 residue 290 ASP Chi-restraints excluded: chain 6 residue 319 THR Chi-restraints excluded: chain 6 residue 338 VAL Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain 7 residue 43 GLN Chi-restraints excluded: chain 7 residue 44 ILE Chi-restraints excluded: chain 7 residue 48 VAL Chi-restraints excluded: chain 7 residue 95 ASP Chi-restraints excluded: chain 7 residue 101 LEU Chi-restraints excluded: chain 7 residue 139 LYS Chi-restraints excluded: chain 7 residue 201 ASP Chi-restraints excluded: chain 7 residue 232 VAL Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 274 LEU Chi-restraints excluded: chain 7 residue 310 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 259 GLU Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 40 TYR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 148 ASP Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 113 MET Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 36 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 114 GLN Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 334 GLU Chi-restraints excluded: chain M residue 339 GLN Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 182 ASP Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 195 VAL Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 287 CYS Chi-restraints excluded: chain N residue 298 ILE Chi-restraints excluded: chain N residue 303 ARG Chi-restraints excluded: chain N residue 322 GLN Chi-restraints excluded: chain N residue 323 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 63 ILE Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 201 ASP Chi-restraints excluded: chain O residue 232 VAL Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain O residue 320 MET Chi-restraints excluded: chain O residue 321 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain P residue 201 ASP Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain P residue 318 PHE Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 77 TYR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 119 GLU Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain Q residue 184 ILE Chi-restraints excluded: chain Q residue 225 ASN Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 265 ASN Chi-restraints excluded: chain Q residue 287 CYS Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain Q residue 309 VAL Chi-restraints excluded: chain Q residue 321 ILE Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 234 ASP Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 290 ASP Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 197 ILE Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 248 VAL Chi-restraints excluded: chain S residue 260 ASN Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 95 ASP Chi-restraints excluded: chain T residue 113 MET Chi-restraints excluded: chain T residue 142 MET Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 174 ASP Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain T residue 248 VAL Chi-restraints excluded: chain T residue 260 ASN Chi-restraints excluded: chain T residue 309 VAL Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain T residue 316 ARG Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 126 ILE Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 175 LYS Chi-restraints excluded: chain U residue 240 VAL Chi-restraints excluded: chain U residue 287 ASP Chi-restraints excluded: chain U residue 300 SER Chi-restraints excluded: chain U residue 425 VAL Chi-restraints excluded: chain V residue 43 GLU Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 99 ILE Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 183 THR Chi-restraints excluded: chain V residue 274 VAL Chi-restraints excluded: chain V residue 288 THR Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 347 THR Chi-restraints excluded: chain V residue 374 SER Chi-restraints excluded: chain V residue 474 THR Chi-restraints excluded: chain W residue 64 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 195 ILE Chi-restraints excluded: chain W residue 445 CYS Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 64 VAL Chi-restraints excluded: chain X residue 170 ARG Chi-restraints excluded: chain X residue 252 TYR Chi-restraints excluded: chain X residue 258 MET Chi-restraints excluded: chain X residue 359 LEU Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 493 GLN Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 123 CYS Chi-restraints excluded: chain Y residue 144 MET Chi-restraints excluded: chain Y residue 206 VAL Chi-restraints excluded: chain Y residue 222 ILE Chi-restraints excluded: chain Y residue 240 VAL Chi-restraints excluded: chain Y residue 255 MET Chi-restraints excluded: chain Y residue 287 ASP Chi-restraints excluded: chain Y residue 424 VAL Chi-restraints excluded: chain Y residue 474 THR Chi-restraints excluded: chain Y residue 494 VAL Chi-restraints excluded: chain Z residue 45 VAL Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 99 ILE Chi-restraints excluded: chain Z residue 186 SER Chi-restraints excluded: chain Z residue 220 THR Chi-restraints excluded: chain Z residue 252 TYR Chi-restraints excluded: chain Z residue 258 MET Chi-restraints excluded: chain Z residue 338 SER Chi-restraints excluded: chain Z residue 349 ASN Chi-restraints excluded: chain Z residue 455 ILE Chi-restraints excluded: chain Z residue 498 MET Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 46 ASP Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 91 ARG Chi-restraints excluded: chain a residue 159 THR Chi-restraints excluded: chain a residue 274 VAL Chi-restraints excluded: chain a residue 325 LEU Chi-restraints excluded: chain a residue 346 ASP Chi-restraints excluded: chain a residue 349 ASN Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 465 VAL Chi-restraints excluded: chain b residue 43 GLU Chi-restraints excluded: chain b residue 52 ASN Chi-restraints excluded: chain b residue 61 ASP Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 296 LEU Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 325 LEU Chi-restraints excluded: chain b residue 347 THR Chi-restraints excluded: chain b residue 427 LEU Chi-restraints excluded: chain b residue 450 SER Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 96 TYR Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 160 SER Chi-restraints excluded: chain c residue 211 TYR Chi-restraints excluded: chain c residue 220 THR Chi-restraints excluded: chain c residue 287 ASP Chi-restraints excluded: chain c residue 442 TRP Chi-restraints excluded: chain c residue 453 MET Chi-restraints excluded: chain c residue 489 ILE Chi-restraints excluded: chain c residue 493 GLN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 137 MET Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 221 TRP Chi-restraints excluded: chain d residue 242 ASP Chi-restraints excluded: chain d residue 256 GLU Chi-restraints excluded: chain d residue 258 MET Chi-restraints excluded: chain d residue 287 ASP Chi-restraints excluded: chain d residue 348 ASP Chi-restraints excluded: chain d residue 462 GLN Chi-restraints excluded: chain d residue 474 THR Chi-restraints excluded: chain d residue 481 LYS Chi-restraints excluded: chain e residue 183 THR Chi-restraints excluded: chain e residue 206 VAL Chi-restraints excluded: chain e residue 287 ASP Chi-restraints excluded: chain e residue 340 ASN Chi-restraints excluded: chain e residue 349 ASN Chi-restraints excluded: chain e residue 426 THR Chi-restraints excluded: chain e residue 466 MET Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 74 ILE Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 287 ASP Chi-restraints excluded: chain f residue 288 THR Chi-restraints excluded: chain f residue 338 SER Chi-restraints excluded: chain f residue 340 ASN Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 40 TYR Chi-restraints excluded: chain g residue 48 VAL Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 77 TYR Chi-restraints excluded: chain g residue 103 ASP Chi-restraints excluded: chain g residue 119 GLU Chi-restraints excluded: chain g residue 136 LEU Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 177 THR Chi-restraints excluded: chain g residue 248 VAL Chi-restraints excluded: chain g residue 258 VAL Chi-restraints excluded: chain g residue 290 ASP Chi-restraints excluded: chain g residue 301 SER Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain g residue 319 THR Chi-restraints excluded: chain g residue 321 ILE Chi-restraints excluded: chain g residue 340 LEU Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain h residue 88 MET Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain h residue 103 ASP Chi-restraints excluded: chain h residue 113 MET Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain h residue 136 LEU Chi-restraints excluded: chain h residue 333 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1578 random chunks: chunk 1383 optimal weight: 9.9990 chunk 1457 optimal weight: 7.9990 chunk 1329 optimal weight: 2.9990 chunk 1417 optimal weight: 5.9990 chunk 1456 optimal weight: 5.9990 chunk 853 optimal weight: 8.9990 chunk 617 optimal weight: 10.0000 chunk 1112 optimal weight: 0.9980 chunk 434 optimal weight: 20.0000 chunk 1280 optimal weight: 1.9990 chunk 1340 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 115 ASN 1 225 ASN ** 3 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 225 ASN ** 6 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 130 GLN 7 164 GLN B 130 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 ASN J 322 GLN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 ASN ** S 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 257 GLN X 72 ASN X 266 ASN Y 39 ASN ** Y 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 436 GLN a 462 GLN ** b 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 299 ASN ** c 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 181 ASN e 379 GLN ** f 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 125 GLN ** h 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN ** h 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 127208 Z= 0.293 Angle : 0.597 12.173 172106 Z= 0.315 Chirality : 0.043 0.203 18442 Planarity : 0.005 0.062 22762 Dihedral : 4.969 57.348 17514 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.14 % Rotamer: Outliers : 3.51 % Allowed : 18.06 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.06 (0.06), residues: 15739 helix: 1.24 (0.08), residues: 4898 sheet: -0.80 (0.09), residues: 3024 loop : -2.00 (0.06), residues: 7817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP d 94 HIS 0.006 0.001 HIS 7 82 PHE 0.027 0.002 PHE c 147 TYR 0.024 0.001 TYR K 245 ARG 0.008 0.000 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1939 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 464 poor density : 1475 time to evaluate : 10.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 148 ASP cc_start: 0.8207 (p0) cc_final: 0.7959 (p0) REVERT: 2 119 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: 2 295 ARG cc_start: 0.8151 (mtt-85) cc_final: 0.7876 (tmt170) REVERT: 2 333 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7342 (p0) REVERT: 3 110 ARG cc_start: 0.8291 (mmm-85) cc_final: 0.7909 (mtt-85) REVERT: 3 116 MET cc_start: 0.6799 (mtp) cc_final: 0.6537 (mtm) REVERT: 3 119 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: 3 219 ASP cc_start: 0.8340 (p0) cc_final: 0.8075 (p0) REVERT: 3 334 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8062 (mt-10) REVERT: 4 130 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8195 (mm-40) REVERT: 5 43 GLN cc_start: 0.7764 (pt0) cc_final: 0.7546 (mt0) REVERT: 5 313 ASP cc_start: 0.4568 (OUTLIER) cc_final: 0.4007 (p0) REVERT: 6 129 MET cc_start: 0.7980 (tpt) cc_final: 0.7231 (tpt) REVERT: 6 159 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7941 (mm-30) REVERT: 6 265 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7633 (p0) REVERT: 6 269 ASP cc_start: 0.6435 (p0) cc_final: 0.6146 (p0) REVERT: 7 3 MET cc_start: 0.7421 (tpp) cc_final: 0.7104 (mmm) REVERT: 7 128 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7999 (tm-30) REVERT: 7 232 VAL cc_start: 0.7184 (OUTLIER) cc_final: 0.6953 (p) REVERT: 7 278 GLN cc_start: 0.8925 (mm110) cc_final: 0.8575 (mm-40) REVERT: A 95 ASP cc_start: 0.8385 (p0) cc_final: 0.8091 (p0) REVERT: B 103 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8127 (p0) REVERT: C 331 ASP cc_start: 0.8363 (t0) cc_final: 0.7727 (t0) REVERT: D 119 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: D 209 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8490 (tmm-80) REVERT: E 50 MET cc_start: 0.8874 (ttp) cc_final: 0.8535 (ttp) REVERT: E 116 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6999 (pmm) REVERT: E 270 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7893 (p0) REVERT: F 129 MET cc_start: 0.8629 (tpp) cc_final: 0.8034 (tpt) REVERT: F 185 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6181 (mt-10) REVERT: F 333 ASP cc_start: 0.7968 (p0) cc_final: 0.7602 (p0) REVERT: G 97 ASP cc_start: 0.8296 (p0) cc_final: 0.7795 (p0) REVERT: G 327 MET cc_start: 0.8313 (mmm) cc_final: 0.7815 (mmt) REVERT: H 83 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8192 (tm-30) REVERT: H 270 ASN cc_start: 0.6045 (OUTLIER) cc_final: 0.5451 (p0) REVERT: H 290 ASP cc_start: 0.7632 (t70) cc_final: 0.7289 (t0) REVERT: I 50 MET cc_start: 0.7536 (tpt) cc_final: 0.6969 (tpt) REVERT: I 73 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8316 (p90) REVERT: I 334 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7923 (tp30) REVERT: J 40 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7766 (p90) REVERT: J 278 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7242 (tt0) REVERT: J 296 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7019 (tp30) REVERT: K 3 MET cc_start: 0.7025 (tpp) cc_final: 0.6692 (ttm) REVERT: K 88 MET cc_start: 0.3302 (tpt) cc_final: 0.2583 (tpt) REVERT: K 234 ASP cc_start: 0.7947 (m-30) cc_final: 0.7705 (m-30) REVERT: L 205 TRP cc_start: 0.9370 (t-100) cc_final: 0.9101 (t-100) REVERT: L 272 MET cc_start: 0.8286 (ptm) cc_final: 0.8076 (ptm) REVERT: L 327 MET cc_start: 0.8578 (mmm) cc_final: 0.8276 (mmm) REVERT: M 113 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7166 (mpp) REVERT: M 119 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: M 339 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7677 (tp40) REVERT: N 22 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8840 (tt) REVERT: O 128 GLU cc_start: 0.8108 (tp30) cc_final: 0.7303 (tp30) REVERT: O 320 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7234 (ttm) REVERT: P 165 SER cc_start: 0.8715 (p) cc_final: 0.8489 (p) REVERT: Q 4 TYR cc_start: 0.7735 (m-80) cc_final: 0.7524 (m-80) REVERT: Q 91 ARG cc_start: 0.7007 (ttp80) cc_final: 0.5779 (tpt170) REVERT: Q 296 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: R 32 TYR cc_start: 0.8082 (m-80) cc_final: 0.7839 (m-80) REVERT: S 135 VAL cc_start: 0.9145 (t) cc_final: 0.8910 (t) REVERT: S 226 SER cc_start: 0.9109 (m) cc_final: 0.8732 (p) REVERT: T 172 LYS cc_start: 0.8272 (mmmm) cc_final: 0.7731 (mmmm) REVERT: T 316 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7946 (mtm-85) REVERT: U 126 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8041 (mp) REVERT: U 258 MET cc_start: 0.8663 (mtp) cc_final: 0.8377 (mtm) REVERT: V 418 GLU cc_start: 0.8367 (tp30) cc_final: 0.8102 (tp30) REVERT: X 125 CYS cc_start: 0.7069 (m) cc_final: 0.6635 (m) REVERT: X 493 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8623 (mt0) REVERT: Y 120 GLU cc_start: 0.7965 (tp30) cc_final: 0.7356 (pp20) REVERT: Y 123 CYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7572 (p) REVERT: Y 442 TRP cc_start: 0.7908 (m100) cc_final: 0.7612 (m100) REVERT: Z 215 MET cc_start: 0.7153 (ttm) cc_final: 0.6636 (ttt) REVERT: Z 349 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.7494 (p0) REVERT: a 123 CYS cc_start: 0.6177 (p) cc_final: 0.5473 (p) REVERT: a 346 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8191 (m-30) REVERT: a 397 MET cc_start: 0.7157 (tpp) cc_final: 0.6780 (tpp) REVERT: a 462 GLN cc_start: 0.7571 (tt0) cc_final: 0.7364 (tt0) REVERT: a 463 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8028 (tm-30) REVERT: b 376 ASN cc_start: 0.8246 (t0) cc_final: 0.8025 (t0) REVERT: b 453 MET cc_start: 0.7798 (ptp) cc_final: 0.7523 (ptp) REVERT: c 197 ASP cc_start: 0.7229 (p0) cc_final: 0.6941 (p0) REVERT: c 211 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.8003 (t80) REVERT: c 238 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7298 (tm-30) REVERT: c 493 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8144 (mm-40) REVERT: d 221 TRP cc_start: 0.8976 (OUTLIER) cc_final: 0.8533 (t-100) REVERT: d 422 ARG cc_start: 0.6935 (mtt-85) cc_final: 0.6507 (mtt-85) REVERT: d 439 ARG cc_start: 0.8158 (mtt90) cc_final: 0.7869 (mtt-85) REVERT: d 462 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7934 (mt0) REVERT: e 101 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6565 (tm-30) REVERT: e 125 CYS cc_start: 0.8616 (m) cc_final: 0.8015 (m) REVERT: e 144 MET cc_start: 0.7903 (tpp) cc_final: 0.7633 (tpp) REVERT: e 334 MET cc_start: 0.8278 (tpp) cc_final: 0.7834 (tpp) REVERT: e 430 LYS cc_start: 0.7337 (tppt) cc_final: 0.7111 (tppt) REVERT: f 110 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6504 (mt-10) REVERT: f 377 TYR cc_start: 0.8200 (m-80) cc_final: 0.7856 (m-80) REVERT: g 40 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: g 77 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: g 340 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8867 (mm) REVERT: h 32 TYR cc_start: 0.7355 (m-10) cc_final: 0.6812 (m-10) REVERT: h 72 GLU cc_start: 0.8363 (pt0) cc_final: 0.7672 (pm20) REVERT: h 136 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8398 (mm) outliers start: 464 outliers final: 372 residues processed: 1825 average time/residue: 0.9643 time to fit residues: 3118.9867 Evaluate side-chains 1842 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 410 poor density : 1432 time to evaluate : 9.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 77 TYR Chi-restraints excluded: chain 0 residue 114 GLN Chi-restraints excluded: chain 0 residue 185 GLU Chi-restraints excluded: chain 0 residue 248 VAL Chi-restraints excluded: chain 0 residue 251 VAL Chi-restraints excluded: chain 0 residue 282 LEU Chi-restraints excluded: chain 0 residue 323 SER Chi-restraints excluded: chain 0 residue 335 PHE Chi-restraints excluded: chain 0 residue 337 SER Chi-restraints excluded: chain 0 residue 338 VAL Chi-restraints excluded: chain 1 residue 16 LYS Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 158 GLU Chi-restraints excluded: chain 1 residue 168 THR Chi-restraints excluded: chain 1 residue 177 THR Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 251 VAL Chi-restraints excluded: chain 1 residue 282 LEU Chi-restraints excluded: chain 1 residue 301 SER Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 1 residue 320 MET Chi-restraints excluded: chain 1 residue 323 SER Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 2 residue 48 VAL Chi-restraints excluded: chain 2 residue 63 ILE Chi-restraints excluded: chain 2 residue 72 GLU Chi-restraints excluded: chain 2 residue 119 GLU Chi-restraints excluded: chain 2 residue 132 VAL Chi-restraints excluded: chain 2 residue 189 LEU Chi-restraints excluded: chain 2 residue 294 GLN Chi-restraints excluded: chain 2 residue 311 THR Chi-restraints excluded: chain 2 residue 319 THR Chi-restraints excluded: chain 2 residue 333 ASP Chi-restraints excluded: chain 2 residue 337 SER Chi-restraints excluded: chain 2 residue 340 LEU Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 62 VAL Chi-restraints excluded: chain 3 residue 74 THR Chi-restraints excluded: chain 3 residue 84 VAL Chi-restraints excluded: chain 3 residue 95 ASP Chi-restraints excluded: chain 3 residue 119 GLU Chi-restraints excluded: chain 3 residue 136 LEU Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 3 residue 194 VAL Chi-restraints excluded: chain 3 residue 247 ASP Chi-restraints excluded: chain 3 residue 323 SER Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 36 THR Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 54 VAL Chi-restraints excluded: chain 4 residue 84 VAL Chi-restraints excluded: chain 4 residue 126 VAL Chi-restraints excluded: chain 4 residue 130 GLN Chi-restraints excluded: chain 4 residue 258 VAL Chi-restraints excluded: chain 4 residue 328 LEU Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 35 THR Chi-restraints excluded: chain 5 residue 36 THR Chi-restraints excluded: chain 5 residue 48 VAL Chi-restraints excluded: chain 5 residue 49 ASN Chi-restraints excluded: chain 5 residue 50 MET Chi-restraints excluded: chain 5 residue 52 LEU Chi-restraints excluded: chain 5 residue 74 THR Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 150 VAL Chi-restraints excluded: chain 5 residue 161 ASN Chi-restraints excluded: chain 5 residue 235 LEU Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 313 ASP Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 121 LEU Chi-restraints excluded: chain 6 residue 154 MET Chi-restraints excluded: chain 6 residue 201 ASP Chi-restraints excluded: chain 6 residue 248 VAL Chi-restraints excluded: chain 6 residue 265 ASN Chi-restraints excluded: chain 6 residue 290 ASP Chi-restraints excluded: chain 6 residue 319 THR Chi-restraints excluded: chain 6 residue 338 VAL Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain 7 residue 43 GLN Chi-restraints excluded: chain 7 residue 48 VAL Chi-restraints excluded: chain 7 residue 101 LEU Chi-restraints excluded: chain 7 residue 139 LYS Chi-restraints excluded: chain 7 residue 201 ASP Chi-restraints excluded: chain 7 residue 232 VAL Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 274 LEU Chi-restraints excluded: chain 7 residue 310 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 259 GLU Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain J residue 40 TYR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 270 ASN Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 148 ASP Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 113 MET Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 36 THR Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 114 GLN Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 334 GLU Chi-restraints excluded: chain M residue 339 GLN Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 182 ASP Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 195 VAL Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 287 CYS Chi-restraints excluded: chain N residue 298 ILE Chi-restraints excluded: chain N residue 322 GLN Chi-restraints excluded: chain N residue 323 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 63 ILE Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 201 ASP Chi-restraints excluded: chain O residue 232 VAL Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain O residue 320 MET Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain P residue 318 PHE Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 77 TYR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 119 GLU Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 262 VAL Chi-restraints excluded: chain Q residue 265 ASN Chi-restraints excluded: chain Q residue 287 CYS Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain Q residue 296 GLU Chi-restraints excluded: chain Q residue 321 ILE Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 234 ASP Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 248 VAL Chi-restraints excluded: chain S residue 260 ASN Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 95 ASP Chi-restraints excluded: chain T residue 113 MET Chi-restraints excluded: chain T residue 142 MET Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 174 ASP Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain T residue 260 ASN Chi-restraints excluded: chain T residue 309 VAL Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain T residue 316 ARG Chi-restraints excluded: chain T residue 327 MET Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 126 ILE Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 175 LYS Chi-restraints excluded: chain U residue 240 VAL Chi-restraints excluded: chain U residue 287 ASP Chi-restraints excluded: chain U residue 300 SER Chi-restraints excluded: chain V residue 43 GLU Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 99 ILE Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 183 THR Chi-restraints excluded: chain V residue 215 MET Chi-restraints excluded: chain V residue 274 VAL Chi-restraints excluded: chain V residue 288 THR Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 347 THR Chi-restraints excluded: chain V residue 374 SER Chi-restraints excluded: chain V residue 474 THR Chi-restraints excluded: chain W residue 64 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 195 ILE Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 64 VAL Chi-restraints excluded: chain X residue 252 TYR Chi-restraints excluded: chain X residue 258 MET Chi-restraints excluded: chain X residue 359 LEU Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 493 GLN Chi-restraints excluded: chain X residue 497 THR Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 123 CYS Chi-restraints excluded: chain Y residue 144 MET Chi-restraints excluded: chain Y residue 206 VAL Chi-restraints excluded: chain Y residue 222 ILE Chi-restraints excluded: chain Y residue 255 MET Chi-restraints excluded: chain Y residue 287 ASP Chi-restraints excluded: chain Y residue 424 VAL Chi-restraints excluded: chain Y residue 474 THR Chi-restraints excluded: chain Z residue 45 VAL Chi-restraints excluded: chain Z residue 50 LEU Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 99 ILE Chi-restraints excluded: chain Z residue 186 SER Chi-restraints excluded: chain Z residue 220 THR Chi-restraints excluded: chain Z residue 252 TYR Chi-restraints excluded: chain Z residue 338 SER Chi-restraints excluded: chain Z residue 349 ASN Chi-restraints excluded: chain Z residue 498 MET Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 91 ARG Chi-restraints excluded: chain a residue 159 THR Chi-restraints excluded: chain a residue 274 VAL Chi-restraints excluded: chain a residue 325 LEU Chi-restraints excluded: chain a residue 346 ASP Chi-restraints excluded: chain a residue 349 ASN Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 465 VAL Chi-restraints excluded: chain b residue 43 GLU Chi-restraints excluded: chain b residue 52 ASN Chi-restraints excluded: chain b residue 61 ASP Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 296 LEU Chi-restraints excluded: chain b residue 325 LEU Chi-restraints excluded: chain b residue 347 THR Chi-restraints excluded: chain b residue 427 LEU Chi-restraints excluded: chain b residue 450 SER Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 160 SER Chi-restraints excluded: chain c residue 211 TYR Chi-restraints excluded: chain c residue 220 THR Chi-restraints excluded: chain c residue 287 ASP Chi-restraints excluded: chain c residue 453 MET Chi-restraints excluded: chain c residue 493 GLN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 96 TYR Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain d residue 221 TRP Chi-restraints excluded: chain d residue 242 ASP Chi-restraints excluded: chain d residue 256 GLU Chi-restraints excluded: chain d residue 258 MET Chi-restraints excluded: chain d residue 287 ASP Chi-restraints excluded: chain d residue 462 GLN Chi-restraints excluded: chain d residue 474 THR Chi-restraints excluded: chain d residue 481 LYS Chi-restraints excluded: chain e residue 206 VAL Chi-restraints excluded: chain e residue 287 ASP Chi-restraints excluded: chain e residue 340 ASN Chi-restraints excluded: chain e residue 349 ASN Chi-restraints excluded: chain e residue 426 THR Chi-restraints excluded: chain e residue 466 MET Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 74 ILE Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 240 VAL Chi-restraints excluded: chain f residue 258 MET Chi-restraints excluded: chain f residue 287 ASP Chi-restraints excluded: chain f residue 338 SER Chi-restraints excluded: chain f residue 340 ASN Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 40 TYR Chi-restraints excluded: chain g residue 48 VAL Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 77 TYR Chi-restraints excluded: chain g residue 103 ASP Chi-restraints excluded: chain g residue 119 GLU Chi-restraints excluded: chain g residue 136 LEU Chi-restraints excluded: chain g residue 142 MET Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 177 THR Chi-restraints excluded: chain g residue 258 VAL Chi-restraints excluded: chain g residue 301 SER Chi-restraints excluded: chain g residue 319 THR Chi-restraints excluded: chain g residue 321 ILE Chi-restraints excluded: chain g residue 340 LEU Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain h residue 88 MET Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain h residue 103 ASP Chi-restraints excluded: chain h residue 113 MET Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain h residue 136 LEU Chi-restraints excluded: chain h residue 269 ASP Chi-restraints excluded: chain h residue 333 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1578 random chunks: chunk 1412 optimal weight: 4.9990 chunk 930 optimal weight: 10.0000 chunk 1498 optimal weight: 9.9990 chunk 914 optimal weight: 2.9990 chunk 710 optimal weight: 0.9990 chunk 1041 optimal weight: 9.9990 chunk 1572 optimal weight: 10.0000 chunk 1446 optimal weight: 0.6980 chunk 1251 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 966 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 125 GLN 1 225 ASN ** 3 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 225 ASN 7 130 GLN B 130 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 ASN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 ASN S 43 GLN ** V 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 257 GLN X 72 ASN X 266 ASN X 332 HIS Y 39 ASN ** Y 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 436 GLN b 78 GLN ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 356 GLN ** c 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 181 ASN e 379 GLN ** f 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 127208 Z= 0.228 Angle : 0.561 15.293 172106 Z= 0.294 Chirality : 0.042 0.199 18442 Planarity : 0.004 0.056 22762 Dihedral : 4.686 57.633 17514 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.25 % Favored : 93.63 % Rotamer: Outliers : 3.22 % Allowed : 18.48 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.07), residues: 15739 helix: 1.44 (0.08), residues: 4907 sheet: -0.68 (0.09), residues: 3026 loop : -1.90 (0.06), residues: 7806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP d 94 HIS 0.005 0.001 HIS 7 82 PHE 0.026 0.001 PHE K 34 TYR 0.020 0.001 TYR b 361 ARG 0.010 0.000 ARG V 495 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31478 Ramachandran restraints generated. 15739 Oldfield, 0 Emsley, 15739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1924 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 426 poor density : 1498 time to evaluate : 13.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 41 LEU cc_start: 0.9154 (mt) cc_final: 0.8665 (mt) REVERT: 2 119 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: 2 295 ARG cc_start: 0.8167 (mtt-85) cc_final: 0.7872 (ttt-90) REVERT: 2 333 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7176 (p0) REVERT: 3 110 ARG cc_start: 0.8251 (mmm-85) cc_final: 0.7870 (mtt-85) REVERT: 3 116 MET cc_start: 0.6703 (mtp) cc_final: 0.6497 (mtm) REVERT: 3 119 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: 3 129 MET cc_start: 0.9147 (tpp) cc_final: 0.8878 (tpp) REVERT: 3 219 ASP cc_start: 0.8302 (p0) cc_final: 0.8063 (p0) REVERT: 3 334 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8046 (mt-10) REVERT: 4 130 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8299 (mm-40) REVERT: 5 313 ASP cc_start: 0.4518 (OUTLIER) cc_final: 0.3990 (p0) REVERT: 6 129 MET cc_start: 0.7925 (tpt) cc_final: 0.7271 (tpt) REVERT: 6 265 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7653 (p0) REVERT: 6 269 ASP cc_start: 0.6372 (p0) cc_final: 0.6062 (p0) REVERT: 7 3 MET cc_start: 0.7458 (tpp) cc_final: 0.7157 (mmm) REVERT: 7 128 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8107 (tm-30) REVERT: 7 232 VAL cc_start: 0.7104 (OUTLIER) cc_final: 0.6867 (p) REVERT: 7 278 GLN cc_start: 0.8818 (mm110) cc_final: 0.8457 (mm-40) REVERT: B 103 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7911 (p0) REVERT: B 128 GLU cc_start: 0.8469 (tp30) cc_final: 0.7998 (tp30) REVERT: B 129 MET cc_start: 0.9102 (tpp) cc_final: 0.8739 (tpp) REVERT: C 90 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8216 (tt) REVERT: C 331 ASP cc_start: 0.8374 (t0) cc_final: 0.7743 (t0) REVERT: D 119 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: D 209 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8511 (tmm-80) REVERT: E 50 MET cc_start: 0.8806 (ttp) cc_final: 0.8467 (ttp) REVERT: E 270 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7722 (p0) REVERT: F 129 MET cc_start: 0.8575 (tpp) cc_final: 0.8068 (tpt) REVERT: F 185 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6129 (mt-10) REVERT: F 333 ASP cc_start: 0.7876 (p0) cc_final: 0.7484 (p0) REVERT: G 97 ASP cc_start: 0.8341 (p0) cc_final: 0.7809 (p0) REVERT: G 327 MET cc_start: 0.8325 (mmm) cc_final: 0.7829 (mmt) REVERT: H 83 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8054 (tm-30) REVERT: H 270 ASN cc_start: 0.6070 (OUTLIER) cc_final: 0.5415 (p0) REVERT: H 290 ASP cc_start: 0.7612 (t70) cc_final: 0.7244 (t0) REVERT: I 50 MET cc_start: 0.7439 (tpt) cc_final: 0.6864 (tpt) REVERT: I 73 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8305 (p90) REVERT: I 334 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7924 (tp30) REVERT: J 40 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7931 (p90) REVERT: J 278 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7260 (tt0) REVERT: J 296 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6998 (tp30) REVERT: K 3 MET cc_start: 0.7058 (tpp) cc_final: 0.6755 (ttm) REVERT: K 88 MET cc_start: 0.3234 (tpt) cc_final: 0.2538 (tpt) REVERT: L 327 MET cc_start: 0.8546 (mmm) cc_final: 0.8238 (mmm) REVERT: M 113 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7091 (mpp) REVERT: M 119 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: N 22 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8826 (tt) REVERT: O 239 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8710 (t) REVERT: O 320 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.7119 (ttm) REVERT: Q 91 ARG cc_start: 0.6953 (ttp80) cc_final: 0.5737 (tpt170) REVERT: Q 296 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: Q 317 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6988 (mm-30) REVERT: R 32 TYR cc_start: 0.8059 (m-80) cc_final: 0.7802 (m-80) REVERT: S 135 VAL cc_start: 0.9088 (t) cc_final: 0.8844 (t) REVERT: S 226 SER cc_start: 0.9087 (m) cc_final: 0.8741 (p) REVERT: T 172 LYS cc_start: 0.8193 (mmmm) cc_final: 0.7663 (mmmm) REVERT: T 316 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7891 (mtm-85) REVERT: U 126 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8049 (mp) REVERT: U 258 MET cc_start: 0.8711 (mtp) cc_final: 0.8435 (mtm) REVERT: X 125 CYS cc_start: 0.7082 (m) cc_final: 0.6639 (m) REVERT: X 170 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7982 (mtp180) REVERT: X 179 ASN cc_start: 0.9175 (m-40) cc_final: 0.8788 (m-40) REVERT: X 493 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8616 (mt0) REVERT: Y 120 GLU cc_start: 0.7943 (tp30) cc_final: 0.7347 (pp20) REVERT: Y 123 CYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7559 (p) REVERT: Y 442 TRP cc_start: 0.7837 (m100) cc_final: 0.7603 (m100) REVERT: Z 215 MET cc_start: 0.7070 (ttm) cc_final: 0.6584 (ttt) REVERT: Z 349 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.7439 (p0) REVERT: a 123 CYS cc_start: 0.6189 (p) cc_final: 0.5500 (p) REVERT: a 346 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8153 (m-30) REVERT: a 380 MET cc_start: 0.7359 (ptt) cc_final: 0.6988 (ptp) REVERT: a 397 MET cc_start: 0.7196 (tpp) cc_final: 0.6787 (tpp) REVERT: a 463 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7988 (tm-30) REVERT: b 376 ASN cc_start: 0.8180 (t0) cc_final: 0.7966 (t0) REVERT: c 197 ASP cc_start: 0.7215 (p0) cc_final: 0.6946 (p0) REVERT: c 238 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7401 (tm-30) REVERT: c 325 LEU cc_start: 0.8379 (tp) cc_final: 0.8126 (tp) REVERT: c 493 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8093 (mm-40) REVERT: d 46 ASP cc_start: 0.8190 (m-30) cc_final: 0.7970 (m-30) REVERT: d 221 TRP cc_start: 0.8968 (OUTLIER) cc_final: 0.8406 (t60) REVERT: d 422 ARG cc_start: 0.6998 (mtt-85) cc_final: 0.6670 (mtt-85) REVERT: d 439 ARG cc_start: 0.8122 (mtt90) cc_final: 0.7839 (mtt-85) REVERT: d 462 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: e 101 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6051 (tm-30) REVERT: e 125 CYS cc_start: 0.8604 (m) cc_final: 0.7990 (m) REVERT: e 144 MET cc_start: 0.7867 (tpp) cc_final: 0.7577 (tpp) REVERT: e 334 MET cc_start: 0.8270 (tpp) cc_final: 0.7844 (tpp) REVERT: f 110 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6458 (mt-10) REVERT: f 348 ASP cc_start: 0.7589 (t0) cc_final: 0.6884 (p0) REVERT: f 377 TYR cc_start: 0.8167 (m-80) cc_final: 0.7879 (m-80) REVERT: g 40 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: g 77 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: g 340 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8847 (mm) REVERT: h 32 TYR cc_start: 0.7311 (m-10) cc_final: 0.6944 (m-10) REVERT: h 72 GLU cc_start: 0.8288 (pt0) cc_final: 0.7657 (pm20) REVERT: h 136 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8452 (mm) REVERT: h 282 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7823 (mm) outliers start: 426 outliers final: 356 residues processed: 1817 average time/residue: 0.9881 time to fit residues: 3177.9251 Evaluate side-chains 1845 residues out of total 13215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 395 poor density : 1450 time to evaluate : 10.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 39 VAL Chi-restraints excluded: chain 0 residue 77 TYR Chi-restraints excluded: chain 0 residue 185 GLU Chi-restraints excluded: chain 0 residue 248 VAL Chi-restraints excluded: chain 0 residue 251 VAL Chi-restraints excluded: chain 0 residue 282 LEU Chi-restraints excluded: chain 0 residue 323 SER Chi-restraints excluded: chain 0 residue 337 SER Chi-restraints excluded: chain 0 residue 338 VAL Chi-restraints excluded: chain 1 residue 16 LYS Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 74 THR Chi-restraints excluded: chain 1 residue 158 GLU Chi-restraints excluded: chain 1 residue 168 THR Chi-restraints excluded: chain 1 residue 177 THR Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 251 VAL Chi-restraints excluded: chain 1 residue 282 LEU Chi-restraints excluded: chain 1 residue 301 SER Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 1 residue 320 MET Chi-restraints excluded: chain 1 residue 323 SER Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 2 residue 48 VAL Chi-restraints excluded: chain 2 residue 63 ILE Chi-restraints excluded: chain 2 residue 72 GLU Chi-restraints excluded: chain 2 residue 119 GLU Chi-restraints excluded: chain 2 residue 132 VAL Chi-restraints excluded: chain 2 residue 189 LEU Chi-restraints excluded: chain 2 residue 294 GLN Chi-restraints excluded: chain 2 residue 311 THR Chi-restraints excluded: chain 2 residue 319 THR Chi-restraints excluded: chain 2 residue 333 ASP Chi-restraints excluded: chain 2 residue 337 SER Chi-restraints excluded: chain 2 residue 340 LEU Chi-restraints excluded: chain 3 residue 16 LYS Chi-restraints excluded: chain 3 residue 62 VAL Chi-restraints excluded: chain 3 residue 74 THR Chi-restraints excluded: chain 3 residue 84 VAL Chi-restraints excluded: chain 3 residue 95 ASP Chi-restraints excluded: chain 3 residue 119 GLU Chi-restraints excluded: chain 3 residue 136 LEU Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 3 residue 194 VAL Chi-restraints excluded: chain 3 residue 323 SER Chi-restraints excluded: chain 4 residue 36 THR Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 84 VAL Chi-restraints excluded: chain 4 residue 126 VAL Chi-restraints excluded: chain 4 residue 130 GLN Chi-restraints excluded: chain 4 residue 219 ASP Chi-restraints excluded: chain 4 residue 258 VAL Chi-restraints excluded: chain 4 residue 328 LEU Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 35 THR Chi-restraints excluded: chain 5 residue 36 THR Chi-restraints excluded: chain 5 residue 48 VAL Chi-restraints excluded: chain 5 residue 49 ASN Chi-restraints excluded: chain 5 residue 50 MET Chi-restraints excluded: chain 5 residue 52 LEU Chi-restraints excluded: chain 5 residue 74 THR Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 150 VAL Chi-restraints excluded: chain 5 residue 161 ASN Chi-restraints excluded: chain 5 residue 235 LEU Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 313 ASP Chi-restraints excluded: chain 6 residue 154 MET Chi-restraints excluded: chain 6 residue 201 ASP Chi-restraints excluded: chain 6 residue 248 VAL Chi-restraints excluded: chain 6 residue 265 ASN Chi-restraints excluded: chain 6 residue 290 ASP Chi-restraints excluded: chain 6 residue 319 THR Chi-restraints excluded: chain 6 residue 338 VAL Chi-restraints excluded: chain 7 residue 35 THR Chi-restraints excluded: chain 7 residue 43 GLN Chi-restraints excluded: chain 7 residue 48 VAL Chi-restraints excluded: chain 7 residue 101 LEU Chi-restraints excluded: chain 7 residue 139 LYS Chi-restraints excluded: chain 7 residue 201 ASP Chi-restraints excluded: chain 7 residue 232 VAL Chi-restraints excluded: chain 7 residue 258 VAL Chi-restraints excluded: chain 7 residue 274 LEU Chi-restraints excluded: chain 7 residue 310 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 259 GLU Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain J residue 40 TYR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 270 ASN Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 148 ASP Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 114 GLN Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 334 GLU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 182 ASP Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 195 VAL Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 287 CYS Chi-restraints excluded: chain N residue 298 ILE Chi-restraints excluded: chain N residue 322 GLN Chi-restraints excluded: chain N residue 323 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 63 ILE Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 201 ASP Chi-restraints excluded: chain O residue 232 VAL Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain O residue 320 MET Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain P residue 157 SER Chi-restraints excluded: chain P residue 214 VAL Chi-restraints excluded: chain P residue 318 PHE Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 77 TYR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 262 VAL Chi-restraints excluded: chain Q residue 265 ASN Chi-restraints excluded: chain Q residue 287 CYS Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain Q residue 296 GLU Chi-restraints excluded: chain Q residue 309 VAL Chi-restraints excluded: chain Q residue 321 ILE Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 234 ASP Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain S residue 197 ILE Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 260 ASN Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 95 ASP Chi-restraints excluded: chain T residue 142 MET Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 174 ASP Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain T residue 260 ASN Chi-restraints excluded: chain T residue 309 VAL Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain T residue 316 ARG Chi-restraints excluded: chain T residue 327 MET Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 126 ILE Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 175 LYS Chi-restraints excluded: chain U residue 287 ASP Chi-restraints excluded: chain U residue 300 SER Chi-restraints excluded: chain U residue 334 MET Chi-restraints excluded: chain V residue 43 GLU Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 99 ILE Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 183 THR Chi-restraints excluded: chain V residue 215 MET Chi-restraints excluded: chain V residue 274 VAL Chi-restraints excluded: chain V residue 288 THR Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain V residue 347 THR Chi-restraints excluded: chain V residue 374 SER Chi-restraints excluded: chain V residue 474 THR Chi-restraints excluded: chain W residue 64 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 195 ILE Chi-restraints excluded: chain W residue 445 CYS Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 64 VAL Chi-restraints excluded: chain X residue 170 ARG Chi-restraints excluded: chain X residue 252 TYR Chi-restraints excluded: chain X residue 258 MET Chi-restraints excluded: chain X residue 359 LEU Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 493 GLN Chi-restraints excluded: chain X residue 497 THR Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 123 CYS Chi-restraints excluded: chain Y residue 144 MET Chi-restraints excluded: chain Y residue 206 VAL Chi-restraints excluded: chain Y residue 255 MET Chi-restraints excluded: chain Y residue 287 ASP Chi-restraints excluded: chain Y residue 424 VAL Chi-restraints excluded: chain Y residue 474 THR Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 99 ILE Chi-restraints excluded: chain Z residue 186 SER Chi-restraints excluded: chain Z residue 220 THR Chi-restraints excluded: chain Z residue 252 TYR Chi-restraints excluded: chain Z residue 338 SER Chi-restraints excluded: chain Z residue 349 ASN Chi-restraints excluded: chain Z residue 498 MET Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 64 VAL Chi-restraints excluded: chain a residue 91 ARG Chi-restraints excluded: chain a residue 274 VAL Chi-restraints excluded: chain a residue 346 ASP Chi-restraints excluded: chain a residue 349 ASN Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 465 VAL Chi-restraints excluded: chain b residue 43 GLU Chi-restraints excluded: chain b residue 52 ASN Chi-restraints excluded: chain b residue 61 ASP Chi-restraints excluded: chain b residue 296 LEU Chi-restraints excluded: chain b residue 347 THR Chi-restraints excluded: chain b residue 427 LEU Chi-restraints excluded: chain b residue 450 SER Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 160 SER Chi-restraints excluded: chain c residue 220 THR Chi-restraints excluded: chain c residue 277 MET Chi-restraints excluded: chain c residue 287 ASP Chi-restraints excluded: chain c residue 453 MET Chi-restraints excluded: chain c residue 493 GLN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 96 TYR Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain d residue 221 TRP Chi-restraints excluded: chain d residue 256 GLU Chi-restraints excluded: chain d residue 258 MET Chi-restraints excluded: chain d residue 287 ASP Chi-restraints excluded: chain d residue 462 GLN Chi-restraints excluded: chain d residue 474 THR Chi-restraints excluded: chain d residue 481 LYS Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 206 VAL Chi-restraints excluded: chain e residue 287 ASP Chi-restraints excluded: chain e residue 340 ASN Chi-restraints excluded: chain e residue 349 ASN Chi-restraints excluded: chain f residue 74 ILE Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 240 VAL Chi-restraints excluded: chain f residue 287 ASP Chi-restraints excluded: chain f residue 338 SER Chi-restraints excluded: chain f residue 340 ASN Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 40 TYR Chi-restraints excluded: chain g residue 48 VAL Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 77 TYR Chi-restraints excluded: chain g residue 103 ASP Chi-restraints excluded: chain g residue 119 GLU Chi-restraints excluded: chain g residue 136 LEU Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 258 VAL Chi-restraints excluded: chain g residue 319 THR Chi-restraints excluded: chain g residue 321 ILE Chi-restraints excluded: chain g residue 340 LEU Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 74 THR Chi-restraints excluded: chain h residue 88 MET Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain h residue 103 ASP Chi-restraints excluded: chain h residue 113 MET Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain h residue 136 LEU Chi-restraints excluded: chain h residue 269 ASP Chi-restraints excluded: chain h residue 282 LEU Chi-restraints excluded: chain h residue 322 GLN Chi-restraints excluded: chain h residue 333 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1578 random chunks: chunk 767 optimal weight: 10.0000 chunk 994 optimal weight: 9.9990 chunk 1333 optimal weight: 10.0000 chunk 383 optimal weight: 4.9990 chunk 1154 optimal weight: 0.9990 chunk 184 optimal weight: 0.0980 chunk 347 optimal weight: 4.9990 chunk 1253 optimal weight: 8.9990 chunk 524 optimal weight: 8.9990 chunk 1287 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 125 GLN 0 276 ASN 1 225 ASN ** 3 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 130 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 ASN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 ASN ** V 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 257 GLN X 72 ASN X 266 ASN Y 39 ASN ** Y 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 436 GLN ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 181 ASN e 57 ASN e 379 GLN ** f 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 299 ASN ** h 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.123028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.110902 restraints weight = 192683.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.109938 restraints weight = 327723.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.109850 restraints weight = 308348.494| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 127208 Z= 0.267 Angle : 0.576 14.228 172106 Z= 0.302 Chirality : 0.043 0.198 18442 Planarity : 0.005 0.057 22762 Dihedral : 4.699 58.494 17514 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.16 % Favored : 93.72 % Rotamer: Outliers : 3.31 % Allowed : 18.55 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.07), residues: 15739 helix: 1.42 (0.08), residues: 4907 sheet: -0.70 (0.09), residues: 2976 loop : -1.90 (0.06), residues: 7856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP d 94 HIS 0.005 0.001 HIS Z 235 PHE 0.025 0.001 PHE c 147 TYR 0.023 0.001 TYR 2 178 ARG 0.011 0.000 ARG V 495 =============================================================================== Job complete usr+sys time: 39885.83 seconds wall clock time: 689 minutes 26.81 seconds (41366.81 seconds total)