Starting phenix.real_space_refine on Mon Mar 25 00:25:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzk_26914/03_2024/7uzk_26914_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzk_26914/03_2024/7uzk_26914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzk_26914/03_2024/7uzk_26914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzk_26914/03_2024/7uzk_26914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzk_26914/03_2024/7uzk_26914_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzk_26914/03_2024/7uzk_26914_updated.pdb" } resolution = 3.0 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 1.197 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 226 5.16 5 C 28656 2.51 5 N 7766 2.21 5 O 8595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 349": "OD1" <-> "OD2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 349": "OD1" <-> "OD2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 330": "OD1" <-> "OD2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 330": "OD1" <-> "OD2" Residue "F TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 250": "OD1" <-> "OD2" Residue "G PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 305": "OE1" <-> "OE2" Residue "G ARG 332": "NH1" <-> "NH2" Residue "G TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 365": "OE1" <-> "OE2" Residue "G TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 160": "OE1" <-> "OE2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 226": "OD1" <-> "OD2" Residue "K PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 210": "OE1" <-> "OE2" Residue "K PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 103": "OD1" <-> "OD2" Residue "M PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 89": "OE1" <-> "OE2" Residue "O PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 63": "OE1" <-> "OE2" Residue "Q PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 90": "OE1" <-> "OE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 63": "OE1" <-> "OE2" Residue "T PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 134": "OD1" <-> "OD2" Residue "T TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45246 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4568 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 558} Chain breaks: 2 Chain: "B" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4657 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 570} Chain: "C" Number of atoms: 4648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4648 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 3603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3603 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Chain: "E" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3632 Classifications: {'peptide': 464} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 436} Chain breaks: 1 Chain: "F" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3576 Classifications: {'peptide': 457} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 429} Chain breaks: 1 Chain: "G" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2919 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 9, 'TRANS': 348} Chain breaks: 1 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1689 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 3, 'TRANS': 203} Chain breaks: 1 Chain: "I" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1341 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain: "J" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1807 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain: "K" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1773 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 5, 'TRANS': 212} Chain: "L" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "M" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "N" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 929 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "O" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 929 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "Q" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2122 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 9, 'TRANS': 252} Chain: "R" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2126 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain: "S" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2147 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain: "T" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1376 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.09, per 1000 atoms: 0.51 Number of scatterers: 45246 At special positions: 0 Unit cell: (173.84, 185.5, 195.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 226 16.00 P 2 15.00 Mg 1 11.99 O 8595 8.00 N 7766 7.00 C 28656 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: 17.06 Conformation dependent library (CDL) restraints added in 7.9 seconds 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10716 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 190 helices and 42 sheets defined 49.2% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.24 Creating SS restraints... Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 259 through 265 Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.554A pdb=" N ARG A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 320 through 340 removed outlier: 3.579A pdb=" N GLU A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 removed outlier: 3.637A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 388 removed outlier: 4.395A pdb=" N GLY A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 382 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 383 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 386 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU A 387 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 460 through 468 removed outlier: 4.239A pdb=" N GLU A 463 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 465 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A 466 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 468 " --> pdb=" O TYR A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 496 removed outlier: 3.844A pdb=" N GLU A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 534 through 558 Processing helix chain 'A' and resid 567 through 582 removed outlier: 6.897A pdb=" N GLU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 586 No H-bonds generated for 'chain 'A' and resid 584 through 586' Processing helix chain 'A' and resid 594 through 614 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.928A pdb=" N GLN B 261 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 263 " --> pdb=" O SER B 260 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 265 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR B 266 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 320 through 340 removed outlier: 5.120A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 378 through 388 removed outlier: 3.847A pdb=" N ARG B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 420 through 428 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 472 through 496 removed outlier: 3.710A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 518 Processing helix chain 'B' and resid 534 through 558 Processing helix chain 'B' and resid 567 through 586 removed outlier: 6.844A pdb=" N GLU B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 281 through 293 Proline residue: C 292 - end of helix Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 320 through 340 removed outlier: 3.558A pdb=" N THR C 329 " --> pdb=" O SER C 326 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 331 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 339 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 378 through 388 removed outlier: 4.019A pdb=" N ARG C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 437 through 442 removed outlier: 3.607A pdb=" N ARG C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 472 through 496 removed outlier: 3.832A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 518 Processing helix chain 'C' and resid 534 through 558 Processing helix chain 'C' and resid 567 through 586 removed outlier: 6.688A pdb=" N GLU C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LYS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 614 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 175 through 178 No H-bonds generated for 'chain 'D' and resid 175 through 178' Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 238 through 250 Processing helix chain 'D' and resid 254 through 256 No H-bonds generated for 'chain 'D' and resid 254 through 256' Processing helix chain 'D' and resid 269 through 287 removed outlier: 3.552A pdb=" N THR D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Proline residue: D 275 - end of helix removed outlier: 3.583A pdb=" N LEU D 279 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU D 283 " --> pdb=" O THR D 280 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 286 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR D 287 " --> pdb=" O PHE D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.579A pdb=" N ILE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 364 through 371 removed outlier: 3.622A pdb=" N TYR D 371 " --> pdb=" O ASP D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 402 through 405 No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 415 through 439 removed outlier: 4.198A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 446 through 461 Processing helix chain 'D' and resid 473 through 486 removed outlier: 4.472A pdb=" N ILE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 497 through 503 Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 238 through 250 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 268 through 287 Proline residue: E 275 - end of helix Processing helix chain 'E' and resid 300 through 313 Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 325 through 335 removed outlier: 4.623A pdb=" N TYR E 328 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP E 330 " --> pdb=" O MET E 327 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA E 332 " --> pdb=" O THR E 329 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 335 " --> pdb=" O ALA E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 364 through 372 Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 402 through 405 No H-bonds generated for 'chain 'E' and resid 402 through 405' Processing helix chain 'E' and resid 415 through 439 removed outlier: 3.728A pdb=" N ASP E 431 " --> pdb=" O ALA E 427 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA E 437 " --> pdb=" O GLN E 433 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 461 removed outlier: 3.753A pdb=" N GLN E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 486 removed outlier: 4.121A pdb=" N ILE E 486 " --> pdb=" O GLN E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 497 through 503 Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 238 through 250 Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 270 through 287 Proline residue: F 275 - end of helix Processing helix chain 'F' and resid 300 through 314 Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 327 through 335 removed outlier: 3.570A pdb=" N ILE F 334 " --> pdb=" O ASP F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 364 through 370 Processing helix chain 'F' and resid 381 through 385 Processing helix chain 'F' and resid 402 through 404 No H-bonds generated for 'chain 'F' and resid 402 through 404' Processing helix chain 'F' and resid 415 through 439 removed outlier: 3.501A pdb=" N ALA F 437 " --> pdb=" O GLN F 433 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 443 No H-bonds generated for 'chain 'F' and resid 441 through 443' Processing helix chain 'F' and resid 446 through 461 removed outlier: 3.519A pdb=" N GLN F 456 " --> pdb=" O LEU F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 486 removed outlier: 4.258A pdb=" N ILE F 486 " --> pdb=" O GLN F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing helix chain 'F' and resid 497 through 503 Processing helix chain 'G' and resid 15 through 26 Processing helix chain 'G' and resid 48 through 80 removed outlier: 4.072A pdb=" N GLY G 53 " --> pdb=" O ASP G 49 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET G 76 " --> pdb=" O VAL G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 90 Processing helix chain 'G' and resid 98 through 103 Processing helix chain 'G' and resid 118 through 157 removed outlier: 3.994A pdb=" N LEU G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 191 through 201 removed outlier: 4.752A pdb=" N ASN G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR G 201 " --> pdb=" O ILE G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 243 removed outlier: 3.739A pdb=" N VAL G 234 " --> pdb=" O LYS G 231 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP G 235 " --> pdb=" O LYS G 232 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG G 238 " --> pdb=" O ASP G 235 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS G 239 " --> pdb=" O ASP G 236 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA G 241 " --> pdb=" O ARG G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 309 removed outlier: 3.575A pdb=" N MET G 265 " --> pdb=" O ASP G 261 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN G 266 " --> pdb=" O LYS G 262 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Proline residue: G 278 - end of helix Processing helix chain 'G' and resid 328 through 342 removed outlier: 6.085A pdb=" N HIS G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU G 342 " --> pdb=" O LEU G 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 76 removed outlier: 3.955A pdb=" N LYS H 49 " --> pdb=" O ARG H 45 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU H 60 " --> pdb=" O MET H 56 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 83 No H-bonds generated for 'chain 'H' and resid 80 through 83' Processing helix chain 'H' and resid 129 through 174 removed outlier: 4.007A pdb=" N ALA H 141 " --> pdb=" O ASN H 137 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU H 160 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA H 161 " --> pdb=" O THR H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 222 removed outlier: 4.234A pdb=" N LYS H 204 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE H 205 " --> pdb=" O ARG H 201 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU H 207 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 107 removed outlier: 3.520A pdb=" N GLN I 67 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET I 76 " --> pdb=" O SER I 73 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP I 89 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU I 102 " --> pdb=" O LYS I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 127 removed outlier: 3.695A pdb=" N VAL I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 159 Proline residue: I 142 - end of helix removed outlier: 3.642A pdb=" N LYS I 145 " --> pdb=" O PRO I 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL I 148 " --> pdb=" O LYS I 145 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE I 152 " --> pdb=" O GLN I 149 " (cutoff:3.500A) Proline residue: I 153 - end of helix removed outlier: 3.833A pdb=" N THR I 159 " --> pdb=" O LYS I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 206 removed outlier: 4.007A pdb=" N GLN I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 216 Processing helix chain 'J' and resid 5 through 107 removed outlier: 3.525A pdb=" N LYS J 52 " --> pdb=" O THR J 48 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLU J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN J 66 " --> pdb=" O LYS J 62 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN J 71 " --> pdb=" O GLN J 67 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS J 107 " --> pdb=" O SER J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 127 removed outlier: 3.667A pdb=" N LEU J 121 " --> pdb=" O ASP J 117 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN J 126 " --> pdb=" O GLN J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 159 Proline residue: J 142 - end of helix removed outlier: 3.714A pdb=" N LYS J 145 " --> pdb=" O PRO J 142 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE J 152 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Proline residue: J 153 - end of helix removed outlier: 3.618A pdb=" N ILE J 157 " --> pdb=" O MET J 154 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR J 159 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 206 Processing helix chain 'J' and resid 208 through 216 removed outlier: 3.615A pdb=" N GLY J 213 " --> pdb=" O PRO J 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 107 removed outlier: 3.633A pdb=" N GLU K 20 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA K 34 " --> pdb=" O ASP K 31 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN K 39 " --> pdb=" O GLU K 36 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS K 42 " --> pdb=" O ASN K 39 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL K 46 " --> pdb=" O GLY K 43 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN K 47 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU K 58 " --> pdb=" O GLU K 55 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS K 82 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG K 85 " --> pdb=" O LYS K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 127 removed outlier: 3.604A pdb=" N LEU K 121 " --> pdb=" O ASP K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 159 removed outlier: 3.775A pdb=" N PHE K 141 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Proline residue: K 142 - end of helix removed outlier: 3.844A pdb=" N LYS K 145 " --> pdb=" O PRO K 142 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL K 148 " --> pdb=" O LYS K 145 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE K 152 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Proline residue: K 153 - end of helix removed outlier: 3.648A pdb=" N ILE K 157 " --> pdb=" O MET K 154 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR K 159 " --> pdb=" O LYS K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 216 removed outlier: 3.561A pdb=" N GLN K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Proline residue: K 209 - end of helix Processing helix chain 'L' and resid 14 through 18 Processing helix chain 'L' and resid 47 through 57 removed outlier: 4.347A pdb=" N PHE L 52 " --> pdb=" O ILE L 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN L 54 " --> pdb=" O ASP L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 79 removed outlier: 3.597A pdb=" N MET L 73 " --> pdb=" O TYR L 69 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL L 74 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N HIS L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 109 Processing helix chain 'M' and resid 56 through 103 removed outlier: 3.662A pdb=" N SER M 71 " --> pdb=" O GLY M 67 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ASP M 93 " --> pdb=" O GLU M 89 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU M 94 " --> pdb=" O GLN M 90 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA M 101 " --> pdb=" O ASP M 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 104 removed outlier: 3.710A pdb=" N ALA N 36 " --> pdb=" O ARG N 32 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS N 37 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA N 42 " --> pdb=" O GLU N 38 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N SER N 65 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N HIS N 66 " --> pdb=" O ALA N 62 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER N 68 " --> pdb=" O GLY N 64 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER N 71 " --> pdb=" O GLY N 67 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLU N 72 " --> pdb=" O SER N 68 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL N 73 " --> pdb=" O CYS N 69 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP N 93 " --> pdb=" O GLU N 89 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU N 94 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 89 removed outlier: 3.936A pdb=" N LYS O 34 " --> pdb=" O ASN O 30 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU O 45 " --> pdb=" O GLN O 41 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER O 71 " --> pdb=" O GLY O 67 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU O 72 " --> pdb=" O SER O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 104 Processing helix chain 'Q' and resid 15 through 36 Processing helix chain 'Q' and resid 43 through 55 removed outlier: 5.001A pdb=" N ASP Q 51 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL Q 52 " --> pdb=" O ASP Q 48 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N TRP Q 55 " --> pdb=" O ASP Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 70 Processing helix chain 'Q' and resid 78 through 97 removed outlier: 3.519A pdb=" N LEU Q 88 " --> pdb=" O ARG Q 84 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU Q 94 " --> pdb=" O GLU Q 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 117 Processing helix chain 'Q' and resid 121 through 123 No H-bonds generated for 'chain 'Q' and resid 121 through 123' Processing helix chain 'Q' and resid 125 through 139 Processing helix chain 'Q' and resid 147 through 166 Processing helix chain 'Q' and resid 173 through 187 removed outlier: 3.715A pdb=" N LYS Q 180 " --> pdb=" O ASN Q 176 " (cutoff:3.500A) Processing helix chain 'Q' and resid 193 through 206 Processing helix chain 'Q' and resid 219 through 233 removed outlier: 3.748A pdb=" N TYR Q 232 " --> pdb=" O THR Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 251 removed outlier: 3.777A pdb=" N SER Q 251 " --> pdb=" O SER Q 247 " (cutoff:3.500A) Processing helix chain 'Q' and resid 257 through 273 Processing helix chain 'R' and resid 15 through 36 Processing helix chain 'R' and resid 43 through 55 removed outlier: 3.928A pdb=" N ASP R 48 " --> pdb=" O LYS R 44 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASP R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL R 52 " --> pdb=" O ASP R 48 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N TRP R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 70 Processing helix chain 'R' and resid 78 through 97 Processing helix chain 'R' and resid 105 through 117 Processing helix chain 'R' and resid 125 through 141 removed outlier: 3.898A pdb=" N TYR R 139 " --> pdb=" O GLN R 135 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS R 141 " --> pdb=" O THR R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 166 Processing helix chain 'R' and resid 173 through 187 Processing helix chain 'R' and resid 193 through 206 Processing helix chain 'R' and resid 219 through 236 removed outlier: 3.516A pdb=" N MET R 229 " --> pdb=" O LEU R 225 " (cutoff:3.500A) Proline residue: R 235 - end of helix Processing helix chain 'R' and resid 240 through 251 removed outlier: 3.751A pdb=" N SER R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER R 251 " --> pdb=" O SER R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 273 Processing helix chain 'S' and resid 15 through 36 Processing helix chain 'S' and resid 43 through 48 Processing helix chain 'S' and resid 50 through 53 No H-bonds generated for 'chain 'S' and resid 50 through 53' Processing helix chain 'S' and resid 62 through 70 Processing helix chain 'S' and resid 78 through 97 removed outlier: 3.606A pdb=" N LEU S 88 " --> pdb=" O ARG S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 116 Processing helix chain 'S' and resid 121 through 123 No H-bonds generated for 'chain 'S' and resid 121 through 123' Processing helix chain 'S' and resid 125 through 140 removed outlier: 3.532A pdb=" N TYR S 139 " --> pdb=" O GLN S 135 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 166 Processing helix chain 'S' and resid 173 through 187 Processing helix chain 'S' and resid 193 through 206 Processing helix chain 'S' and resid 219 through 233 removed outlier: 3.830A pdb=" N TYR S 232 " --> pdb=" O THR S 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 240 through 251 Processing helix chain 'S' and resid 257 through 273 Processing helix chain 'T' and resid 64 through 71 removed outlier: 3.556A pdb=" N GLN T 69 " --> pdb=" O MET T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 78 No H-bonds generated for 'chain 'T' and resid 76 through 78' Processing helix chain 'T' and resid 89 through 92 No H-bonds generated for 'chain 'T' and resid 89 through 92' Processing helix chain 'T' and resid 96 through 103 Processing sheet with id= A, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.547A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= C, first strand: chain 'A' and resid 183 through 186 removed outlier: 5.251A pdb=" N GLU A 134 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE A 166 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE A 155 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N HIS A 164 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 199 through 203 removed outlier: 5.942A pdb=" N GLU A 195 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL A 176 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 431 through 433 removed outlier: 8.571A pdb=" N THR A 246 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 406 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE A 248 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY A 408 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 271 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N MET A 347 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 273 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 295 through 298 Processing sheet with id= G, first strand: chain 'A' and resid 401 through 404 removed outlier: 4.206A pdb=" N ARG A 391 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.651A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 87 through 90 Processing sheet with id= J, first strand: chain 'B' and resid 183 through 186 removed outlier: 5.453A pdb=" N GLU B 134 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE B 166 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE B 155 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS B 164 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.310A pdb=" N GLU B 193 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 219 through 221 removed outlier: 4.103A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 406 through 410 removed outlier: 6.618A pdb=" N VAL B 431 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N TRP B 433 " --> pdb=" O PRO B 249 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 295 through 297 Processing sheet with id= O, first strand: chain 'C' and resid 18 through 20 removed outlier: 6.623A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= Q, first strand: chain 'C' and resid 98 through 100 removed outlier: 8.944A pdb=" N PHE C 99 " --> pdb=" O THR C 309 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU C 311 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE C 272 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL C 312 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR C 274 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ASN C 314 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY C 276 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER C 403 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET C 346 " --> pdb=" O SER C 403 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER C 405 " --> pdb=" O MET C 346 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA C 348 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 407 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 183 through 186 removed outlier: 7.029A pdb=" N ILE C 166 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE C 155 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS C 164 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.240A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE C 179 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 191 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU C 203 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU C 193 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU C 201 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 295 through 297 Processing sheet with id= U, first strand: chain 'C' and resid 401 through 404 removed outlier: 4.326A pdb=" N ARG C 391 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 50 through 54 removed outlier: 6.534A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU D 88 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 120 through 123 Processing sheet with id= X, first strand: chain 'D' and resid 130 through 133 removed outlier: 3.981A pdb=" N ARG D 130 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER D 347 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL D 295 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR D 349 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU D 297 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE D 351 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 376 through 378 Processing sheet with id= Z, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.286A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 120 through 123 Processing sheet with id= AB, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.918A pdb=" N ARG E 130 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N CYS E 258 " --> pdb=" O PHE E 227 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS E 292 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL E 230 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU E 294 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA E 232 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE E 296 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE E 351 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE E 191 " --> pdb=" O LEU E 354 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.748A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AE, first strand: chain 'F' and resid 130 through 133 removed outlier: 3.905A pdb=" N ARG F 130 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER F 347 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL F 295 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR F 349 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU F 297 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE F 351 " --> pdb=" O LEU F 297 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 376 through 378 Processing sheet with id= AG, first strand: chain 'G' and resid 370 through 375 removed outlier: 6.533A pdb=" N GLU G 3 " --> pdb=" O PRO G 323 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 247 through 249 removed outlier: 4.486A pdb=" N LEU G 186 " --> pdb=" O ARG G 249 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 92 through 101 Processing sheet with id= AJ, first strand: chain 'I' and resid 164 through 167 Processing sheet with id= AK, first strand: chain 'J' and resid 164 through 167 Processing sheet with id= AL, first strand: chain 'K' and resid 164 through 167 Processing sheet with id= AM, first strand: chain 'L' and resid 36 through 38 removed outlier: 9.114A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA L 9 " --> pdb=" O GLY L 62 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE L 64 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE L 11 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE L 66 " --> pdb=" O ILE L 11 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA L 87 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE L 66 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU L 89 " --> pdb=" O ILE L 66 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'T' and resid 151 through 155 removed outlier: 4.236A pdb=" N ILE T 121 " --> pdb=" O PHE T 147 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR T 219 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU T 85 " --> pdb=" O THR T 219 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'T' and resid 164 through 167 Processing sheet with id= AP, first strand: chain 'T' and resid 190 through 192 2235 hydrogen bonds defined for protein. 5970 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: 16.70 Time building geometry restraints manager: 18.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 9259 1.32 - 1.45: 9796 1.45 - 1.57: 26581 1.57 - 1.70: 1 1.70 - 1.83: 398 Bond restraints: 46035 Sorted by residual: bond pdb=" C ALA T 76 " pdb=" N ARG T 77 " ideal model delta sigma weight residual 1.335 1.474 -0.139 1.30e-02 5.92e+03 1.15e+02 bond pdb=" C PRO G 113 " pdb=" N ILE G 114 " ideal model delta sigma weight residual 1.334 1.459 -0.125 1.26e-02 6.30e+03 9.84e+01 bond pdb=" C LEU F 484 " pdb=" N ARG F 485 " ideal model delta sigma weight residual 1.334 1.205 0.129 1.38e-02 5.25e+03 8.72e+01 bond pdb=" C ARG T 77 " pdb=" N VAL T 78 " ideal model delta sigma weight residual 1.332 1.249 0.084 1.06e-02 8.90e+03 6.21e+01 bond pdb=" C4 ADP C 701 " pdb=" C5 ADP C 701 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.07e+01 ... (remaining 46030 not shown) Histogram of bond angle deviations from ideal: 96.72 - 104.38: 664 104.38 - 112.03: 18565 112.03 - 119.69: 20630 119.69 - 127.35: 21907 127.35 - 135.00: 366 Bond angle restraints: 62132 Sorted by residual: angle pdb=" O LEU F 484 " pdb=" C LEU F 484 " pdb=" N ARG F 485 " ideal model delta sigma weight residual 122.22 113.99 8.23 1.17e+00 7.31e-01 4.95e+01 angle pdb=" CA LEU F 484 " pdb=" C LEU F 484 " pdb=" N ARG F 485 " ideal model delta sigma weight residual 117.63 125.31 -7.68 1.25e+00 6.40e-01 3.78e+01 angle pdb=" CA ASP D 359 " pdb=" CB ASP D 359 " pdb=" CG ASP D 359 " ideal model delta sigma weight residual 112.60 118.56 -5.96 1.00e+00 1.00e+00 3.55e+01 angle pdb=" O PRO G 113 " pdb=" C PRO G 113 " pdb=" N ILE G 114 " ideal model delta sigma weight residual 123.03 129.75 -6.72 1.13e+00 7.83e-01 3.54e+01 angle pdb=" N GLN H 91 " pdb=" CA GLN H 91 " pdb=" C GLN H 91 " ideal model delta sigma weight residual 112.92 120.02 -7.10 1.23e+00 6.61e-01 3.34e+01 ... (remaining 62127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.57: 27172 22.57 - 45.14: 938 45.14 - 67.70: 153 67.70 - 90.27: 58 90.27 - 112.84: 1 Dihedral angle restraints: 28322 sinusoidal: 11711 harmonic: 16611 Sorted by residual: dihedral pdb=" CA GLY B 396 " pdb=" C GLY B 396 " pdb=" N ASN B 397 " pdb=" CA ASN B 397 " ideal model delta harmonic sigma weight residual -180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ASP C 349 " pdb=" C ASP C 349 " pdb=" N SER C 350 " pdb=" CA SER C 350 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ALA H 90 " pdb=" C ALA H 90 " pdb=" N GLN H 91 " pdb=" CA GLN H 91 " ideal model delta harmonic sigma weight residual 180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 28319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 5815 0.119 - 0.237: 1045 0.237 - 0.356: 97 0.356 - 0.475: 10 0.475 - 0.593: 2 Chirality restraints: 6969 Sorted by residual: chirality pdb=" CA ASN C 397 " pdb=" N ASN C 397 " pdb=" C ASN C 397 " pdb=" CB ASN C 397 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.80e+00 chirality pdb=" CA ASP E 299 " pdb=" N ASP E 299 " pdb=" C ASP E 299 " pdb=" CB ASP E 299 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" CA LYS A 139 " pdb=" N LYS A 139 " pdb=" C LYS A 139 " pdb=" CB LYS A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.07e+00 ... (remaining 6966 not shown) Planarity restraints: 8036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 303 " -0.163 2.00e-02 2.50e+03 9.20e-02 1.69e+02 pdb=" CG TYR D 303 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR D 303 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR D 303 " 0.073 2.00e-02 2.50e+03 pdb=" CE1 TYR D 303 " 0.066 2.00e-02 2.50e+03 pdb=" CE2 TYR D 303 " 0.055 2.00e-02 2.50e+03 pdb=" CZ TYR D 303 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 303 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 122 " -0.137 2.00e-02 2.50e+03 7.88e-02 1.55e+02 pdb=" CG TRP R 122 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP R 122 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP R 122 " 0.051 2.00e-02 2.50e+03 pdb=" NE1 TRP R 122 " 0.080 2.00e-02 2.50e+03 pdb=" CE2 TRP R 122 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 122 " 0.107 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 122 " -0.106 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 122 " 0.054 2.00e-02 2.50e+03 pdb=" CH2 TRP R 122 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 122 " -0.130 2.00e-02 2.50e+03 7.69e-02 1.48e+02 pdb=" CG TRP Q 122 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 122 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 122 " 0.042 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 122 " 0.082 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 122 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 122 " 0.104 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 122 " -0.103 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 122 " 0.057 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 122 " -0.085 2.00e-02 2.50e+03 ... (remaining 8033 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5609 2.80 - 3.32: 44990 3.32 - 3.85: 72900 3.85 - 4.37: 91726 4.37 - 4.90: 153540 Nonbonded interactions: 368765 Sorted by model distance: nonbonded pdb=" OH TYR H 112 " pdb=" O ARG L 4 " model vdw 2.272 2.440 nonbonded pdb=" OH TYR F 303 " pdb=" OD1 ASP F 330 " model vdw 2.508 2.440 nonbonded pdb=" OG SER G 179 " pdb=" OE1 GLU O 15 " model vdw 2.521 2.440 nonbonded pdb=" OE2 GLU L 90 " pdb=" OG SER L 104 " model vdw 2.527 2.440 nonbonded pdb=" OG SER G 83 " pdb=" OD1 ASP G 85 " model vdw 2.528 2.440 ... (remaining 368760 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 16 through 250 or resid 258 through 412 or resid 418 throu \ gh 615)) selection = (chain 'C' and (resid 16 through 250 or resid 258 through 412 or resid 418 throu \ gh 615)) } ncs_group { reference = (chain 'D' and (resid 38 through 213 or resid 226 through 506)) selection = (chain 'E' and (resid 38 through 213 or resid 226 through 506)) selection = chain 'F' } ncs_group { reference = (chain 'J' and resid 9 through 226) selection = chain 'K' } ncs_group { reference = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'Q' selection = (chain 'R' and resid 13 through 274) selection = (chain 'S' and resid 13 through 274) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 11.330 Check model and map are aligned: 0.700 Set scattering table: 0.440 Process input model: 115.110 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.250 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:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.012 0.142 46035 Z= 0.784 Angle : 1.741 14.518 62132 Z= 1.182 Chirality : 0.089 0.593 6969 Planarity : 0.014 0.142 8036 Dihedral : 12.770 112.840 17606 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 0.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.64 % Favored : 97.20 % Rotamer: Outliers : 0.30 % Allowed : 2.94 % Favored : 96.75 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.95 % 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: -0.44 (0.10), residues: 5650 helix: -0.23 (0.09), residues: 2840 sheet: 0.29 (0.19), residues: 631 loop : -0.31 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.163 0.023 TRP C 567 HIS 0.010 0.003 HIS D 415 PHE 0.072 0.012 PHE R 213 TYR 0.163 0.018 TYR D 303 ARG 0.011 0.001 ARG E 471 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1286 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1271 time to evaluate : 5.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLN cc_start: 0.8758 (tp40) cc_final: 0.8376 (pt0) REVERT: A 163 LYS cc_start: 0.8857 (mmtm) cc_final: 0.8458 (mmtt) REVERT: A 173 ARG cc_start: 0.8467 (ptt-90) cc_final: 0.8082 (ptt180) REVERT: A 193 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7387 (mp0) REVERT: A 401 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8193 (mt-10) REVERT: A 492 ILE cc_start: 0.8155 (mt) cc_final: 0.7875 (mp) REVERT: A 584 MET cc_start: 0.8821 (mtm) cc_final: 0.8449 (mtm) REVERT: B 136 ILE cc_start: 0.8938 (mm) cc_final: 0.8659 (mp) REVERT: B 195 GLU cc_start: 0.7468 (tt0) cc_final: 0.6774 (tt0) REVERT: B 297 GLU cc_start: 0.7874 (tt0) cc_final: 0.7670 (tt0) REVERT: B 393 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8081 (tptt) REVERT: B 401 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7927 (mt-10) REVERT: B 484 GLN cc_start: 0.8216 (tp40) cc_final: 0.7859 (tp-100) REVERT: C 56 ARG cc_start: 0.8459 (ttm170) cc_final: 0.8042 (ttp-170) REVERT: C 84 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8600 (mmtp) REVERT: C 108 ASP cc_start: 0.8016 (m-30) cc_final: 0.7754 (m-30) REVERT: C 130 ASP cc_start: 0.8141 (m-30) cc_final: 0.7885 (m-30) REVERT: C 289 ARG cc_start: 0.8839 (ttp80) cc_final: 0.8613 (ttp-170) REVERT: C 293 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7581 (mm-30) REVERT: C 356 GLU cc_start: 0.8410 (tt0) cc_final: 0.8118 (mt-10) REVERT: C 371 ASP cc_start: 0.8740 (m-30) cc_final: 0.8487 (m-30) REVERT: C 438 LYS cc_start: 0.8313 (mttt) cc_final: 0.7961 (mmtm) REVERT: C 484 GLN cc_start: 0.8429 (tp40) cc_final: 0.8059 (mm-40) REVERT: C 485 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6913 (mt-10) REVERT: C 487 GLU cc_start: 0.8129 (tp30) cc_final: 0.7542 (tm-30) REVERT: C 517 ASP cc_start: 0.7868 (m-30) cc_final: 0.7567 (m-30) REVERT: C 584 MET cc_start: 0.8500 (mtm) cc_final: 0.8147 (mtm) REVERT: D 48 LYS cc_start: 0.8986 (mttt) cc_final: 0.8693 (mmmm) REVERT: D 93 LYS cc_start: 0.9018 (tttt) cc_final: 0.8772 (ttmt) REVERT: D 245 LYS cc_start: 0.8429 (tttm) cc_final: 0.8176 (ttpt) REVERT: D 250 GLU cc_start: 0.7714 (tt0) cc_final: 0.7468 (pt0) REVERT: D 321 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.7899 (mmm-85) REVERT: D 493 LYS cc_start: 0.8214 (mttt) cc_final: 0.7922 (pmtt) REVERT: D 494 ARG cc_start: 0.8464 (mmp80) cc_final: 0.8258 (mmt180) REVERT: E 126 ASP cc_start: 0.8588 (m-30) cc_final: 0.8346 (m-30) REVERT: E 315 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7762 (mp0) REVERT: E 460 LYS cc_start: 0.8860 (mttt) cc_final: 0.8454 (mtpm) REVERT: F 168 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7735 (mp0) REVERT: F 242 ARG cc_start: 0.7997 (mtt90) cc_final: 0.7427 (mtt90) REVERT: F 245 LYS cc_start: 0.7978 (tttm) cc_final: 0.7585 (ttmt) REVERT: F 410 MET cc_start: 0.8449 (mmt) cc_final: 0.8071 (mmt) REVERT: F 435 MET cc_start: 0.8852 (ttp) cc_final: 0.8552 (ttm) REVERT: F 452 LEU cc_start: 0.8756 (tp) cc_final: 0.8543 (mt) REVERT: F 491 MET cc_start: 0.8776 (mtp) cc_final: 0.8552 (mtp) REVERT: G 111 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9152 (mtpt) REVERT: G 114 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8456 (pt) REVERT: G 194 HIS cc_start: 0.7657 (t-90) cc_final: 0.7185 (t70) REVERT: H 62 MET cc_start: 0.8267 (mmt) cc_final: 0.8023 (mpt) REVERT: H 130 GLN cc_start: 0.7832 (mm110) cc_final: 0.7356 (pm20) REVERT: I 89 ASP cc_start: 0.7550 (m-30) cc_final: 0.6822 (m-30) REVERT: I 93 ASP cc_start: 0.7999 (m-30) cc_final: 0.7749 (m-30) REVERT: I 99 LYS cc_start: 0.8083 (tttt) cc_final: 0.7465 (mttt) REVERT: I 161 LYS cc_start: 0.8119 (mttp) cc_final: 0.7573 (ptmt) REVERT: I 185 ASN cc_start: 0.7731 (t0) cc_final: 0.7412 (t0) REVERT: I 208 MET cc_start: 0.9102 (mmt) cc_final: 0.8637 (mmm) REVERT: J 41 GLU cc_start: 0.7957 (tp30) cc_final: 0.7663 (tp30) REVERT: J 57 TYR cc_start: 0.8150 (m-80) cc_final: 0.7851 (m-80) REVERT: J 61 GLU cc_start: 0.7845 (tt0) cc_final: 0.7577 (mt-10) REVERT: J 76 MET cc_start: 0.7341 (mtm) cc_final: 0.6767 (tmm) REVERT: J 85 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7128 (mmt180) REVERT: J 94 LEU cc_start: 0.8265 (tm) cc_final: 0.8056 (tp) REVERT: J 182 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8343 (mt-10) REVERT: J 191 LYS cc_start: 0.8840 (pttt) cc_final: 0.8501 (pttp) REVERT: J 197 GLU cc_start: 0.8178 (mp0) cc_final: 0.7207 (mp0) REVERT: J 201 ASP cc_start: 0.7722 (t0) cc_final: 0.7276 (m-30) REVERT: J 207 MET cc_start: 0.8115 (ptm) cc_final: 0.7830 (ptm) REVERT: K 60 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7820 (ttmm) REVERT: K 93 ASP cc_start: 0.7896 (m-30) cc_final: 0.7653 (m-30) REVERT: K 108 ASP cc_start: 0.7118 (t0) cc_final: 0.6433 (t0) REVERT: K 212 ARG cc_start: 0.8356 (ttt-90) cc_final: 0.8128 (ttt180) REVERT: M 98 ASN cc_start: 0.8352 (m-40) cc_final: 0.8115 (m-40) REVERT: M 112 GLU cc_start: 0.8174 (pm20) cc_final: 0.7973 (pt0) REVERT: N 48 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7540 (ttp-170) REVERT: O 80 LYS cc_start: 0.8100 (mttt) cc_final: 0.7792 (mttm) REVERT: O 97 ASP cc_start: 0.7969 (m-30) cc_final: 0.7740 (m-30) REVERT: Q 16 GLU cc_start: 0.8096 (tp30) cc_final: 0.7857 (tp30) REVERT: R 50 GLN cc_start: 0.7976 (tp40) cc_final: 0.7279 (tp40) REVERT: R 54 ILE cc_start: 0.8956 (tt) cc_final: 0.8685 (pt) REVERT: R 105 LEU cc_start: 0.7625 (mt) cc_final: 0.6936 (mp) REVERT: R 117 GLN cc_start: 0.8583 (mt0) cc_final: 0.8363 (mt0) REVERT: R 135 GLN cc_start: 0.8375 (tt0) cc_final: 0.7881 (tt0) REVERT: R 231 ASP cc_start: 0.8881 (m-30) cc_final: 0.8669 (m-30) REVERT: S 60 TYR cc_start: 0.8209 (m-80) cc_final: 0.7872 (m-80) REVERT: S 67 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6930 (mm-30) REVERT: T 185 ASP cc_start: 0.8809 (p0) cc_final: 0.8547 (p0) outliers start: 15 outliers final: 8 residues processed: 1280 average time/residue: 1.7913 time to fit residues: 2744.7404 Evaluate side-chains 838 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 828 time to evaluate : 4.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain T residue 153 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 475 optimal weight: 0.9980 chunk 426 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 441 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 268 optimal weight: 0.9980 chunk 328 optimal weight: 0.9980 chunk 511 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 HIS C 523 ASN D 38 ASN F 382 GLN F 482 GLN G 88 GLN ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS I 100 GLN I 219 ASN J 39 ASN J 67 GLN J 205 GLN J 219 ASN L 46 ASN L 57 ASN L 81 HIS M 90 GLN N 66 HIS ** O 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN Q 117 GLN Q 222 GLN R 142 ASN S 149 ASN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 135 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 46035 Z= 0.215 Angle : 0.610 7.437 62132 Z= 0.322 Chirality : 0.043 0.201 6969 Planarity : 0.005 0.045 8036 Dihedral : 5.873 110.429 6236 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.05 % Favored : 97.93 % Rotamer: Outliers : 2.42 % Allowed : 11.96 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 0.88 (0.11), residues: 5650 helix: 1.28 (0.10), residues: 2823 sheet: 0.35 (0.19), residues: 668 loop : -0.16 (0.14), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 567 HIS 0.007 0.001 HIS K 14 PHE 0.024 0.002 PHE H 155 TYR 0.027 0.001 TYR H 112 ARG 0.011 0.001 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 859 time to evaluate : 5.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8093 (p90) cc_final: 0.7734 (p90) REVERT: A 163 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8298 (mmtt) REVERT: A 173 ARG cc_start: 0.8444 (ptt-90) cc_final: 0.7985 (ptt180) REVERT: A 193 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7341 (mt-10) REVERT: A 231 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7726 (mp10) REVERT: A 492 ILE cc_start: 0.8231 (mt) cc_final: 0.8028 (mp) REVERT: A 565 ILE cc_start: 0.8940 (mm) cc_final: 0.8738 (mt) REVERT: A 571 ARG cc_start: 0.7763 (ttp80) cc_final: 0.7538 (ttp-170) REVERT: A 584 MET cc_start: 0.8841 (mtm) cc_final: 0.8488 (mtm) REVERT: B 195 GLU cc_start: 0.7489 (tt0) cc_final: 0.6861 (tt0) REVERT: B 297 GLU cc_start: 0.7879 (tt0) cc_final: 0.7647 (tt0) REVERT: B 401 GLU cc_start: 0.8223 (mt-10) cc_final: 0.8010 (mt-10) REVERT: B 452 ILE cc_start: 0.8491 (tp) cc_final: 0.8088 (pt) REVERT: B 462 ASP cc_start: 0.7002 (p0) cc_final: 0.6715 (p0) REVERT: B 466 ASP cc_start: 0.7855 (t70) cc_final: 0.7603 (m-30) REVERT: B 471 GLU cc_start: 0.8121 (pm20) cc_final: 0.7822 (pm20) REVERT: B 540 MET cc_start: 0.8225 (mtp) cc_final: 0.7942 (mtm) REVERT: B 604 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7298 (tm) REVERT: C 17 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7846 (m) REVERT: C 56 ARG cc_start: 0.8448 (ttm170) cc_final: 0.7985 (ttp-170) REVERT: C 84 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8601 (mmtp) REVERT: C 108 ASP cc_start: 0.7984 (m-30) cc_final: 0.7720 (m-30) REVERT: C 286 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.6506 (tp30) REVERT: C 289 ARG cc_start: 0.8478 (ttp80) cc_final: 0.7804 (ttp-170) REVERT: C 293 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7618 (mm-30) REVERT: C 294 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8389 (tt) REVERT: C 297 GLU cc_start: 0.8533 (tt0) cc_final: 0.8276 (tt0) REVERT: C 301 LYS cc_start: 0.7716 (tttm) cc_final: 0.7515 (ttpp) REVERT: C 303 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8070 (mm-30) REVERT: C 356 GLU cc_start: 0.7922 (tt0) cc_final: 0.7637 (mt-10) REVERT: C 438 LYS cc_start: 0.8298 (mttt) cc_final: 0.7845 (mmtm) REVERT: C 459 ARG cc_start: 0.7339 (mmp-170) cc_final: 0.6913 (mmp-170) REVERT: C 484 GLN cc_start: 0.8231 (tp40) cc_final: 0.7978 (mm-40) REVERT: C 485 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7004 (mt-10) REVERT: C 487 GLU cc_start: 0.8009 (tp30) cc_final: 0.7320 (tt0) REVERT: C 513 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6784 (ttmt) REVERT: D 93 LYS cc_start: 0.8997 (tttt) cc_final: 0.8737 (ttmt) REVERT: D 245 LYS cc_start: 0.8329 (tttm) cc_final: 0.8055 (ttpt) REVERT: D 250 GLU cc_start: 0.7628 (tt0) cc_final: 0.7270 (pt0) REVERT: D 321 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.8046 (mmm-85) REVERT: D 382 GLN cc_start: 0.8063 (mm110) cc_final: 0.7607 (mt0) REVERT: E 137 LYS cc_start: 0.8498 (ttpp) cc_final: 0.8159 (mtpm) REVERT: E 315 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7681 (mp0) REVERT: F 108 LYS cc_start: 0.8845 (tttt) cc_final: 0.8641 (ttpp) REVERT: F 154 MET cc_start: 0.9076 (mmm) cc_final: 0.8823 (tpt) REVERT: F 242 ARG cc_start: 0.7849 (mtt90) cc_final: 0.7399 (mtt90) REVERT: F 245 LYS cc_start: 0.7936 (tttm) cc_final: 0.7620 (ttpt) REVERT: F 358 ASN cc_start: 0.8208 (m-40) cc_final: 0.7980 (t0) REVERT: F 435 MET cc_start: 0.8732 (ttp) cc_final: 0.8505 (ttm) REVERT: I 87 ARG cc_start: 0.7159 (mtt90) cc_final: 0.6875 (mtm180) REVERT: I 89 ASP cc_start: 0.7356 (m-30) cc_final: 0.6858 (m-30) REVERT: I 99 LYS cc_start: 0.8190 (tttt) cc_final: 0.7721 (mttt) REVERT: I 115 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7303 (mp) REVERT: I 117 ASP cc_start: 0.8018 (m-30) cc_final: 0.7672 (m-30) REVERT: I 161 LYS cc_start: 0.8112 (mttp) cc_final: 0.7564 (ptmt) REVERT: I 201 ASP cc_start: 0.7830 (t0) cc_final: 0.7433 (m-30) REVERT: I 208 MET cc_start: 0.8792 (mmt) cc_final: 0.8458 (mmm) REVERT: I 226 ASP cc_start: 0.7602 (t0) cc_final: 0.7140 (m-30) REVERT: J 22 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7812 (tm-30) REVERT: J 41 GLU cc_start: 0.7940 (tp30) cc_final: 0.7604 (tp30) REVERT: J 45 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8916 (mm) REVERT: J 61 GLU cc_start: 0.7819 (tt0) cc_final: 0.7568 (mt-10) REVERT: J 76 MET cc_start: 0.7307 (mtm) cc_final: 0.6989 (tmm) REVERT: J 85 ARG cc_start: 0.7558 (mtt180) cc_final: 0.6960 (mmt180) REVERT: J 94 LEU cc_start: 0.8373 (tm) cc_final: 0.8160 (tp) REVERT: J 99 LYS cc_start: 0.7809 (tttt) cc_final: 0.7362 (ttmp) REVERT: J 197 GLU cc_start: 0.7885 (mp0) cc_final: 0.7143 (mp0) REVERT: J 201 ASP cc_start: 0.7574 (t0) cc_final: 0.7128 (m-30) REVERT: K 108 ASP cc_start: 0.6983 (t0) cc_final: 0.6650 (t0) REVERT: K 117 ASP cc_start: 0.8006 (m-30) cc_final: 0.7748 (t0) REVERT: K 168 ASP cc_start: 0.7780 (t70) cc_final: 0.7576 (t70) REVERT: L 57 ASN cc_start: 0.7757 (t160) cc_final: 0.7556 (t0) REVERT: N 53 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8220 (ttpp) REVERT: N 81 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7344 (mtp) REVERT: N 93 ASP cc_start: 0.7410 (m-30) cc_final: 0.7192 (m-30) REVERT: Q 16 GLU cc_start: 0.7780 (tp30) cc_final: 0.7527 (tp30) REVERT: Q 47 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7405 (mm-30) REVERT: Q 64 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: Q 107 LEU cc_start: 0.6904 (mt) cc_final: 0.6680 (tp) REVERT: Q 117 GLN cc_start: 0.8493 (mm-40) cc_final: 0.7928 (mp-120) REVERT: Q 205 LYS cc_start: 0.7982 (tptt) cc_final: 0.7279 (mptt) REVERT: R 34 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6706 (tm130) REVERT: R 50 GLN cc_start: 0.7590 (tp40) cc_final: 0.6927 (tp40) REVERT: R 117 GLN cc_start: 0.8657 (mt0) cc_final: 0.8324 (mp10) REVERT: R 135 GLN cc_start: 0.8181 (tt0) cc_final: 0.7956 (tt0) REVERT: S 34 GLN cc_start: 0.7188 (tt0) cc_final: 0.6967 (tm-30) REVERT: S 60 TYR cc_start: 0.8200 (m-80) cc_final: 0.7944 (m-80) REVERT: S 67 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6956 (mm-30) REVERT: S 77 ASP cc_start: 0.7507 (t0) cc_final: 0.6967 (t70) REVERT: S 161 MET cc_start: 0.7229 (ttp) cc_final: 0.6870 (ttp) REVERT: S 197 TYR cc_start: 0.6788 (m-80) cc_final: 0.6539 (m-80) REVERT: S 210 GLU cc_start: 0.7523 (pm20) cc_final: 0.7124 (tp30) REVERT: S 223 LYS cc_start: 0.8400 (tptt) cc_final: 0.8131 (tptt) outliers start: 120 outliers final: 31 residues processed: 914 average time/residue: 1.6331 time to fit residues: 1819.0669 Evaluate side-chains 767 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 725 time to evaluate : 5.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain N residue 81 MET Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain T residue 135 HIS Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 284 optimal weight: 10.0000 chunk 158 optimal weight: 0.0470 chunk 425 optimal weight: 6.9990 chunk 348 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 512 optimal weight: 4.9990 chunk 553 optimal weight: 3.9990 chunk 456 optimal weight: 4.9990 chunk 507 optimal weight: 0.5980 chunk 174 optimal weight: 6.9990 chunk 410 optimal weight: 40.0000 overall best weight: 2.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS C 157 ASN C 164 HIS D 38 ASN D 42 GLN E 209 GLN F 181 ASN F 382 GLN F 482 GLN G 88 GLN ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 HIS I 100 GLN J 221 ASN ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 ASN L 67 ASN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 HIS M 90 GLN ** O 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN R 142 ASN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 135 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 46035 Z= 0.348 Angle : 0.619 10.552 62132 Z= 0.323 Chirality : 0.045 0.197 6969 Planarity : 0.005 0.046 8036 Dihedral : 5.461 110.227 6221 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.37 % Allowed : 13.11 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 0.89 (0.11), residues: 5650 helix: 1.41 (0.10), residues: 2815 sheet: 0.29 (0.19), residues: 683 loop : -0.32 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 567 HIS 0.019 0.002 HIS K 14 PHE 0.031 0.002 PHE H 155 TYR 0.027 0.002 TYR S 139 ARG 0.008 0.001 ARG L 4 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 767 time to evaluate : 5.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8852 (m) REVERT: A 163 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8381 (mmtt) REVERT: A 193 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7379 (mt-10) REVERT: A 231 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7889 (mp10) REVERT: A 492 ILE cc_start: 0.8266 (mt) cc_final: 0.8049 (mp) REVERT: A 564 LYS cc_start: 0.8216 (ptpp) cc_final: 0.7513 (mtpt) REVERT: A 571 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7543 (ttm170) REVERT: A 584 MET cc_start: 0.8999 (mtm) cc_final: 0.8539 (mtm) REVERT: B 195 GLU cc_start: 0.7546 (tt0) cc_final: 0.6899 (tt0) REVERT: B 297 GLU cc_start: 0.7990 (tt0) cc_final: 0.7735 (tt0) REVERT: B 401 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8047 (mt-10) REVERT: C 17 THR cc_start: 0.8254 (p) cc_final: 0.7886 (m) REVERT: C 56 ARG cc_start: 0.8525 (ttm170) cc_final: 0.8011 (ttp-170) REVERT: C 84 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8570 (mmtp) REVERT: C 108 ASP cc_start: 0.8062 (m-30) cc_final: 0.7773 (m-30) REVERT: C 279 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7887 (tp30) REVERT: C 286 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.6588 (tp30) REVERT: C 289 ARG cc_start: 0.8587 (ttp80) cc_final: 0.7643 (ttp-170) REVERT: C 293 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7587 (mm-30) REVERT: C 297 GLU cc_start: 0.8477 (tt0) cc_final: 0.8194 (tt0) REVERT: C 301 LYS cc_start: 0.7643 (tttm) cc_final: 0.7425 (ttpp) REVERT: C 303 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: C 356 GLU cc_start: 0.8040 (tt0) cc_final: 0.7629 (mt-10) REVERT: C 438 LYS cc_start: 0.8327 (mttt) cc_final: 0.7857 (mmtm) REVERT: C 485 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7107 (mt-10) REVERT: C 487 GLU cc_start: 0.8017 (tp30) cc_final: 0.7290 (tm-30) REVERT: C 491 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: C 513 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6927 (ttmt) REVERT: C 540 MET cc_start: 0.8466 (mtp) cc_final: 0.8141 (mtp) REVERT: C 580 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7853 (mttp) REVERT: C 591 LYS cc_start: 0.8331 (tppp) cc_final: 0.7938 (tppt) REVERT: D 93 LYS cc_start: 0.8927 (tttt) cc_final: 0.8669 (ttmt) REVERT: D 250 GLU cc_start: 0.7479 (tt0) cc_final: 0.7057 (pt0) REVERT: D 382 GLN cc_start: 0.8103 (mm110) cc_final: 0.7730 (mt0) REVERT: E 95 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8800 (t) REVERT: E 137 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8116 (mtpm) REVERT: E 299 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7840 (t0) REVERT: E 315 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7886 (mp0) REVERT: E 342 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: E 367 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7626 (t70) REVERT: E 374 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8794 (pm20) REVERT: E 491 MET cc_start: 0.9158 (mmm) cc_final: 0.8951 (mtt) REVERT: F 81 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8355 (mttp) REVERT: F 96 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8537 (m) REVERT: F 108 LYS cc_start: 0.8916 (tttt) cc_final: 0.8652 (ttpp) REVERT: F 154 MET cc_start: 0.9129 (mmm) cc_final: 0.8871 (tpt) REVERT: F 242 ARG cc_start: 0.7927 (mtt90) cc_final: 0.7458 (mtm110) REVERT: F 245 LYS cc_start: 0.7915 (tttm) cc_final: 0.7607 (ttmt) REVERT: F 250 GLU cc_start: 0.8112 (tt0) cc_final: 0.7862 (tt0) REVERT: F 358 ASN cc_start: 0.8141 (m-40) cc_final: 0.7909 (t0) REVERT: G 211 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7503 (mmt180) REVERT: I 89 ASP cc_start: 0.7360 (m-30) cc_final: 0.6956 (m-30) REVERT: I 99 LYS cc_start: 0.8214 (tttt) cc_final: 0.7829 (mttm) REVERT: I 115 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7249 (mp) REVERT: I 117 ASP cc_start: 0.8108 (m-30) cc_final: 0.7659 (m-30) REVERT: I 161 LYS cc_start: 0.8146 (mttp) cc_final: 0.7589 (ptmt) REVERT: I 208 MET cc_start: 0.8853 (mmt) cc_final: 0.8468 (mmm) REVERT: J 41 GLU cc_start: 0.7865 (tp30) cc_final: 0.7607 (tp30) REVERT: J 59 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7555 (ttmt) REVERT: J 76 MET cc_start: 0.7303 (mtm) cc_final: 0.6915 (tmm) REVERT: J 85 ARG cc_start: 0.7486 (mtt180) cc_final: 0.6887 (mmt-90) REVERT: J 99 LYS cc_start: 0.7849 (tttt) cc_final: 0.7387 (ttmp) REVERT: J 157 ILE cc_start: 0.8538 (mp) cc_final: 0.8290 (pt) REVERT: J 197 GLU cc_start: 0.7854 (mp0) cc_final: 0.7150 (mp0) REVERT: J 201 ASP cc_start: 0.7622 (t0) cc_final: 0.7204 (m-30) REVERT: K 60 LYS cc_start: 0.7618 (mtpp) cc_final: 0.7212 (ttmt) REVERT: K 117 ASP cc_start: 0.7917 (m-30) cc_final: 0.7559 (m-30) REVERT: L 57 ASN cc_start: 0.7995 (t0) cc_final: 0.7617 (t0) REVERT: N 53 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8147 (ttpp) REVERT: N 93 ASP cc_start: 0.7288 (m-30) cc_final: 0.7082 (m-30) REVERT: O 91 ASN cc_start: 0.8865 (m-40) cc_final: 0.8451 (m110) REVERT: Q 117 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8023 (mp-120) REVERT: Q 205 LYS cc_start: 0.8073 (tptt) cc_final: 0.7289 (mptt) REVERT: R 34 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6788 (tm130) REVERT: R 50 GLN cc_start: 0.7493 (tp-100) cc_final: 0.6974 (tp40) REVERT: R 58 LYS cc_start: 0.7837 (tppt) cc_final: 0.7537 (tptm) REVERT: R 117 GLN cc_start: 0.8648 (mt0) cc_final: 0.8316 (mp10) REVERT: R 135 GLN cc_start: 0.8241 (tt0) cc_final: 0.7681 (tt0) REVERT: R 259 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8153 (tm) REVERT: S 34 GLN cc_start: 0.7333 (tt0) cc_final: 0.7094 (tm-30) REVERT: S 161 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6961 (ttp) REVERT: S 195 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7273 (mp0) REVERT: S 197 TYR cc_start: 0.6761 (m-80) cc_final: 0.6466 (m-80) REVERT: S 199 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8784 (tm) REVERT: S 210 GLU cc_start: 0.7657 (pm20) cc_final: 0.7356 (tp30) outliers start: 167 outliers final: 68 residues processed: 854 average time/residue: 1.6580 time to fit residues: 1726.0756 Evaluate side-chains 803 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 715 time to evaluate : 5.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 580 LYS Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 111 HIS Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 199 LEU Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 161 MET Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 201 LYS Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 97 LYS Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain T residue 150 ASN Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 506 optimal weight: 4.9990 chunk 385 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 244 optimal weight: 0.0980 chunk 343 optimal weight: 0.6980 chunk 514 optimal weight: 8.9990 chunk 544 optimal weight: 30.0000 chunk 268 optimal weight: 1.9990 chunk 487 optimal weight: 5.9990 chunk 146 optimal weight: 0.0170 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN C 65 GLN C 157 ASN D 42 GLN D 345 ASN E 133 ASN F 382 GLN F 482 GLN G 88 GLN ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN J 39 ASN J 67 GLN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN R 142 ASN R 165 GLN S 117 GLN S 142 ASN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 46035 Z= 0.155 Angle : 0.514 11.258 62132 Z= 0.268 Chirality : 0.040 0.189 6969 Planarity : 0.004 0.058 8036 Dihedral : 4.903 100.566 6221 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.56 % Allowed : 14.62 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 1.18 (0.11), residues: 5650 helix: 1.72 (0.10), residues: 2823 sheet: 0.31 (0.19), residues: 694 loop : -0.26 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 19 HIS 0.011 0.001 HIS K 14 PHE 0.020 0.001 PHE B 547 TYR 0.035 0.001 TYR G 253 ARG 0.013 0.000 ARG M 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 791 time to evaluate : 5.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8623 (mmtm) cc_final: 0.8346 (mmtt) REVERT: A 193 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 231 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7801 (mp10) REVERT: A 552 ARG cc_start: 0.8277 (mtp180) cc_final: 0.7955 (mtp-110) REVERT: A 564 LYS cc_start: 0.8241 (ptpp) cc_final: 0.7624 (mtpt) REVERT: A 571 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7537 (ttm170) REVERT: A 584 MET cc_start: 0.8989 (mtm) cc_final: 0.8545 (mtm) REVERT: B 194 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.8000 (pt) REVERT: B 195 GLU cc_start: 0.7551 (tt0) cc_final: 0.7037 (tm-30) REVERT: B 297 GLU cc_start: 0.7939 (tt0) cc_final: 0.7699 (tt0) REVERT: B 346 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.8902 (ttt) REVERT: B 401 GLU cc_start: 0.8218 (mt-10) cc_final: 0.8015 (mt-10) REVERT: B 437 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7868 (tppp) REVERT: B 452 ILE cc_start: 0.8533 (tp) cc_final: 0.8236 (pt) REVERT: B 462 ASP cc_start: 0.7006 (p0) cc_final: 0.6408 (p0) REVERT: B 466 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7258 (m-30) REVERT: B 530 ARG cc_start: 0.8064 (ptp-110) cc_final: 0.7821 (ptp-170) REVERT: C 56 ARG cc_start: 0.8466 (ttm170) cc_final: 0.7959 (ttp-170) REVERT: C 84 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8551 (mmtp) REVERT: C 108 ASP cc_start: 0.8015 (m-30) cc_final: 0.7726 (m-30) REVERT: C 123 ASN cc_start: 0.8718 (t0) cc_final: 0.8499 (t0) REVERT: C 293 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7568 (mm-30) REVERT: C 297 GLU cc_start: 0.8251 (tt0) cc_final: 0.7929 (tt0) REVERT: C 303 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8176 (mm-30) REVERT: C 356 GLU cc_start: 0.8095 (tt0) cc_final: 0.7719 (mt-10) REVERT: C 399 GLU cc_start: 0.8247 (tp30) cc_final: 0.7845 (tp30) REVERT: C 438 LYS cc_start: 0.8335 (mttt) cc_final: 0.7830 (mmtm) REVERT: C 459 ARG cc_start: 0.7514 (mmp-170) cc_final: 0.7151 (mmp-170) REVERT: C 485 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7028 (mt-10) REVERT: C 487 GLU cc_start: 0.7954 (tp30) cc_final: 0.7274 (tt0) REVERT: C 491 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: C 513 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6855 (ttmt) REVERT: C 540 MET cc_start: 0.8406 (mtp) cc_final: 0.8126 (mtp) REVERT: D 250 GLU cc_start: 0.7471 (tt0) cc_final: 0.7040 (pt0) REVERT: D 382 GLN cc_start: 0.8099 (mm110) cc_final: 0.7737 (mt0) REVERT: E 137 LYS cc_start: 0.8514 (ttpp) cc_final: 0.8231 (mtpm) REVERT: E 141 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7594 (ptm160) REVERT: E 315 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7776 (mp0) REVERT: E 342 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7878 (tm-30) REVERT: E 374 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8734 (pm20) REVERT: E 423 TYR cc_start: 0.9238 (t80) cc_final: 0.9033 (t80) REVERT: E 493 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8084 (mtpp) REVERT: F 81 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8434 (mttp) REVERT: F 108 LYS cc_start: 0.8869 (tttt) cc_final: 0.8605 (ttpp) REVERT: F 154 MET cc_start: 0.9074 (mmm) cc_final: 0.8850 (tpt) REVERT: F 242 ARG cc_start: 0.7822 (mtt90) cc_final: 0.7405 (mtt90) REVERT: F 245 LYS cc_start: 0.7938 (tttm) cc_final: 0.7641 (ttmt) REVERT: F 250 GLU cc_start: 0.8047 (tt0) cc_final: 0.7841 (tt0) REVERT: F 358 ASN cc_start: 0.8113 (m-40) cc_final: 0.7848 (t0) REVERT: F 410 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8093 (mmt) REVERT: G 211 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7464 (mmt180) REVERT: I 89 ASP cc_start: 0.7364 (m-30) cc_final: 0.6989 (m-30) REVERT: I 99 LYS cc_start: 0.8207 (tttt) cc_final: 0.7834 (mttm) REVERT: I 115 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7146 (mp) REVERT: I 117 ASP cc_start: 0.7884 (m-30) cc_final: 0.7437 (m-30) REVERT: I 161 LYS cc_start: 0.8113 (mttp) cc_final: 0.7621 (ptmt) REVERT: I 184 TYR cc_start: 0.8656 (m-80) cc_final: 0.8443 (m-80) REVERT: I 208 MET cc_start: 0.8735 (mmt) cc_final: 0.8465 (mmm) REVERT: I 226 ASP cc_start: 0.7654 (m-30) cc_final: 0.7392 (m-30) REVERT: J 39 ASN cc_start: 0.8412 (m-40) cc_final: 0.8185 (t0) REVERT: J 41 GLU cc_start: 0.7899 (tp30) cc_final: 0.7574 (tp30) REVERT: J 59 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7584 (ttmt) REVERT: J 76 MET cc_start: 0.7393 (mtm) cc_final: 0.7010 (tmm) REVERT: J 85 ARG cc_start: 0.7582 (mtt180) cc_final: 0.6930 (mmt-90) REVERT: J 99 LYS cc_start: 0.7847 (tttt) cc_final: 0.7372 (ttmm) REVERT: J 157 ILE cc_start: 0.8546 (mp) cc_final: 0.8326 (pt) REVERT: J 197 GLU cc_start: 0.7828 (mp0) cc_final: 0.7135 (mp0) REVERT: J 201 ASP cc_start: 0.7614 (t0) cc_final: 0.7242 (m-30) REVERT: K 60 LYS cc_start: 0.7537 (mtpp) cc_final: 0.7162 (ttmt) REVERT: K 117 ASP cc_start: 0.7962 (m-30) cc_final: 0.7612 (m-30) REVERT: L 57 ASN cc_start: 0.7799 (t0) cc_final: 0.7458 (t0) REVERT: L 69 TYR cc_start: 0.7946 (p90) cc_final: 0.7546 (p90) REVERT: N 53 LYS cc_start: 0.8574 (ttmm) cc_final: 0.8165 (ttpp) REVERT: O 91 ASN cc_start: 0.8830 (m-40) cc_final: 0.8291 (m110) REVERT: Q 42 LEU cc_start: 0.7303 (mt) cc_final: 0.6545 (mt) REVERT: Q 107 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6347 (pp) REVERT: Q 117 GLN cc_start: 0.8475 (mm-40) cc_final: 0.7965 (mp10) REVERT: Q 205 LYS cc_start: 0.8009 (tptt) cc_final: 0.7237 (mptt) REVERT: R 34 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6636 (tm-30) REVERT: R 50 GLN cc_start: 0.7443 (tp-100) cc_final: 0.7060 (tp40) REVERT: R 58 LYS cc_start: 0.7815 (tppt) cc_final: 0.7594 (tptm) REVERT: R 117 GLN cc_start: 0.8524 (mt0) cc_final: 0.8295 (mp10) REVERT: R 135 GLN cc_start: 0.8181 (tt0) cc_final: 0.7633 (tt0) REVERT: R 259 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8118 (tm) REVERT: S 141 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8239 (tptt) REVERT: S 161 MET cc_start: 0.7350 (ttp) cc_final: 0.6965 (ttp) REVERT: S 195 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7302 (mp0) REVERT: S 197 TYR cc_start: 0.6767 (m-80) cc_final: 0.6449 (m-80) REVERT: S 199 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8808 (tm) REVERT: S 201 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6815 (tppp) REVERT: S 223 LYS cc_start: 0.8648 (tptt) cc_final: 0.8374 (tptt) outliers start: 127 outliers final: 40 residues processed: 863 average time/residue: 1.6733 time to fit residues: 1756.7714 Evaluate side-chains 789 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 727 time to evaluate : 5.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain H residue 111 HIS Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 201 LYS Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 453 optimal weight: 9.9990 chunk 308 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 405 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 chunk 464 optimal weight: 7.9990 chunk 376 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 277 optimal weight: 4.9990 chunk 488 optimal weight: 20.0000 chunk 137 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 157 ASN B 224 ASN ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN C 157 ASN D 42 GLN D 54 ASN F 382 GLN F 482 GLN G 88 GLN ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 GLN J 221 ASN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 142 ASN R 142 ASN R 184 HIS S 165 GLN T 56 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 46035 Z= 0.389 Angle : 0.616 11.241 62132 Z= 0.318 Chirality : 0.045 0.193 6969 Planarity : 0.005 0.069 8036 Dihedral : 5.199 107.491 6221 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.61 % Allowed : 14.91 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 0.94 (0.11), residues: 5650 helix: 1.60 (0.10), residues: 2827 sheet: 0.19 (0.20), residues: 670 loop : -0.49 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 567 HIS 0.018 0.001 HIS G 194 PHE 0.032 0.002 PHE H 155 TYR 0.046 0.002 TYR G 223 ARG 0.010 0.001 ARG R 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 738 time to evaluate : 5.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8882 (m) REVERT: A 151 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8510 (m-30) REVERT: A 163 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8271 (mmtt) REVERT: A 193 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7323 (mt-10) REVERT: A 231 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7842 (mp10) REVERT: A 487 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7501 (tp30) REVERT: A 571 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7533 (ttm170) REVERT: B 195 GLU cc_start: 0.7572 (tt0) cc_final: 0.6914 (tt0) REVERT: B 297 GLU cc_start: 0.8019 (tt0) cc_final: 0.7772 (tt0) REVERT: B 346 MET cc_start: 0.9407 (OUTLIER) cc_final: 0.9014 (ttt) REVERT: B 401 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8016 (mt-10) REVERT: B 437 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7868 (tppp) REVERT: B 462 ASP cc_start: 0.7006 (p0) cc_final: 0.6428 (p0) REVERT: B 466 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7170 (m-30) REVERT: B 513 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7112 (ttmt) REVERT: B 530 ARG cc_start: 0.8124 (ptp-110) cc_final: 0.7915 (ptp-170) REVERT: C 56 ARG cc_start: 0.8514 (ttm170) cc_final: 0.7988 (ttp-170) REVERT: C 84 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8614 (mmtp) REVERT: C 108 ASP cc_start: 0.8110 (m-30) cc_final: 0.7781 (m-30) REVERT: C 123 ASN cc_start: 0.8763 (t0) cc_final: 0.8494 (t0) REVERT: C 220 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8842 (mtpp) REVERT: C 279 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7886 (tp30) REVERT: C 286 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: C 293 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7622 (mm-30) REVERT: C 297 GLU cc_start: 0.8244 (tt0) cc_final: 0.7994 (tt0) REVERT: C 347 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8456 (mpp) REVERT: C 356 GLU cc_start: 0.8164 (tt0) cc_final: 0.7705 (mt-10) REVERT: C 399 GLU cc_start: 0.8293 (tp30) cc_final: 0.7878 (tp30) REVERT: C 438 LYS cc_start: 0.8357 (mttt) cc_final: 0.7849 (mmtm) REVERT: C 485 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7070 (mt-10) REVERT: C 487 GLU cc_start: 0.7968 (tp30) cc_final: 0.7283 (tt0) REVERT: C 491 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: C 513 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6766 (ttmt) REVERT: C 517 ASP cc_start: 0.8187 (m-30) cc_final: 0.7835 (m-30) REVERT: D 250 GLU cc_start: 0.7485 (tt0) cc_final: 0.7065 (pt0) REVERT: D 382 GLN cc_start: 0.8078 (mm110) cc_final: 0.7666 (mt0) REVERT: D 452 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7226 (mp) REVERT: D 485 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7344 (mtt-85) REVERT: E 95 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8761 (t) REVERT: E 137 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8282 (mtpm) REVERT: E 141 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7747 (ptm160) REVERT: E 234 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.9131 (mtm) REVERT: E 315 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7966 (mp0) REVERT: E 342 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: E 367 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7698 (t70) REVERT: E 374 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8685 (pm20) REVERT: F 81 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8345 (mttp) REVERT: F 108 LYS cc_start: 0.8896 (tttt) cc_final: 0.8622 (ttpp) REVERT: F 242 ARG cc_start: 0.7916 (mtt90) cc_final: 0.7474 (mtm110) REVERT: F 245 LYS cc_start: 0.7958 (tttm) cc_final: 0.7667 (ttmt) REVERT: F 250 GLU cc_start: 0.8073 (tt0) cc_final: 0.7854 (tt0) REVERT: F 305 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7732 (mt-10) REVERT: F 358 ASN cc_start: 0.8189 (m-40) cc_final: 0.7844 (t0) REVERT: F 410 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7524 (mmt) REVERT: G 211 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7636 (mmt180) REVERT: H 78 ASP cc_start: 0.7109 (m-30) cc_final: 0.6873 (m-30) REVERT: I 89 ASP cc_start: 0.7488 (m-30) cc_final: 0.7070 (m-30) REVERT: I 99 LYS cc_start: 0.8262 (tttt) cc_final: 0.7876 (mttm) REVERT: I 115 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7242 (mp) REVERT: I 117 ASP cc_start: 0.8028 (m-30) cc_final: 0.7466 (m-30) REVERT: I 161 LYS cc_start: 0.8117 (mttp) cc_final: 0.7544 (ptmt) REVERT: I 184 TYR cc_start: 0.8727 (m-80) cc_final: 0.8482 (m-80) REVERT: I 201 ASP cc_start: 0.7905 (t0) cc_final: 0.7417 (m-30) REVERT: I 208 MET cc_start: 0.8934 (mmt) cc_final: 0.8500 (mmm) REVERT: I 226 ASP cc_start: 0.7755 (m-30) cc_final: 0.7195 (m-30) REVERT: J 39 ASN cc_start: 0.8472 (m-40) cc_final: 0.8196 (t0) REVERT: J 41 GLU cc_start: 0.7936 (tp30) cc_final: 0.7607 (tp30) REVERT: J 76 MET cc_start: 0.7459 (mtm) cc_final: 0.6982 (tmm) REVERT: J 85 ARG cc_start: 0.7502 (mtt180) cc_final: 0.6909 (mmt-90) REVERT: J 99 LYS cc_start: 0.7870 (tttt) cc_final: 0.7379 (ttmm) REVERT: J 157 ILE cc_start: 0.8567 (mp) cc_final: 0.8315 (pt) REVERT: J 197 GLU cc_start: 0.7861 (mp0) cc_final: 0.7168 (mp0) REVERT: J 201 ASP cc_start: 0.7600 (t0) cc_final: 0.7191 (m-30) REVERT: K 117 ASP cc_start: 0.7909 (m-30) cc_final: 0.7581 (m-30) REVERT: L 57 ASN cc_start: 0.8113 (t0) cc_final: 0.7673 (t0) REVERT: N 48 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7574 (ttp-170) REVERT: O 91 ASN cc_start: 0.8717 (m-40) cc_final: 0.8490 (m110) REVERT: Q 109 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: Q 117 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8003 (mp10) REVERT: Q 205 LYS cc_start: 0.8105 (tptt) cc_final: 0.7363 (mptt) REVERT: R 34 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6762 (tm130) REVERT: R 50 GLN cc_start: 0.7460 (tp-100) cc_final: 0.7162 (tp40) REVERT: R 117 GLN cc_start: 0.8565 (mt0) cc_final: 0.8319 (mp10) REVERT: R 135 GLN cc_start: 0.8304 (tt0) cc_final: 0.7739 (tt0) REVERT: R 259 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8150 (tm) REVERT: S 141 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8257 (tptt) REVERT: S 161 MET cc_start: 0.7351 (ttp) cc_final: 0.6967 (ttp) REVERT: S 195 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7372 (mp0) REVERT: S 197 TYR cc_start: 0.6854 (m-80) cc_final: 0.6591 (m-80) REVERT: S 199 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8695 (tm) REVERT: T 214 ASP cc_start: 0.8640 (m-30) cc_final: 0.8199 (m-30) outliers start: 179 outliers final: 81 residues processed: 837 average time/residue: 1.6688 time to fit residues: 1707.6750 Evaluate side-chains 823 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 713 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 111 HIS Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain T residue 150 ASN Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 183 optimal weight: 2.9990 chunk 490 optimal weight: 40.0000 chunk 107 optimal weight: 10.0000 chunk 319 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 544 optimal weight: 30.0000 chunk 452 optimal weight: 8.9990 chunk 252 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 140 ASN ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN C 157 ASN D 42 GLN E 461 ASN F 382 GLN F 482 GLN G 23 HIS G 88 GLN ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 221 ASN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 165 GLN R 142 ASN S 165 GLN T 56 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 46035 Z= 0.241 Angle : 0.549 11.095 62132 Z= 0.284 Chirality : 0.042 0.193 6969 Planarity : 0.004 0.052 8036 Dihedral : 4.987 105.215 6221 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.17 % Allowed : 16.16 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 1.03 (0.11), residues: 5650 helix: 1.71 (0.10), residues: 2827 sheet: 0.09 (0.19), residues: 715 loop : -0.45 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 19 HIS 0.005 0.001 HIS G 296 PHE 0.028 0.002 PHE K 141 TYR 0.025 0.001 TYR L 98 ARG 0.012 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 728 time to evaluate : 5.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8849 (m) REVERT: A 102 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8285 (mp) REVERT: A 151 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8461 (m-30) REVERT: A 163 LYS cc_start: 0.8692 (mmtm) cc_final: 0.8280 (mmtt) REVERT: A 193 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7337 (mt-10) REVERT: A 231 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7799 (mp10) REVERT: A 471 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7687 (pm20) REVERT: A 487 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7514 (tp30) REVERT: A 571 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7545 (ttm170) REVERT: A 612 PHE cc_start: 0.8549 (m-80) cc_final: 0.8308 (m-80) REVERT: B 195 GLU cc_start: 0.7583 (tt0) cc_final: 0.6890 (tt0) REVERT: B 297 GLU cc_start: 0.7992 (tt0) cc_final: 0.7776 (tt0) REVERT: B 346 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.8964 (ttt) REVERT: B 401 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8005 (mt-10) REVERT: B 437 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7822 (tppp) REVERT: B 466 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7413 (m-30) REVERT: B 513 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.7051 (ttmt) REVERT: B 530 ARG cc_start: 0.8064 (ptp-110) cc_final: 0.7843 (ptp-170) REVERT: C 56 ARG cc_start: 0.8521 (ttm170) cc_final: 0.7994 (ttp-170) REVERT: C 84 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8607 (mmtp) REVERT: C 108 ASP cc_start: 0.8089 (m-30) cc_final: 0.7780 (m-30) REVERT: C 123 ASN cc_start: 0.8764 (t0) cc_final: 0.8550 (t0) REVERT: C 286 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: C 293 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7615 (mm-30) REVERT: C 297 GLU cc_start: 0.8298 (tt0) cc_final: 0.7968 (tt0) REVERT: C 356 GLU cc_start: 0.8160 (tt0) cc_final: 0.7702 (mt-10) REVERT: C 399 GLU cc_start: 0.8294 (tp30) cc_final: 0.7958 (tp30) REVERT: C 438 LYS cc_start: 0.8271 (mttt) cc_final: 0.7794 (mmtm) REVERT: C 485 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7080 (mt-10) REVERT: C 487 GLU cc_start: 0.7976 (tp30) cc_final: 0.7300 (tt0) REVERT: C 491 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: C 513 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6753 (ttmt) REVERT: C 517 ASP cc_start: 0.8184 (m-30) cc_final: 0.7845 (m-30) REVERT: C 552 ARG cc_start: 0.7293 (ttt-90) cc_final: 0.6994 (mtp-110) REVERT: D 41 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8379 (m) REVERT: D 245 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7674 (mtpp) REVERT: D 250 GLU cc_start: 0.7455 (tt0) cc_final: 0.7131 (pt0) REVERT: D 305 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7857 (mt-10) REVERT: D 382 GLN cc_start: 0.8037 (mm110) cc_final: 0.7650 (mt0) REVERT: E 41 SER cc_start: 0.8086 (m) cc_final: 0.7615 (p) REVERT: E 137 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8279 (mtpm) REVERT: E 141 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7749 (ptm160) REVERT: E 315 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7874 (mp0) REVERT: E 342 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: E 367 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7695 (t70) REVERT: E 374 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8830 (pm20) REVERT: F 81 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8352 (mttp) REVERT: F 108 LYS cc_start: 0.8870 (tttt) cc_final: 0.8593 (ttpp) REVERT: F 242 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7492 (mtm110) REVERT: F 245 LYS cc_start: 0.8027 (tttm) cc_final: 0.7686 (ttmt) REVERT: F 250 GLU cc_start: 0.8024 (tt0) cc_final: 0.7820 (tt0) REVERT: F 305 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7664 (mt-10) REVERT: F 358 ASN cc_start: 0.8174 (m-40) cc_final: 0.7799 (t0) REVERT: F 410 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8052 (mmt) REVERT: G 211 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7581 (mmt180) REVERT: H 63 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7362 (ttm110) REVERT: H 78 ASP cc_start: 0.7017 (m-30) cc_final: 0.6747 (m-30) REVERT: I 89 ASP cc_start: 0.7440 (m-30) cc_final: 0.7019 (m-30) REVERT: I 99 LYS cc_start: 0.8251 (tttt) cc_final: 0.7871 (mttm) REVERT: I 115 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7215 (mp) REVERT: I 117 ASP cc_start: 0.7989 (m-30) cc_final: 0.7449 (m-30) REVERT: I 149 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: I 161 LYS cc_start: 0.8112 (mttp) cc_final: 0.7556 (ptmt) REVERT: I 184 TYR cc_start: 0.8704 (m-80) cc_final: 0.8421 (m-80) REVERT: I 201 ASP cc_start: 0.7892 (t0) cc_final: 0.7424 (m-30) REVERT: I 208 MET cc_start: 0.8882 (mmt) cc_final: 0.8515 (mmm) REVERT: I 226 ASP cc_start: 0.7746 (m-30) cc_final: 0.7174 (m-30) REVERT: J 39 ASN cc_start: 0.8402 (m-40) cc_final: 0.8158 (t0) REVERT: J 41 GLU cc_start: 0.7916 (tp30) cc_final: 0.7583 (tp30) REVERT: J 59 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7550 (ttmt) REVERT: J 76 MET cc_start: 0.7450 (mtm) cc_final: 0.6989 (tmm) REVERT: J 85 ARG cc_start: 0.7463 (mtt180) cc_final: 0.6853 (mmt-90) REVERT: J 99 LYS cc_start: 0.7865 (tttt) cc_final: 0.7367 (ttmm) REVERT: J 157 ILE cc_start: 0.8568 (mp) cc_final: 0.8327 (pt) REVERT: J 197 GLU cc_start: 0.7836 (mp0) cc_final: 0.7136 (mp0) REVERT: J 201 ASP cc_start: 0.7600 (t0) cc_final: 0.7239 (m-30) REVERT: J 221 ASN cc_start: 0.9047 (m110) cc_final: 0.8797 (m110) REVERT: K 117 ASP cc_start: 0.7885 (m-30) cc_final: 0.7553 (m-30) REVERT: L 57 ASN cc_start: 0.8060 (t0) cc_final: 0.7698 (t0) REVERT: N 48 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7559 (ttp-170) REVERT: N 53 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8140 (ttpp) REVERT: O 91 ASN cc_start: 0.8822 (m-40) cc_final: 0.8487 (m110) REVERT: Q 105 LEU cc_start: 0.6491 (mt) cc_final: 0.6198 (mp) REVERT: Q 109 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6310 (mp0) REVERT: Q 117 GLN cc_start: 0.8470 (mm-40) cc_final: 0.7983 (mp10) REVERT: Q 205 LYS cc_start: 0.8134 (tptt) cc_final: 0.7398 (mptt) REVERT: R 34 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6759 (tm130) REVERT: R 47 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7466 (tm-30) REVERT: R 50 GLN cc_start: 0.7442 (tp-100) cc_final: 0.7153 (tp40) REVERT: R 58 LYS cc_start: 0.7727 (tppt) cc_final: 0.7457 (tptp) REVERT: R 117 GLN cc_start: 0.8537 (mt0) cc_final: 0.8314 (mp10) REVERT: R 135 GLN cc_start: 0.8216 (tt0) cc_final: 0.7798 (tt0) REVERT: S 9 LYS cc_start: 0.6536 (OUTLIER) cc_final: 0.6315 (mptp) REVERT: S 141 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8211 (tptt) REVERT: S 197 TYR cc_start: 0.6808 (m-80) cc_final: 0.6539 (m-80) REVERT: S 199 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8704 (tm) REVERT: T 214 ASP cc_start: 0.8648 (m-30) cc_final: 0.8175 (m-30) outliers start: 157 outliers final: 71 residues processed: 822 average time/residue: 1.7530 time to fit residues: 1783.1873 Evaluate side-chains 807 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 706 time to evaluate : 6.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 88 GLN Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 111 HIS Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain T residue 150 ASN Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 525 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 310 optimal weight: 4.9990 chunk 397 optimal weight: 5.9990 chunk 308 optimal weight: 0.9980 chunk 458 optimal weight: 20.0000 chunk 304 optimal weight: 4.9990 chunk 542 optimal weight: 9.9990 chunk 339 optimal weight: 10.0000 chunk 330 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 140 ASN ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN C 157 ASN D 42 GLN F 382 GLN F 482 GLN G 194 HIS ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 GLN J 122 GLN J 194 ASN Q 142 ASN R 142 ASN S 117 GLN S 134 ASN S 165 GLN T 56 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 46035 Z= 0.465 Angle : 0.650 10.910 62132 Z= 0.335 Chirality : 0.047 0.201 6969 Planarity : 0.005 0.097 8036 Dihedral : 5.282 108.106 6221 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.67 % Allowed : 16.28 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.11), residues: 5650 helix: 1.50 (0.10), residues: 2835 sheet: 0.01 (0.19), residues: 682 loop : -0.65 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 19 HIS 0.007 0.001 HIS C 444 PHE 0.034 0.002 PHE H 155 TYR 0.036 0.002 TYR L 98 ARG 0.012 0.001 ARG M 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 718 time to evaluate : 5.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.9229 (OUTLIER) cc_final: 0.8839 (m) REVERT: A 102 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8362 (mp) REVERT: A 151 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8433 (m-30) REVERT: A 163 LYS cc_start: 0.8716 (mmtm) cc_final: 0.8355 (mmtt) REVERT: A 193 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7329 (mt-10) REVERT: A 487 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7522 (tp30) REVERT: A 612 PHE cc_start: 0.8547 (m-80) cc_final: 0.8317 (m-80) REVERT: B 195 GLU cc_start: 0.7669 (tt0) cc_final: 0.7121 (tm-30) REVERT: B 297 GLU cc_start: 0.8055 (tt0) cc_final: 0.7790 (tt0) REVERT: B 346 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.9038 (ttt) REVERT: B 401 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8009 (mt-10) REVERT: B 437 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7817 (tppp) REVERT: B 466 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: B 513 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7116 (ttmt) REVERT: B 530 ARG cc_start: 0.8104 (ptp-110) cc_final: 0.7877 (ptp-170) REVERT: C 56 ARG cc_start: 0.8530 (ttm170) cc_final: 0.8016 (ttp-170) REVERT: C 84 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8611 (mmtp) REVERT: C 108 ASP cc_start: 0.8104 (m-30) cc_final: 0.7779 (m-30) REVERT: C 220 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8868 (mtpp) REVERT: C 279 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: C 286 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: C 293 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7643 (mm-30) REVERT: C 297 GLU cc_start: 0.8401 (tt0) cc_final: 0.7996 (tt0) REVERT: C 347 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8524 (mpp) REVERT: C 356 GLU cc_start: 0.8241 (tt0) cc_final: 0.7750 (mt-10) REVERT: C 399 GLU cc_start: 0.8312 (tp30) cc_final: 0.7933 (tp30) REVERT: C 438 LYS cc_start: 0.8324 (mttt) cc_final: 0.7865 (mmtm) REVERT: C 485 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7095 (mt-10) REVERT: C 487 GLU cc_start: 0.8067 (tp30) cc_final: 0.7323 (tt0) REVERT: C 506 LYS cc_start: 0.7814 (mttp) cc_final: 0.7544 (mttp) REVERT: C 513 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6802 (ttmt) REVERT: C 517 ASP cc_start: 0.8216 (m-30) cc_final: 0.7893 (m-30) REVERT: C 580 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7776 (mttp) REVERT: D 245 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7697 (mtpp) REVERT: D 250 GLU cc_start: 0.7552 (tt0) cc_final: 0.7178 (pt0) REVERT: D 251 ASN cc_start: 0.7182 (OUTLIER) cc_final: 0.6742 (t0) REVERT: D 305 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7907 (mt-10) REVERT: D 382 GLN cc_start: 0.8135 (mm110) cc_final: 0.7747 (mt0) REVERT: D 485 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7290 (mtt-85) REVERT: E 137 LYS cc_start: 0.8575 (ttpp) cc_final: 0.8302 (mtpm) REVERT: E 141 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7775 (ptm160) REVERT: E 250 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7961 (mt-10) REVERT: E 315 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8003 (mt-10) REVERT: E 342 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: E 367 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7792 (t70) REVERT: E 374 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8847 (pm20) REVERT: E 412 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8663 (ttp-170) REVERT: F 81 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8338 (mttp) REVERT: F 108 LYS cc_start: 0.8887 (tttt) cc_final: 0.8628 (ttpp) REVERT: F 242 ARG cc_start: 0.7897 (mtt90) cc_final: 0.7455 (mtm110) REVERT: F 245 LYS cc_start: 0.8015 (tttm) cc_final: 0.7706 (ttmt) REVERT: F 250 GLU cc_start: 0.8045 (tt0) cc_final: 0.7824 (tt0) REVERT: F 305 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7731 (mt-10) REVERT: F 359 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8373 (m-30) REVERT: F 410 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7696 (mmt) REVERT: F 412 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7578 (ttm170) REVERT: G 211 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7582 (mmt180) REVERT: H 78 ASP cc_start: 0.7044 (m-30) cc_final: 0.6799 (m-30) REVERT: I 89 ASP cc_start: 0.7463 (m-30) cc_final: 0.7029 (m-30) REVERT: I 99 LYS cc_start: 0.8292 (tttt) cc_final: 0.7931 (mttm) REVERT: I 115 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7249 (mp) REVERT: I 117 ASP cc_start: 0.8106 (m-30) cc_final: 0.7549 (m-30) REVERT: I 161 LYS cc_start: 0.8071 (mttp) cc_final: 0.7643 (ptmt) REVERT: I 184 TYR cc_start: 0.8774 (m-80) cc_final: 0.8489 (m-80) REVERT: I 201 ASP cc_start: 0.7954 (t0) cc_final: 0.7258 (m-30) REVERT: I 226 ASP cc_start: 0.7801 (m-30) cc_final: 0.7159 (m-30) REVERT: J 41 GLU cc_start: 0.7882 (tp30) cc_final: 0.7639 (tp30) REVERT: J 76 MET cc_start: 0.7503 (mtm) cc_final: 0.6970 (tmm) REVERT: J 81 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7346 (tt) REVERT: J 85 ARG cc_start: 0.7614 (mtt180) cc_final: 0.6850 (mmt180) REVERT: J 99 LYS cc_start: 0.7884 (tttt) cc_final: 0.7382 (ttmm) REVERT: J 157 ILE cc_start: 0.8535 (mp) cc_final: 0.8278 (pt) REVERT: J 177 ILE cc_start: 0.7699 (mm) cc_final: 0.7493 (OUTLIER) REVERT: J 197 GLU cc_start: 0.7872 (mp0) cc_final: 0.7216 (mp0) REVERT: J 201 ASP cc_start: 0.7634 (t0) cc_final: 0.7269 (m-30) REVERT: J 221 ASN cc_start: 0.9075 (m110) cc_final: 0.8851 (m110) REVERT: K 69 LYS cc_start: 0.7486 (mttt) cc_final: 0.7218 (mtmt) REVERT: K 117 ASP cc_start: 0.7919 (m-30) cc_final: 0.7602 (m-30) REVERT: K 192 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8557 (m) REVERT: L 57 ASN cc_start: 0.8272 (t0) cc_final: 0.7845 (t0) REVERT: N 48 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7658 (ttp-170) REVERT: N 53 LYS cc_start: 0.8531 (ttmm) cc_final: 0.8132 (ttpp) REVERT: N 87 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.6622 (m-80) REVERT: O 91 ASN cc_start: 0.8812 (m-40) cc_final: 0.8509 (m110) REVERT: Q 117 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8087 (mp10) REVERT: Q 205 LYS cc_start: 0.8200 (tptt) cc_final: 0.7492 (mptt) REVERT: R 34 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6612 (tm-30) REVERT: R 47 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7496 (tm-30) REVERT: R 50 GLN cc_start: 0.7504 (tp-100) cc_final: 0.7196 (tp40) REVERT: R 58 LYS cc_start: 0.7779 (tppt) cc_final: 0.7506 (tptm) REVERT: R 117 GLN cc_start: 0.8594 (mt0) cc_final: 0.8374 (mp10) REVERT: R 135 GLN cc_start: 0.8300 (tt0) cc_final: 0.7743 (tt0) REVERT: R 142 ASN cc_start: 0.8613 (t160) cc_final: 0.8105 (t0) REVERT: S 9 LYS cc_start: 0.6494 (OUTLIER) cc_final: 0.6227 (mptp) REVERT: S 34 GLN cc_start: 0.7642 (tm-30) cc_final: 0.7392 (tm-30) REVERT: S 141 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8243 (tptt) REVERT: S 197 TYR cc_start: 0.6810 (m-80) cc_final: 0.6605 (m-80) REVERT: S 199 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8719 (tm) REVERT: S 223 LYS cc_start: 0.8695 (tptt) cc_final: 0.8484 (mptt) REVERT: T 172 GLU cc_start: 0.8670 (pm20) cc_final: 0.8383 (pm20) outliers start: 182 outliers final: 85 residues processed: 828 average time/residue: 1.6547 time to fit residues: 1667.5271 Evaluate side-chains 819 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 700 time to evaluate : 5.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 580 LYS Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 412 ARG Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 111 HIS Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 139 GLN Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 149 GLN Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain Q residue 214 GLU Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain T residue 150 ASN Chi-restraints excluded: chain T residue 153 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 335 optimal weight: 20.0000 chunk 216 optimal weight: 0.8980 chunk 324 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 344 optimal weight: 0.5980 chunk 369 optimal weight: 2.9990 chunk 268 optimal weight: 0.0770 chunk 50 optimal weight: 3.9990 chunk 426 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN C 157 ASN D 42 GLN F 265 ASN F 382 GLN F 482 GLN G 88 GLN H 137 ASN I 100 GLN Q 132 GLN S 134 ASN T 56 GLN ** T 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 46035 Z= 0.167 Angle : 0.530 11.664 62132 Z= 0.274 Chirality : 0.040 0.198 6969 Planarity : 0.004 0.058 8036 Dihedral : 4.772 99.211 6221 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.34 % Allowed : 17.83 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 1.10 (0.11), residues: 5650 helix: 1.81 (0.10), residues: 2830 sheet: 0.05 (0.19), residues: 706 loop : -0.48 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 19 HIS 0.005 0.001 HIS T 66 PHE 0.026 0.001 PHE B 547 TYR 0.025 0.001 TYR H 112 ARG 0.013 0.000 ARG M 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 733 time to evaluate : 4.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8749 (m) REVERT: A 102 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8276 (mp) REVERT: A 163 LYS cc_start: 0.8650 (mmtm) cc_final: 0.8258 (mmtt) REVERT: A 173 ARG cc_start: 0.8150 (ptt-90) cc_final: 0.7590 (ptt180) REVERT: A 193 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7350 (mt-10) REVERT: A 231 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7788 (mp10) REVERT: A 487 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7484 (tp30) REVERT: A 557 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8320 (p) REVERT: A 571 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7472 (ttm170) REVERT: A 583 SER cc_start: 0.8532 (p) cc_final: 0.8255 (m) REVERT: B 195 GLU cc_start: 0.7568 (tt0) cc_final: 0.7026 (tm-30) REVERT: B 289 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8207 (ttp-170) REVERT: B 297 GLU cc_start: 0.8030 (tt0) cc_final: 0.7783 (tt0) REVERT: B 346 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.8972 (ttt) REVERT: B 401 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7970 (mt-10) REVERT: B 437 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7821 (tppp) REVERT: B 452 ILE cc_start: 0.8546 (tp) cc_final: 0.8247 (pt) REVERT: B 466 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: B 513 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7134 (ttmt) REVERT: B 530 ARG cc_start: 0.8039 (ptp-110) cc_final: 0.7777 (ptp-170) REVERT: C 56 ARG cc_start: 0.8513 (ttm170) cc_final: 0.8008 (ttp-170) REVERT: C 84 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8641 (mmtp) REVERT: C 108 ASP cc_start: 0.7966 (m-30) cc_final: 0.7693 (m-30) REVERT: C 279 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: C 293 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7587 (mm-30) REVERT: C 297 GLU cc_start: 0.8244 (tt0) cc_final: 0.7857 (tt0) REVERT: C 356 GLU cc_start: 0.8160 (tt0) cc_final: 0.7731 (mt-10) REVERT: C 438 LYS cc_start: 0.8311 (mttt) cc_final: 0.7848 (mmtm) REVERT: C 485 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7040 (mt-10) REVERT: C 487 GLU cc_start: 0.7925 (tp30) cc_final: 0.7280 (tt0) REVERT: C 491 GLU cc_start: 0.7474 (tt0) cc_final: 0.7258 (tm-30) REVERT: C 513 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6712 (ttmt) REVERT: C 517 ASP cc_start: 0.8177 (m-30) cc_final: 0.7866 (m-30) REVERT: C 552 ARG cc_start: 0.7241 (ttt-90) cc_final: 0.6956 (mtp-110) REVERT: D 245 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7612 (mtpp) REVERT: D 250 GLU cc_start: 0.7517 (tt0) cc_final: 0.7111 (mt-10) REVERT: D 305 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7835 (mt-10) REVERT: D 382 GLN cc_start: 0.8033 (mm110) cc_final: 0.7605 (mt0) REVERT: E 41 SER cc_start: 0.8119 (m) cc_final: 0.7706 (p) REVERT: E 95 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8799 (t) REVERT: E 137 LYS cc_start: 0.8484 (ttpp) cc_final: 0.8261 (mtpm) REVERT: E 315 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7769 (mp0) REVERT: E 342 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: E 367 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7686 (t70) REVERT: E 374 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8622 (pm20) REVERT: F 81 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8410 (mttp) REVERT: F 108 LYS cc_start: 0.8857 (tttt) cc_final: 0.8581 (ttpp) REVERT: F 242 ARG cc_start: 0.7874 (mtt90) cc_final: 0.7508 (mtm110) REVERT: F 245 LYS cc_start: 0.8044 (tttm) cc_final: 0.7699 (ttmt) REVERT: F 250 GLU cc_start: 0.7998 (tt0) cc_final: 0.7795 (tt0) REVERT: F 305 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7618 (mt-10) REVERT: F 359 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: F 410 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7838 (mtt) REVERT: F 452 LEU cc_start: 0.8346 (mt) cc_final: 0.8065 (mt) REVERT: G 211 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7558 (mmt180) REVERT: H 78 ASP cc_start: 0.6913 (m-30) cc_final: 0.6592 (m-30) REVERT: I 89 ASP cc_start: 0.7397 (m-30) cc_final: 0.7026 (m-30) REVERT: I 99 LYS cc_start: 0.8229 (tttt) cc_final: 0.7890 (mttm) REVERT: I 115 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7190 (mp) REVERT: I 117 ASP cc_start: 0.7969 (m-30) cc_final: 0.7481 (m-30) REVERT: I 149 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: I 161 LYS cc_start: 0.8045 (mttp) cc_final: 0.7662 (ptmt) REVERT: I 184 TYR cc_start: 0.8704 (m-80) cc_final: 0.8470 (m-80) REVERT: I 201 ASP cc_start: 0.7855 (t0) cc_final: 0.7393 (m-30) REVERT: I 208 MET cc_start: 0.8786 (mmt) cc_final: 0.8470 (mmm) REVERT: I 226 ASP cc_start: 0.7806 (m-30) cc_final: 0.7184 (m-30) REVERT: J 41 GLU cc_start: 0.7892 (tp30) cc_final: 0.7632 (tp30) REVERT: J 59 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7561 (ttmt) REVERT: J 76 MET cc_start: 0.7454 (mtm) cc_final: 0.6957 (tmm) REVERT: J 85 ARG cc_start: 0.7513 (mtt180) cc_final: 0.6843 (mmt180) REVERT: J 99 LYS cc_start: 0.7854 (tttt) cc_final: 0.7363 (ttmm) REVERT: J 157 ILE cc_start: 0.8526 (mp) cc_final: 0.8306 (pt) REVERT: J 197 GLU cc_start: 0.7818 (mp0) cc_final: 0.7150 (mp0) REVERT: J 201 ASP cc_start: 0.7546 (t0) cc_final: 0.7205 (m-30) REVERT: J 208 MET cc_start: 0.8705 (mmm) cc_final: 0.8489 (mmm) REVERT: J 221 ASN cc_start: 0.9097 (m110) cc_final: 0.8869 (m110) REVERT: K 117 ASP cc_start: 0.7959 (m-30) cc_final: 0.7585 (m-30) REVERT: K 192 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8366 (m) REVERT: L 57 ASN cc_start: 0.7977 (t0) cc_final: 0.7688 (t0) REVERT: M 107 ARG cc_start: 0.7841 (mtm110) cc_final: 0.7503 (mtm110) REVERT: N 48 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7557 (ttp-170) REVERT: N 53 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8114 (ttpp) REVERT: O 91 ASN cc_start: 0.8791 (m-40) cc_final: 0.8485 (m110) REVERT: Q 117 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8038 (mp10) REVERT: Q 205 LYS cc_start: 0.8155 (tptt) cc_final: 0.7434 (mptt) REVERT: R 34 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.6768 (tm130) REVERT: R 47 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7521 (tm-30) REVERT: R 50 GLN cc_start: 0.7489 (tp-100) cc_final: 0.7198 (tp40) REVERT: R 135 GLN cc_start: 0.8201 (tt0) cc_final: 0.7942 (tt0) REVERT: R 142 ASN cc_start: 0.8608 (t160) cc_final: 0.8053 (t0) REVERT: S 9 LYS cc_start: 0.6554 (OUTLIER) cc_final: 0.6326 (mptp) REVERT: S 141 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8303 (tptt) REVERT: S 197 TYR cc_start: 0.6828 (m-80) cc_final: 0.6620 (m-80) REVERT: S 199 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8739 (tm) REVERT: S 223 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8513 (mptt) outliers start: 116 outliers final: 51 residues processed: 803 average time/residue: 1.6795 time to fit residues: 1640.3427 Evaluate side-chains 779 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 699 time to evaluate : 5.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 111 HIS Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 214 GLU Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 223 LYS Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain T residue 150 ASN Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 493 optimal weight: 6.9990 chunk 519 optimal weight: 6.9990 chunk 474 optimal weight: 6.9990 chunk 505 optimal weight: 0.5980 chunk 304 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 397 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 456 optimal weight: 5.9990 chunk 478 optimal weight: 0.9980 chunk 503 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN D 42 GLN F 265 ASN F 382 GLN F 482 GLN G 88 GLN G 194 HIS H 91 GLN ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN I 100 GLN J 39 ASN K 78 GLN N 98 ASN Q 142 ASN R 165 GLN T 56 GLN ** T 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 46035 Z= 0.405 Angle : 0.634 11.940 62132 Z= 0.326 Chirality : 0.045 0.234 6969 Planarity : 0.005 0.060 8036 Dihedral : 5.090 106.040 6221 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.70 % Allowed : 17.93 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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 (0.11), residues: 5650 helix: 1.64 (0.10), residues: 2835 sheet: -0.07 (0.19), residues: 705 loop : -0.62 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 567 HIS 0.006 0.001 HIS G 194 PHE 0.039 0.002 PHE K 141 TYR 0.023 0.002 TYR H 112 ARG 0.014 0.001 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 713 time to evaluate : 6.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8386 (mp) REVERT: A 163 LYS cc_start: 0.8632 (mmtm) cc_final: 0.8331 (mmtt) REVERT: A 193 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7375 (mt-10) REVERT: A 231 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7789 (mp10) REVERT: A 487 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7513 (tp30) REVERT: A 583 SER cc_start: 0.8465 (p) cc_final: 0.8176 (m) REVERT: A 612 PHE cc_start: 0.8530 (m-80) cc_final: 0.8301 (m-80) REVERT: B 58 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: B 195 GLU cc_start: 0.7693 (tt0) cc_final: 0.7133 (tm-30) REVERT: B 297 GLU cc_start: 0.8061 (tt0) cc_final: 0.7811 (tt0) REVERT: B 346 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.9027 (ttt) REVERT: B 401 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7987 (mt-10) REVERT: B 437 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7663 (tptm) REVERT: B 466 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7494 (m-30) REVERT: B 513 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.7092 (ttmt) REVERT: B 530 ARG cc_start: 0.8065 (ptp-110) cc_final: 0.7825 (ptp-170) REVERT: B 540 MET cc_start: 0.8319 (mtp) cc_final: 0.8021 (mtm) REVERT: B 604 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7636 (tm) REVERT: C 56 ARG cc_start: 0.8520 (ttm170) cc_final: 0.8010 (ttp-170) REVERT: C 84 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8622 (mmtp) REVERT: C 108 ASP cc_start: 0.7986 (m-30) cc_final: 0.7716 (m-30) REVERT: C 220 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8835 (mtpp) REVERT: C 279 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: C 293 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7667 (mm-30) REVERT: C 297 GLU cc_start: 0.8302 (tt0) cc_final: 0.7935 (tt0) REVERT: C 356 GLU cc_start: 0.8242 (tt0) cc_final: 0.7747 (mt-10) REVERT: C 438 LYS cc_start: 0.8418 (mttt) cc_final: 0.7958 (mmtm) REVERT: C 485 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7097 (mt-10) REVERT: C 487 GLU cc_start: 0.7989 (tp30) cc_final: 0.7302 (tt0) REVERT: C 491 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: C 506 LYS cc_start: 0.7771 (mttp) cc_final: 0.7540 (mttp) REVERT: C 513 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6960 (ttmt) REVERT: C 552 ARG cc_start: 0.7209 (ttt-90) cc_final: 0.6911 (mtp-110) REVERT: D 245 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7638 (mtpp) REVERT: D 250 GLU cc_start: 0.7589 (tt0) cc_final: 0.7188 (mt-10) REVERT: D 305 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7902 (mt-10) REVERT: D 382 GLN cc_start: 0.8046 (mm110) cc_final: 0.7648 (mt0) REVERT: E 41 SER cc_start: 0.8383 (m) cc_final: 0.7938 (p) REVERT: E 95 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8750 (t) REVERT: E 137 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8301 (mtpm) REVERT: E 141 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7750 (ptm160) REVERT: E 315 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7983 (mt-10) REVERT: E 342 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: E 367 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7734 (t70) REVERT: E 374 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8817 (pm20) REVERT: E 493 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8206 (mtpp) REVERT: F 81 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8321 (mttp) REVERT: F 108 LYS cc_start: 0.8879 (tttt) cc_final: 0.8609 (ttpp) REVERT: F 242 ARG cc_start: 0.7889 (mtt90) cc_final: 0.7460 (mtm110) REVERT: F 245 LYS cc_start: 0.8016 (tttm) cc_final: 0.7712 (ttmt) REVERT: F 250 GLU cc_start: 0.8086 (tt0) cc_final: 0.7876 (tt0) REVERT: F 305 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7695 (mt-10) REVERT: F 359 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8328 (m-30) REVERT: F 410 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7908 (mtt) REVERT: G 27 THR cc_start: 0.6893 (m) cc_final: 0.6327 (p) REVERT: G 211 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7603 (mmt180) REVERT: H 78 ASP cc_start: 0.6965 (m-30) cc_final: 0.6630 (m-30) REVERT: I 89 ASP cc_start: 0.7471 (m-30) cc_final: 0.7045 (m-30) REVERT: I 99 LYS cc_start: 0.8252 (tttt) cc_final: 0.7930 (mttm) REVERT: I 115 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7234 (mp) REVERT: I 117 ASP cc_start: 0.8071 (m-30) cc_final: 0.7529 (m-30) REVERT: I 131 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7378 (mtp-110) REVERT: I 149 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7541 (mp10) REVERT: I 161 LYS cc_start: 0.8067 (mttp) cc_final: 0.7636 (ptmt) REVERT: I 184 TYR cc_start: 0.8770 (m-80) cc_final: 0.8511 (m-80) REVERT: I 201 ASP cc_start: 0.7950 (t0) cc_final: 0.7254 (m-30) REVERT: I 226 ASP cc_start: 0.7871 (m-30) cc_final: 0.7212 (m-30) REVERT: J 41 GLU cc_start: 0.7948 (tp30) cc_final: 0.7663 (tp30) REVERT: J 76 MET cc_start: 0.7514 (mtm) cc_final: 0.6952 (tmm) REVERT: J 85 ARG cc_start: 0.7586 (mtt180) cc_final: 0.6845 (mmt180) REVERT: J 99 LYS cc_start: 0.7882 (tttt) cc_final: 0.7383 (ttmm) REVERT: J 157 ILE cc_start: 0.8531 (mp) cc_final: 0.8294 (pt) REVERT: J 177 ILE cc_start: 0.7483 (mm) cc_final: 0.7131 (OUTLIER) REVERT: J 197 GLU cc_start: 0.7877 (mp0) cc_final: 0.7189 (mp0) REVERT: J 201 ASP cc_start: 0.7602 (t0) cc_final: 0.7245 (m-30) REVERT: J 221 ASN cc_start: 0.9087 (m110) cc_final: 0.8851 (m110) REVERT: K 54 MET cc_start: 0.7541 (mmm) cc_final: 0.7333 (mmt) REVERT: K 117 ASP cc_start: 0.7925 (m-30) cc_final: 0.7565 (m-30) REVERT: K 192 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8506 (m) REVERT: L 57 ASN cc_start: 0.8218 (t0) cc_final: 0.7847 (t0) REVERT: N 48 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7586 (ttp-170) REVERT: N 53 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8063 (ttpp) REVERT: N 87 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.6717 (m-80) REVERT: O 91 ASN cc_start: 0.8783 (m-40) cc_final: 0.8454 (m110) REVERT: Q 117 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8085 (mp10) REVERT: Q 205 LYS cc_start: 0.8233 (tptt) cc_final: 0.7538 (mptt) REVERT: R 34 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: R 47 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7516 (tm-30) REVERT: R 50 GLN cc_start: 0.7537 (tp-100) cc_final: 0.7253 (tp40) REVERT: R 135 GLN cc_start: 0.8245 (tt0) cc_final: 0.7748 (tt0) REVERT: R 142 ASN cc_start: 0.8643 (t160) cc_final: 0.8120 (t0) REVERT: R 205 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.7037 (mmtp) REVERT: S 9 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.6258 (mptp) REVERT: S 141 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8282 (tptt) REVERT: S 197 TYR cc_start: 0.6869 (m-80) cc_final: 0.6664 (m-80) REVERT: S 223 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8523 (mptt) REVERT: T 172 GLU cc_start: 0.8685 (pm20) cc_final: 0.8356 (pm20) outliers start: 134 outliers final: 68 residues processed: 791 average time/residue: 1.6903 time to fit residues: 1629.7032 Evaluate side-chains 790 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 691 time to evaluate : 5.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 88 GLN Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 111 HIS Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain O residue 29 LYS Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain Q residue 214 GLU Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 223 LYS Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain T residue 150 ASN Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 332 optimal weight: 1.9990 chunk 534 optimal weight: 9.9990 chunk 326 optimal weight: 0.6980 chunk 253 optimal weight: 0.9980 chunk 371 optimal weight: 0.8980 chunk 560 optimal weight: 1.9990 chunk 516 optimal weight: 0.9980 chunk 446 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 344 optimal weight: 0.7980 chunk 273 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN D 42 GLN F 265 ASN F 382 GLN G 88 GLN ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN I 100 GLN N 98 ASN S 117 GLN T 56 GLN ** T 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 46035 Z= 0.200 Angle : 0.562 12.580 62132 Z= 0.289 Chirality : 0.041 0.224 6969 Planarity : 0.004 0.069 8036 Dihedral : 4.870 101.638 6221 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.04 % Allowed : 18.72 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 1.03 (0.11), residues: 5650 helix: 1.78 (0.10), residues: 2830 sheet: -0.04 (0.19), residues: 716 loop : -0.52 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 19 HIS 0.005 0.001 HIS T 66 PHE 0.028 0.001 PHE K 141 TYR 0.025 0.001 TYR H 112 ARG 0.014 0.000 ARG B 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 708 time to evaluate : 4.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8739 (m) REVERT: A 102 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8304 (mp) REVERT: A 163 LYS cc_start: 0.8612 (mmtm) cc_final: 0.8260 (mmtt) REVERT: A 173 ARG cc_start: 0.8168 (ptt-90) cc_final: 0.7504 (ptt180) REVERT: A 193 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7468 (mt-10) REVERT: A 231 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7796 (mp10) REVERT: A 487 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7488 (tp30) REVERT: A 557 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8344 (p) REVERT: A 571 ARG cc_start: 0.7834 (ttp80) cc_final: 0.7441 (ttm170) REVERT: B 195 GLU cc_start: 0.7711 (tt0) cc_final: 0.7164 (tm-30) REVERT: B 289 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8227 (ttp-170) REVERT: B 297 GLU cc_start: 0.8047 (tt0) cc_final: 0.7804 (tt0) REVERT: B 346 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.8990 (ttt) REVERT: B 401 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7946 (mt-10) REVERT: B 437 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7671 (tptm) REVERT: B 466 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: B 513 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7152 (ttmt) REVERT: B 530 ARG cc_start: 0.8022 (ptp-110) cc_final: 0.7763 (ptp-170) REVERT: B 540 MET cc_start: 0.8134 (mtp) cc_final: 0.7836 (mtm) REVERT: C 56 ARG cc_start: 0.8513 (ttm170) cc_final: 0.8010 (ttp-170) REVERT: C 61 MET cc_start: 0.8966 (mtm) cc_final: 0.8661 (ttm) REVERT: C 84 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8615 (mmtp) REVERT: C 108 ASP cc_start: 0.7968 (m-30) cc_final: 0.7706 (m-30) REVERT: C 220 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8796 (mtpp) REVERT: C 279 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: C 293 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7585 (mm-30) REVERT: C 297 GLU cc_start: 0.8264 (tt0) cc_final: 0.7885 (tt0) REVERT: C 356 GLU cc_start: 0.8203 (tt0) cc_final: 0.7710 (mt-10) REVERT: C 438 LYS cc_start: 0.8397 (mttt) cc_final: 0.7938 (mmtm) REVERT: C 485 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7043 (mt-10) REVERT: C 487 GLU cc_start: 0.7988 (tp30) cc_final: 0.7306 (tt0) REVERT: C 491 GLU cc_start: 0.7471 (tt0) cc_final: 0.7253 (tm-30) REVERT: C 513 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6764 (ttmt) REVERT: C 517 ASP cc_start: 0.8111 (m-30) cc_final: 0.7821 (m-30) REVERT: C 552 ARG cc_start: 0.7194 (ttt-90) cc_final: 0.6906 (mtp-110) REVERT: D 245 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7612 (mtpp) REVERT: D 250 GLU cc_start: 0.7557 (tt0) cc_final: 0.7170 (mt-10) REVERT: D 305 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7868 (mt-10) REVERT: D 382 GLN cc_start: 0.8013 (mm110) cc_final: 0.7644 (mt0) REVERT: D 410 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7963 (mtt) REVERT: E 41 SER cc_start: 0.8282 (m) cc_final: 0.7858 (p) REVERT: E 95 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8818 (t) REVERT: E 137 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8263 (mtpm) REVERT: E 315 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7792 (mp0) REVERT: E 342 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: E 367 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7714 (t70) REVERT: E 374 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8699 (pm20) REVERT: E 493 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8186 (mtpp) REVERT: F 81 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8376 (mttp) REVERT: F 108 LYS cc_start: 0.8863 (tttt) cc_final: 0.8561 (ttpp) REVERT: F 242 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7451 (mtm110) REVERT: F 245 LYS cc_start: 0.7987 (tttm) cc_final: 0.7701 (ttmt) REVERT: F 305 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7663 (mt-10) REVERT: F 410 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7880 (mtt) REVERT: F 452 LEU cc_start: 0.8386 (mt) cc_final: 0.8092 (mt) REVERT: G 211 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7586 (mmt180) REVERT: H 78 ASP cc_start: 0.6909 (m-30) cc_final: 0.6565 (m-30) REVERT: I 89 ASP cc_start: 0.7445 (m-30) cc_final: 0.7036 (m-30) REVERT: I 99 LYS cc_start: 0.8216 (tttt) cc_final: 0.7915 (mttm) REVERT: I 115 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7230 (mp) REVERT: I 117 ASP cc_start: 0.8003 (m-30) cc_final: 0.7471 (m-30) REVERT: I 131 ARG cc_start: 0.7597 (ttp80) cc_final: 0.7354 (mtp-110) REVERT: I 149 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7536 (mp10) REVERT: I 161 LYS cc_start: 0.8039 (mttp) cc_final: 0.7653 (ptmt) REVERT: I 184 TYR cc_start: 0.8742 (m-80) cc_final: 0.8511 (m-80) REVERT: I 201 ASP cc_start: 0.7931 (t0) cc_final: 0.7259 (m-30) REVERT: I 208 MET cc_start: 0.8853 (mmt) cc_final: 0.8502 (mmm) REVERT: I 226 ASP cc_start: 0.7865 (m-30) cc_final: 0.7209 (m-30) REVERT: J 41 GLU cc_start: 0.7925 (tp30) cc_final: 0.7642 (tp30) REVERT: J 76 MET cc_start: 0.7438 (mtm) cc_final: 0.6931 (tmm) REVERT: J 85 ARG cc_start: 0.7523 (mtt180) cc_final: 0.6894 (mmt-90) REVERT: J 99 LYS cc_start: 0.7861 (tttt) cc_final: 0.7370 (ttmm) REVERT: J 157 ILE cc_start: 0.8518 (mp) cc_final: 0.8298 (pt) REVERT: J 177 ILE cc_start: 0.7610 (mm) cc_final: 0.7331 (OUTLIER) REVERT: J 197 GLU cc_start: 0.7788 (mp0) cc_final: 0.7101 (mp0) REVERT: J 201 ASP cc_start: 0.7567 (t0) cc_final: 0.7219 (m-30) REVERT: J 221 ASN cc_start: 0.9097 (m110) cc_final: 0.8868 (m110) REVERT: K 54 MET cc_start: 0.7523 (mmm) cc_final: 0.7314 (mmt) REVERT: K 117 ASP cc_start: 0.7900 (m-30) cc_final: 0.7523 (m-30) REVERT: K 192 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8416 (m) REVERT: L 57 ASN cc_start: 0.8159 (t0) cc_final: 0.7866 (t0) REVERT: M 107 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7656 (mtm110) REVERT: N 48 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7565 (ttp-170) REVERT: N 53 LYS cc_start: 0.8468 (ttmm) cc_final: 0.8071 (ttpp) REVERT: O 91 ASN cc_start: 0.8757 (m-40) cc_final: 0.8453 (m110) REVERT: Q 117 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8020 (mp10) REVERT: Q 205 LYS cc_start: 0.8184 (tptt) cc_final: 0.7478 (mptt) REVERT: R 34 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6751 (tm130) REVERT: R 47 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7523 (tm-30) REVERT: R 50 GLN cc_start: 0.7521 (tp-100) cc_final: 0.7243 (tp40) REVERT: R 142 ASN cc_start: 0.8636 (t160) cc_final: 0.8091 (t0) REVERT: R 205 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.7045 (mmtp) REVERT: S 9 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.6302 (mptp) REVERT: S 141 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8255 (tptt) REVERT: S 197 TYR cc_start: 0.6880 (m-80) cc_final: 0.6676 (m-80) outliers start: 101 outliers final: 57 residues processed: 773 average time/residue: 1.6871 time to fit residues: 1589.8828 Evaluate side-chains 778 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 693 time to evaluate : 5.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 111 HIS Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain J residue 149 GLN Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain Q residue 214 GLU Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain R residue 59 ASN Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain T residue 150 ASN Chi-restraints excluded: chain T residue 153 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 354 optimal weight: 0.9990 chunk 475 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 411 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 447 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 459 optimal weight: 9.9990 chunk 56 optimal weight: 0.0270 chunk 82 optimal weight: 5.9990 overall best weight: 2.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN D 42 GLN F 265 ASN F 382 GLN G 194 HIS ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN I 100 GLN N 98 ASN Q 142 ASN R 117 GLN ** T 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.175972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.137507 restraints weight = 55180.787| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.11 r_work: 0.3231 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 46035 Z= 0.386 Angle : 0.631 12.469 62132 Z= 0.324 Chirality : 0.045 0.221 6969 Planarity : 0.005 0.069 8036 Dihedral : 5.087 105.513 6221 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.24 % Allowed : 18.70 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 0.86 (0.11), residues: 5650 helix: 1.65 (0.10), residues: 2828 sheet: -0.10 (0.19), residues: 700 loop : -0.63 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 19 HIS 0.007 0.001 HIS G 194 PHE 0.033 0.002 PHE H 155 TYR 0.024 0.002 TYR H 112 ARG 0.015 0.001 ARG B 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23838.88 seconds wall clock time: 421 minutes 42.20 seconds (25302.20 seconds total)