Starting phenix.real_space_refine on Mon Apr 15 08:46:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh5_11214/04_2024/6zh5_11214.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh5_11214/04_2024/6zh5_11214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh5_11214/04_2024/6zh5_11214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh5_11214/04_2024/6zh5_11214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh5_11214/04_2024/6zh5_11214.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh5_11214/04_2024/6zh5_11214.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 16 7.16 5 S 96 5.16 5 C 21480 2.51 5 N 6192 2.21 5 O 6624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z GLU 12": "OE1" <-> "OE2" Residue "Z ARG 40": "NH1" <-> "NH2" Residue "Z GLU 46": "OE1" <-> "OE2" Residue "Z GLU 54": "OE1" <-> "OE2" Residue "Z GLU 58": "OE1" <-> "OE2" Residue "Z ASP 72": "OD1" <-> "OD2" Residue "Z ASP 88": "OD1" <-> "OD2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z GLU 138": "OE1" <-> "OE2" Residue "Z GLU 172": "OE1" <-> "OE2" Residue "Z ASP 183": "OD1" <-> "OD2" Residue "Z GLU 187": "OE1" <-> "OE2" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C ARG 40": "NH1" <-> "NH2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E GLU 54": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E ASP 88": "OD1" <-> "OD2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G ARG 40": "NH1" <-> "NH2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "G ASP 88": "OD1" <-> "OD2" Residue "G GLU 131": "OE1" <-> "OE2" Residue "G GLU 138": "OE1" <-> "OE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G ASP 183": "OD1" <-> "OD2" Residue "G GLU 187": "OE1" <-> "OE2" Residue "H GLU 12": "OE1" <-> "OE2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H ASP 88": "OD1" <-> "OD2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 138": "OE1" <-> "OE2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "H ASP 183": "OD1" <-> "OD2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I GLU 58": "OE1" <-> "OE2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "I ASP 88": "OD1" <-> "OD2" Residue "I GLU 131": "OE1" <-> "OE2" Residue "I GLU 138": "OE1" <-> "OE2" Residue "I GLU 172": "OE1" <-> "OE2" Residue "I ASP 183": "OD1" <-> "OD2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "J GLU 12": "OE1" <-> "OE2" Residue "J ARG 40": "NH1" <-> "NH2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J GLU 58": "OE1" <-> "OE2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "J ASP 88": "OD1" <-> "OD2" Residue "J GLU 131": "OE1" <-> "OE2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "J GLU 172": "OE1" <-> "OE2" Residue "J ASP 183": "OD1" <-> "OD2" Residue "J GLU 187": "OE1" <-> "OE2" Residue "K GLU 12": "OE1" <-> "OE2" Residue "K ARG 40": "NH1" <-> "NH2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K GLU 54": "OE1" <-> "OE2" Residue "K GLU 58": "OE1" <-> "OE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K ASP 88": "OD1" <-> "OD2" Residue "K GLU 131": "OE1" <-> "OE2" Residue "K GLU 138": "OE1" <-> "OE2" Residue "K GLU 172": "OE1" <-> "OE2" Residue "K ASP 183": "OD1" <-> "OD2" Residue "K GLU 187": "OE1" <-> "OE2" Residue "L GLU 12": "OE1" <-> "OE2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L GLU 54": "OE1" <-> "OE2" Residue "L GLU 58": "OE1" <-> "OE2" Residue "L ASP 72": "OD1" <-> "OD2" Residue "L ASP 88": "OD1" <-> "OD2" Residue "L GLU 131": "OE1" <-> "OE2" Residue "L GLU 138": "OE1" <-> "OE2" Residue "L GLU 172": "OE1" <-> "OE2" Residue "L ASP 183": "OD1" <-> "OD2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "M GLU 12": "OE1" <-> "OE2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M ASP 72": "OD1" <-> "OD2" Residue "M ASP 88": "OD1" <-> "OD2" Residue "M GLU 131": "OE1" <-> "OE2" Residue "M GLU 138": "OE1" <-> "OE2" Residue "M GLU 172": "OE1" <-> "OE2" Residue "M ASP 183": "OD1" <-> "OD2" Residue "M GLU 187": "OE1" <-> "OE2" Residue "N GLU 12": "OE1" <-> "OE2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N ASP 72": "OD1" <-> "OD2" Residue "N ASP 88": "OD1" <-> "OD2" Residue "N GLU 131": "OE1" <-> "OE2" Residue "N GLU 138": "OE1" <-> "OE2" Residue "N GLU 172": "OE1" <-> "OE2" Residue "N ASP 183": "OD1" <-> "OD2" Residue "N GLU 187": "OE1" <-> "OE2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O ARG 40": "NH1" <-> "NH2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 54": "OE1" <-> "OE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O ASP 72": "OD1" <-> "OD2" Residue "O ASP 88": "OD1" <-> "OD2" Residue "O GLU 131": "OE1" <-> "OE2" Residue "O GLU 138": "OE1" <-> "OE2" Residue "O GLU 172": "OE1" <-> "OE2" Residue "O ASP 183": "OD1" <-> "OD2" Residue "O GLU 187": "OE1" <-> "OE2" Residue "P GLU 12": "OE1" <-> "OE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P GLU 46": "OE1" <-> "OE2" Residue "P GLU 54": "OE1" <-> "OE2" Residue "P GLU 58": "OE1" <-> "OE2" Residue "P ASP 72": "OD1" <-> "OD2" Residue "P ASP 88": "OD1" <-> "OD2" Residue "P GLU 131": "OE1" <-> "OE2" Residue "P GLU 138": "OE1" <-> "OE2" Residue "P GLU 172": "OE1" <-> "OE2" Residue "P ASP 183": "OD1" <-> "OD2" Residue "P GLU 187": "OE1" <-> "OE2" Residue "Q GLU 12": "OE1" <-> "OE2" Residue "Q ARG 40": "NH1" <-> "NH2" Residue "Q GLU 46": "OE1" <-> "OE2" Residue "Q GLU 54": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q ASP 72": "OD1" <-> "OD2" Residue "Q ASP 88": "OD1" <-> "OD2" Residue "Q GLU 131": "OE1" <-> "OE2" Residue "Q GLU 138": "OE1" <-> "OE2" Residue "Q GLU 172": "OE1" <-> "OE2" Residue "Q ASP 183": "OD1" <-> "OD2" Residue "Q GLU 187": "OE1" <-> "OE2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R GLU 54": "OE1" <-> "OE2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R ASP 72": "OD1" <-> "OD2" Residue "R ASP 88": "OD1" <-> "OD2" Residue "R GLU 131": "OE1" <-> "OE2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "R GLU 172": "OE1" <-> "OE2" Residue "R ASP 183": "OD1" <-> "OD2" Residue "R GLU 187": "OE1" <-> "OE2" Residue "S GLU 12": "OE1" <-> "OE2" Residue "S ARG 40": "NH1" <-> "NH2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S GLU 54": "OE1" <-> "OE2" Residue "S GLU 58": "OE1" <-> "OE2" Residue "S ASP 72": "OD1" <-> "OD2" Residue "S ASP 88": "OD1" <-> "OD2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S GLU 138": "OE1" <-> "OE2" Residue "S GLU 172": "OE1" <-> "OE2" Residue "S ASP 183": "OD1" <-> "OD2" Residue "S GLU 187": "OE1" <-> "OE2" Residue "T GLU 12": "OE1" <-> "OE2" Residue "T ARG 40": "NH1" <-> "NH2" Residue "T GLU 46": "OE1" <-> "OE2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "T GLU 58": "OE1" <-> "OE2" Residue "T ASP 72": "OD1" <-> "OD2" Residue "T ASP 88": "OD1" <-> "OD2" Residue "T GLU 131": "OE1" <-> "OE2" Residue "T GLU 138": "OE1" <-> "OE2" Residue "T GLU 172": "OE1" <-> "OE2" Residue "T ASP 183": "OD1" <-> "OD2" Residue "T GLU 187": "OE1" <-> "OE2" Residue "U GLU 12": "OE1" <-> "OE2" Residue "U ARG 40": "NH1" <-> "NH2" Residue "U GLU 46": "OE1" <-> "OE2" Residue "U GLU 54": "OE1" <-> "OE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U ASP 72": "OD1" <-> "OD2" Residue "U ASP 88": "OD1" <-> "OD2" Residue "U GLU 131": "OE1" <-> "OE2" Residue "U GLU 138": "OE1" <-> "OE2" Residue "U GLU 172": "OE1" <-> "OE2" Residue "U ASP 183": "OD1" <-> "OD2" Residue "U GLU 187": "OE1" <-> "OE2" Residue "V GLU 12": "OE1" <-> "OE2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "V GLU 46": "OE1" <-> "OE2" Residue "V GLU 54": "OE1" <-> "OE2" Residue "V GLU 58": "OE1" <-> "OE2" Residue "V ASP 72": "OD1" <-> "OD2" Residue "V ASP 88": "OD1" <-> "OD2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "V GLU 138": "OE1" <-> "OE2" Residue "V GLU 172": "OE1" <-> "OE2" Residue "V ASP 183": "OD1" <-> "OD2" Residue "V GLU 187": "OE1" <-> "OE2" Residue "W GLU 12": "OE1" <-> "OE2" Residue "W ARG 40": "NH1" <-> "NH2" Residue "W GLU 46": "OE1" <-> "OE2" Residue "W GLU 54": "OE1" <-> "OE2" Residue "W GLU 58": "OE1" <-> "OE2" Residue "W ASP 72": "OD1" <-> "OD2" Residue "W ASP 88": "OD1" <-> "OD2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "W GLU 138": "OE1" <-> "OE2" Residue "W GLU 172": "OE1" <-> "OE2" Residue "W ASP 183": "OD1" <-> "OD2" Residue "W GLU 187": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 72": "OD1" <-> "OD2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D ASP 183": "OD1" <-> "OD2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "F GLU 12": "OE1" <-> "OE2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F GLU 54": "OE1" <-> "OE2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F GLU 138": "OE1" <-> "OE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F ASP 183": "OD1" <-> "OD2" Residue "F GLU 187": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 34408 Number of models: 1 Model: "" Number of chains: 35 Chain: "Z" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "A" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "C" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "E" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "G" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "H" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "I" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "K" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "L" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "M" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "N" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "O" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "P" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "Q" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "R" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "S" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "T" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "U" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "V" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "W" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "B" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "D" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "F" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.74, per 1000 atoms: 0.49 Number of scatterers: 34408 At special positions: 0 Unit cell: (128.7, 128.7, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 16 26.01 S 96 16.00 O 6624 8.00 N 6192 7.00 C 21480 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: 13.28 Conformation dependent library (CDL) restraints added in 6.1 seconds 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8016 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 0 sheets defined 80.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'Z' and resid 10 through 36 Processing helix chain 'Z' and resid 45 through 73 removed outlier: 3.699A pdb=" N GLU Z 58 " --> pdb=" O GLU Z 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA Z 99 " --> pdb=" O GLU Z 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET Z 103 " --> pdb=" O ALA Z 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 123 through 134 Processing helix chain 'Z' and resid 134 through 155 Processing helix chain 'Z' and resid 170 through 179 Processing helix chain 'Z' and resid 179 through 191 removed outlier: 3.728A pdb=" N ILE Z 186 " --> pdb=" O HIS Z 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 36 Processing helix chain 'A' and resid 45 through 73 removed outlier: 3.699A pdb=" N GLU A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 121 removed outlier: 3.630A pdb=" N ALA A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 134 through 155 Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'A' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 134 through 155 Processing helix chain 'C' and resid 170 through 179 Processing helix chain 'C' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE C 186 " --> pdb=" O HIS C 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 36 Processing helix chain 'E' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU E 58 " --> pdb=" O GLU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 121 removed outlier: 3.628A pdb=" N ALA E 99 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 134 through 155 Processing helix chain 'E' and resid 170 through 179 Processing helix chain 'E' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU G 58 " --> pdb=" O GLU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 134 Processing helix chain 'G' and resid 134 through 155 Processing helix chain 'G' and resid 170 through 179 Processing helix chain 'G' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE G 186 " --> pdb=" O HIS G 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 36 Processing helix chain 'H' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU H 58 " --> pdb=" O GLU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA H 99 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET H 103 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 134 Processing helix chain 'H' and resid 134 through 155 Processing helix chain 'H' and resid 170 through 179 Processing helix chain 'H' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE H 186 " --> pdb=" O HIS H 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 36 Processing helix chain 'I' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU I 58 " --> pdb=" O GLU I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA I 99 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET I 103 " --> pdb=" O ALA I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 134 through 155 Processing helix chain 'I' and resid 170 through 179 Processing helix chain 'I' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE I 186 " --> pdb=" O HIS I 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 36 Processing helix chain 'J' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 121 removed outlier: 3.628A pdb=" N ALA J 99 " --> pdb=" O GLU J 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET J 103 " --> pdb=" O ALA J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 134 through 155 Processing helix chain 'J' and resid 170 through 179 Processing helix chain 'J' and resid 179 through 191 removed outlier: 3.726A pdb=" N ILE J 186 " --> pdb=" O HIS J 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 36 Processing helix chain 'K' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU K 58 " --> pdb=" O GLU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA K 99 " --> pdb=" O GLU K 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET K 103 " --> pdb=" O ALA K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 134 through 155 Processing helix chain 'K' and resid 170 through 179 Processing helix chain 'K' and resid 179 through 191 removed outlier: 3.726A pdb=" N ILE K 186 " --> pdb=" O HIS K 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 36 Processing helix chain 'L' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU L 58 " --> pdb=" O GLU L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA L 99 " --> pdb=" O GLU L 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 134 Processing helix chain 'L' and resid 134 through 155 Processing helix chain 'L' and resid 170 through 179 Processing helix chain 'L' and resid 179 through 191 removed outlier: 3.726A pdb=" N ILE L 186 " --> pdb=" O HIS L 182 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 36 Processing helix chain 'M' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU M 58 " --> pdb=" O GLU M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA M 99 " --> pdb=" O GLU M 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET M 103 " --> pdb=" O ALA M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 134 Processing helix chain 'M' and resid 134 through 155 Processing helix chain 'M' and resid 170 through 179 Processing helix chain 'M' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE M 186 " --> pdb=" O HIS M 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 36 Processing helix chain 'N' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU N 58 " --> pdb=" O GLU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA N 99 " --> pdb=" O GLU N 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET N 103 " --> pdb=" O ALA N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 134 Processing helix chain 'N' and resid 134 through 155 Processing helix chain 'N' and resid 170 through 179 Processing helix chain 'N' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE N 186 " --> pdb=" O HIS N 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 36 Processing helix chain 'O' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU O 58 " --> pdb=" O GLU O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA O 99 " --> pdb=" O GLU O 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET O 103 " --> pdb=" O ALA O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 134 Processing helix chain 'O' and resid 134 through 155 Processing helix chain 'O' and resid 170 through 179 Processing helix chain 'O' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE O 186 " --> pdb=" O HIS O 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 36 Processing helix chain 'P' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU P 58 " --> pdb=" O GLU P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA P 99 " --> pdb=" O GLU P 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET P 103 " --> pdb=" O ALA P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 123 through 134 Processing helix chain 'P' and resid 134 through 155 Processing helix chain 'P' and resid 170 through 179 Processing helix chain 'P' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE P 186 " --> pdb=" O HIS P 182 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 36 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 3.697A pdb=" N GLU Q 58 " --> pdb=" O GLU Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 121 removed outlier: 3.630A pdb=" N ALA Q 99 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET Q 103 " --> pdb=" O ALA Q 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 134 Processing helix chain 'Q' and resid 134 through 155 Processing helix chain 'Q' and resid 170 through 179 Processing helix chain 'Q' and resid 179 through 191 removed outlier: 3.726A pdb=" N ILE Q 186 " --> pdb=" O HIS Q 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 36 Processing helix chain 'R' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU R 58 " --> pdb=" O GLU R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 121 removed outlier: 3.628A pdb=" N ALA R 99 " --> pdb=" O GLU R 95 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET R 103 " --> pdb=" O ALA R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 134 Processing helix chain 'R' and resid 134 through 155 Processing helix chain 'R' and resid 170 through 179 Processing helix chain 'R' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE R 186 " --> pdb=" O HIS R 182 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 36 Processing helix chain 'S' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU S 58 " --> pdb=" O GLU S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 92 through 121 removed outlier: 3.628A pdb=" N ALA S 99 " --> pdb=" O GLU S 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET S 103 " --> pdb=" O ALA S 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 134 Processing helix chain 'S' and resid 134 through 155 Processing helix chain 'S' and resid 170 through 179 Processing helix chain 'S' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE S 186 " --> pdb=" O HIS S 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 36 Processing helix chain 'T' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU T 58 " --> pdb=" O GLU T 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA T 99 " --> pdb=" O GLU T 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET T 103 " --> pdb=" O ALA T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 123 through 134 Processing helix chain 'T' and resid 134 through 155 Processing helix chain 'T' and resid 170 through 179 Processing helix chain 'T' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE T 186 " --> pdb=" O HIS T 182 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 36 Processing helix chain 'U' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU U 58 " --> pdb=" O GLU U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 92 through 121 removed outlier: 3.630A pdb=" N ALA U 99 " --> pdb=" O GLU U 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET U 103 " --> pdb=" O ALA U 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 123 through 134 Processing helix chain 'U' and resid 134 through 155 Processing helix chain 'U' and resid 170 through 179 Processing helix chain 'U' and resid 179 through 191 removed outlier: 3.726A pdb=" N ILE U 186 " --> pdb=" O HIS U 182 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 36 Processing helix chain 'V' and resid 45 through 73 removed outlier: 3.699A pdb=" N GLU V 58 " --> pdb=" O GLU V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA V 99 " --> pdb=" O GLU V 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET V 103 " --> pdb=" O ALA V 99 " (cutoff:3.500A) Processing helix chain 'V' and resid 123 through 134 Processing helix chain 'V' and resid 134 through 155 Processing helix chain 'V' and resid 170 through 179 Processing helix chain 'V' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE V 186 " --> pdb=" O HIS V 182 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 36 Processing helix chain 'W' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU W 58 " --> pdb=" O GLU W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA W 99 " --> pdb=" O GLU W 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET W 103 " --> pdb=" O ALA W 99 " (cutoff:3.500A) Processing helix chain 'W' and resid 123 through 134 Processing helix chain 'W' and resid 134 through 155 Processing helix chain 'W' and resid 170 through 179 Processing helix chain 'W' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE W 186 " --> pdb=" O HIS W 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 36 Processing helix chain 'B' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 134 through 155 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 179 through 191 removed outlier: 3.726A pdb=" N ILE B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 36 Processing helix chain 'D' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 134 through 155 Processing helix chain 'D' and resid 170 through 179 Processing helix chain 'D' and resid 179 through 191 removed outlier: 3.728A pdb=" N ILE D 186 " --> pdb=" O HIS D 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 36 Processing helix chain 'F' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU F 58 " --> pdb=" O GLU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA F 99 " --> pdb=" O GLU F 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 134 Processing helix chain 'F' and resid 134 through 155 Processing helix chain 'F' and resid 170 through 179 Processing helix chain 'F' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE F 186 " --> pdb=" O HIS F 182 " (cutoff:3.500A) 2664 hydrogen bonds defined for protein. 7992 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: 11.70 Time building geometry restraints manager: 14.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12024 1.34 - 1.46: 7168 1.46 - 1.57: 15584 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 34944 Sorted by residual: bond pdb=" CG ARG G 121 " pdb=" CD ARG G 121 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CG ARG V 121 " pdb=" CD ARG V 121 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CG ARG T 121 " pdb=" CD ARG T 121 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CG ARG U 121 " pdb=" CD ARG U 121 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.72e+00 bond pdb=" CG ARG L 121 " pdb=" CD ARG L 121 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.70e+00 ... (remaining 34939 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 575 107.14 - 113.85: 19823 113.85 - 120.55: 15274 120.55 - 127.26: 11008 127.26 - 133.97: 264 Bond angle restraints: 46944 Sorted by residual: angle pdb=" CB ARG O 121 " pdb=" CG ARG O 121 " pdb=" CD ARG O 121 " ideal model delta sigma weight residual 111.30 121.53 -10.23 2.30e+00 1.89e-01 1.98e+01 angle pdb=" CB ARG C 121 " pdb=" CG ARG C 121 " pdb=" CD ARG C 121 " ideal model delta sigma weight residual 111.30 121.52 -10.22 2.30e+00 1.89e-01 1.97e+01 angle pdb=" CB ARG H 121 " pdb=" CG ARG H 121 " pdb=" CD ARG H 121 " ideal model delta sigma weight residual 111.30 121.52 -10.22 2.30e+00 1.89e-01 1.97e+01 angle pdb=" CB ARG L 121 " pdb=" CG ARG L 121 " pdb=" CD ARG L 121 " ideal model delta sigma weight residual 111.30 121.52 -10.22 2.30e+00 1.89e-01 1.97e+01 angle pdb=" CB ARG G 121 " pdb=" CG ARG G 121 " pdb=" CD ARG G 121 " ideal model delta sigma weight residual 111.30 121.50 -10.20 2.30e+00 1.89e-01 1.97e+01 ... (remaining 46939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 18000 16.82 - 33.63: 1920 33.63 - 50.45: 816 50.45 - 67.27: 264 67.27 - 84.08: 96 Dihedral angle restraints: 21096 sinusoidal: 8736 harmonic: 12360 Sorted by residual: dihedral pdb=" CB GLU J 61 " pdb=" CG GLU J 61 " pdb=" CD GLU J 61 " pdb=" OE1 GLU J 61 " ideal model delta sinusoidal sigma weight residual 0.00 -84.08 84.08 1 3.00e+01 1.11e-03 9.57e+00 dihedral pdb=" CB GLU E 61 " pdb=" CG GLU E 61 " pdb=" CD GLU E 61 " pdb=" OE1 GLU E 61 " ideal model delta sinusoidal sigma weight residual 0.00 -84.07 84.07 1 3.00e+01 1.11e-03 9.57e+00 dihedral pdb=" CB GLU Z 61 " pdb=" CG GLU Z 61 " pdb=" CD GLU Z 61 " pdb=" OE1 GLU Z 61 " ideal model delta sinusoidal sigma weight residual 0.00 -84.05 84.05 1 3.00e+01 1.11e-03 9.56e+00 ... (remaining 21093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2144 0.025 - 0.050: 1797 0.050 - 0.076: 806 0.076 - 0.101: 239 0.101 - 0.126: 54 Chirality restraints: 5040 Sorted by residual: chirality pdb=" CB VAL C 139 " pdb=" CA VAL C 139 " pdb=" CG1 VAL C 139 " pdb=" CG2 VAL C 139 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CB VAL H 139 " pdb=" CA VAL H 139 " pdb=" CG1 VAL H 139 " pdb=" CG2 VAL H 139 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CB VAL I 139 " pdb=" CA VAL I 139 " pdb=" CG1 VAL I 139 " pdb=" CG2 VAL I 139 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 5037 not shown) Planarity restraints: 6240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 121 " -0.041 9.50e-02 1.11e+02 2.37e-02 2.96e+00 pdb=" NE ARG B 121 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 121 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG B 121 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 121 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 121 " -0.040 9.50e-02 1.11e+02 2.32e-02 2.90e+00 pdb=" NE ARG F 121 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG F 121 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG F 121 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG F 121 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 121 " -0.040 9.50e-02 1.11e+02 2.32e-02 2.90e+00 pdb=" NE ARG H 121 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG H 121 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG H 121 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG H 121 " 0.008 2.00e-02 2.50e+03 ... (remaining 6237 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 357 2.59 - 3.17: 30265 3.17 - 3.75: 57123 3.75 - 4.32: 81669 4.32 - 4.90: 132530 Nonbonded interactions: 301944 Sorted by model distance: nonbonded pdb=" OE1 GLU I 131 " pdb="FE FE I 202 " model vdw 2.015 2.260 nonbonded pdb=" OE1 GLU H 131 " pdb="FE FE H 201 " model vdw 2.018 2.260 nonbonded pdb=" OE1 GLU U 131 " pdb="FE FE K 201 " model vdw 2.038 2.260 nonbonded pdb=" OE1 GLU R 131 " pdb="FE FE H 201 " model vdw 2.050 2.260 nonbonded pdb=" OE1 GLU Q 131 " pdb="FE FE J 201 " model vdw 2.066 2.260 ... (remaining 301939 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 191) selection = (chain 'B' and resid 2 through 191) selection = (chain 'C' and resid 2 through 191) selection = (chain 'D' and resid 2 through 191) selection = chain 'E' selection = (chain 'F' and resid 2 through 191) selection = chain 'G' selection = (chain 'H' and resid 2 through 191) selection = (chain 'I' and resid 2 through 191) selection = (chain 'J' and resid 2 through 191) selection = (chain 'K' and resid 2 through 191) selection = (chain 'L' and resid 2 through 191) selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = (chain 'U' and resid 2 through 191) selection = chain 'V' selection = chain 'W' selection = chain 'Z' } 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=0.50 max=1.00 mean=0.99 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.440 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 85.650 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.330 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: 0.010 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 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 : 0.007 0.039 34944 Z= 0.475 Angle : 0.727 10.232 46944 Z= 0.438 Chirality : 0.041 0.126 5040 Planarity : 0.003 0.024 6240 Dihedral : 18.436 84.084 13080 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 12.67 % Allowed : 16.08 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.11), residues: 4176 helix: -1.51 (0.07), residues: 3408 sheet: None (None), residues: 0 loop : -2.43 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP Z 90 HIS 0.004 0.001 HIS A 125 PHE 0.010 0.001 PHE Z 129 TYR 0.006 0.001 TYR N 31 ARG 0.029 0.001 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2000 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 456 poor density : 1544 time to evaluate : 4.099 Fit side-chains REVERT: Z 46 GLU cc_start: 0.8305 (pp20) cc_final: 0.8044 (pp20) REVERT: Z 61 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7846 (mt-10) REVERT: Z 87 GLN cc_start: 0.9134 (mt0) cc_final: 0.8897 (mt0) REVERT: Z 92 LYS cc_start: 0.9142 (mmpt) cc_final: 0.8634 (mmmt) REVERT: Z 95 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: Z 103 MET cc_start: 0.8729 (ttm) cc_final: 0.8517 (ttm) REVERT: Z 176 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8440 (tm-30) REVERT: A 61 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 64 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: A 68 GLU cc_start: 0.8115 (pt0) cc_final: 0.7526 (pt0) REVERT: A 80 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8541 (mm-40) REVERT: A 101 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8824 (tt) REVERT: A 105 LYS cc_start: 0.9123 (mtpt) cc_final: 0.8892 (mtmm) REVERT: A 108 ASN cc_start: 0.9321 (t0) cc_final: 0.8843 (t0) REVERT: A 109 GLN cc_start: 0.8920 (tp40) cc_final: 0.8243 (mm-40) REVERT: A 113 ASP cc_start: 0.8592 (m-30) cc_final: 0.8211 (m-30) REVERT: A 128 ASP cc_start: 0.9070 (OUTLIER) cc_final: 0.8678 (t0) REVERT: A 132 SER cc_start: 0.9559 (OUTLIER) cc_final: 0.9328 (p) REVERT: A 176 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8690 (tm-30) REVERT: C 61 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7841 (mt-10) REVERT: C 80 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8783 (mm-40) REVERT: C 87 GLN cc_start: 0.9210 (mt0) cc_final: 0.8982 (mt0) REVERT: C 92 LYS cc_start: 0.9119 (mmpt) cc_final: 0.8739 (mmmt) REVERT: C 101 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9071 (tt) REVERT: C 109 GLN cc_start: 0.8982 (tp40) cc_final: 0.8776 (tp40) REVERT: C 123 ASP cc_start: 0.9155 (t0) cc_final: 0.8913 (t0) REVERT: C 132 SER cc_start: 0.9640 (OUTLIER) cc_final: 0.9436 (p) REVERT: C 136 ASP cc_start: 0.8425 (t70) cc_final: 0.8132 (t0) REVERT: C 140 LYS cc_start: 0.9229 (mttm) cc_final: 0.8887 (mmtm) REVERT: C 176 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8886 (tm-30) REVERT: E 46 GLU cc_start: 0.8239 (pp20) cc_final: 0.7998 (pp20) REVERT: E 61 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7717 (mt-10) REVERT: E 92 LYS cc_start: 0.9192 (mmpt) cc_final: 0.8681 (mmmt) REVERT: E 95 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7883 (pm20) REVERT: E 123 ASP cc_start: 0.9118 (t0) cc_final: 0.8852 (t0) REVERT: E 140 LYS cc_start: 0.9241 (mttm) cc_final: 0.8959 (mmtm) REVERT: E 176 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8586 (tm-30) REVERT: G 61 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7610 (mt-10) REVERT: G 87 GLN cc_start: 0.9346 (mt0) cc_final: 0.9057 (mt0) REVERT: G 92 LYS cc_start: 0.9160 (mmpt) cc_final: 0.8396 (mmmt) REVERT: G 95 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: G 123 ASP cc_start: 0.9104 (t0) cc_final: 0.8878 (t0) REVERT: H 46 GLU cc_start: 0.8227 (pp20) cc_final: 0.7928 (pp20) REVERT: H 59 LYS cc_start: 0.9050 (mmtm) cc_final: 0.8784 (mptt) REVERT: H 61 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7803 (mt-10) REVERT: H 101 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8819 (tt) REVERT: H 108 ASN cc_start: 0.9275 (t0) cc_final: 0.8973 (t0) REVERT: H 113 ASP cc_start: 0.8555 (m-30) cc_final: 0.8304 (m-30) REVERT: H 123 ASP cc_start: 0.9074 (t0) cc_final: 0.8843 (t70) REVERT: H 140 LYS cc_start: 0.9218 (mttm) cc_final: 0.8964 (mmtm) REVERT: H 176 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8640 (tm-30) REVERT: I 31 TYR cc_start: 0.8899 (m-10) cc_final: 0.8381 (m-10) REVERT: I 46 GLU cc_start: 0.8154 (pp20) cc_final: 0.7940 (pp20) REVERT: I 61 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7734 (mt-10) REVERT: I 80 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8590 (mm-40) REVERT: I 92 LYS cc_start: 0.9025 (mmpt) cc_final: 0.8697 (mmmt) REVERT: I 101 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8863 (tt) REVERT: I 104 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8045 (mm-30) REVERT: I 108 ASN cc_start: 0.9205 (t0) cc_final: 0.8872 (t0) REVERT: I 140 LYS cc_start: 0.9248 (mttm) cc_final: 0.9026 (mmtm) REVERT: I 176 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8646 (tm-30) REVERT: J 46 GLU cc_start: 0.8225 (pp20) cc_final: 0.8010 (pp20) REVERT: J 61 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7714 (mt-10) REVERT: J 80 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8786 (mm-40) REVERT: J 92 LYS cc_start: 0.9209 (mmpt) cc_final: 0.8648 (mmmt) REVERT: J 123 ASP cc_start: 0.9072 (t0) cc_final: 0.8799 (t0) REVERT: J 140 LYS cc_start: 0.9215 (mttm) cc_final: 0.8846 (mmtm) REVERT: J 176 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8623 (tm-30) REVERT: K 46 GLU cc_start: 0.8252 (pp20) cc_final: 0.8045 (pp20) REVERT: K 61 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7738 (mt-10) REVERT: K 80 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8746 (mm-40) REVERT: K 87 GLN cc_start: 0.9240 (mt0) cc_final: 0.9036 (mt0) REVERT: K 92 LYS cc_start: 0.9019 (mmpt) cc_final: 0.8768 (mmmt) REVERT: K 95 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: K 123 ASP cc_start: 0.9089 (t0) cc_final: 0.8835 (t0) REVERT: K 132 SER cc_start: 0.9592 (OUTLIER) cc_final: 0.9392 (p) REVERT: K 140 LYS cc_start: 0.9235 (mttm) cc_final: 0.9011 (mmtp) REVERT: K 176 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8616 (tm-30) REVERT: L 61 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7763 (mt-10) REVERT: L 80 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8658 (mm-40) REVERT: L 87 GLN cc_start: 0.9206 (mt0) cc_final: 0.9002 (mt0) REVERT: L 92 LYS cc_start: 0.9020 (mmpt) cc_final: 0.8592 (mmmt) REVERT: L 101 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9158 (tt) REVERT: L 109 GLN cc_start: 0.9043 (tp40) cc_final: 0.8349 (mm-40) REVERT: L 113 ASP cc_start: 0.8560 (m-30) cc_final: 0.8186 (m-30) REVERT: L 123 ASP cc_start: 0.9119 (t0) cc_final: 0.8864 (t0) REVERT: L 136 ASP cc_start: 0.8277 (t70) cc_final: 0.8035 (t0) REVERT: L 140 LYS cc_start: 0.9209 (mttm) cc_final: 0.8919 (mmtm) REVERT: L 176 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8821 (tm-30) REVERT: M 46 GLU cc_start: 0.8218 (pp20) cc_final: 0.7967 (pp20) REVERT: M 61 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7758 (mt-10) REVERT: M 68 GLU cc_start: 0.8209 (pt0) cc_final: 0.7591 (pt0) REVERT: M 80 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8396 (mm-40) REVERT: M 101 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9049 (tt) REVERT: M 117 LEU cc_start: 0.9434 (tp) cc_final: 0.9227 (OUTLIER) REVERT: M 123 ASP cc_start: 0.9146 (t0) cc_final: 0.8913 (t0) REVERT: M 132 SER cc_start: 0.9576 (OUTLIER) cc_final: 0.9336 (p) REVERT: M 176 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8591 (tm-30) REVERT: N 8 ASN cc_start: 0.8791 (t0) cc_final: 0.8371 (t0) REVERT: N 14 GLU cc_start: 0.8879 (tt0) cc_final: 0.8650 (tt0) REVERT: N 92 LYS cc_start: 0.8965 (mmpt) cc_final: 0.8112 (mmmt) REVERT: N 95 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: N 109 GLN cc_start: 0.8957 (tp40) cc_final: 0.8716 (mm-40) REVERT: O 3 SER cc_start: 0.9201 (t) cc_final: 0.8894 (t) REVERT: O 8 ASN cc_start: 0.8745 (t0) cc_final: 0.8290 (t0) REVERT: O 14 GLU cc_start: 0.8793 (tt0) cc_final: 0.8529 (tt0) REVERT: O 92 LYS cc_start: 0.8969 (mmpt) cc_final: 0.8131 (mmmt) REVERT: O 95 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8090 (pm20) REVERT: P 14 GLU cc_start: 0.8995 (tt0) cc_final: 0.8794 (tt0) REVERT: P 28 SER cc_start: 0.9316 (t) cc_final: 0.9095 (p) REVERT: P 46 GLU cc_start: 0.8235 (pp20) cc_final: 0.7930 (pp20) REVERT: P 61 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7640 (mt-10) REVERT: P 68 GLU cc_start: 0.8229 (pt0) cc_final: 0.7629 (pt0) REVERT: P 80 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8291 (mm-40) REVERT: P 101 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8966 (tt) REVERT: P 123 ASP cc_start: 0.8959 (t0) cc_final: 0.8719 (t0) REVERT: P 132 SER cc_start: 0.9521 (OUTLIER) cc_final: 0.9271 (p) REVERT: P 140 LYS cc_start: 0.9220 (mttm) cc_final: 0.9016 (mmtm) REVERT: Q 46 GLU cc_start: 0.8264 (pp20) cc_final: 0.8019 (pp20) REVERT: Q 59 LYS cc_start: 0.9115 (mmtm) cc_final: 0.8854 (mptt) REVERT: Q 61 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7717 (mt-10) REVERT: Q 80 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8683 (mm-40) REVERT: Q 92 LYS cc_start: 0.9123 (mmpt) cc_final: 0.8579 (mmmt) REVERT: Q 95 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7904 (pm20) REVERT: Q 123 ASP cc_start: 0.9028 (t0) cc_final: 0.8751 (t70) REVERT: Q 176 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8586 (tm-30) REVERT: R 61 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7792 (mt-10) REVERT: R 80 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8838 (mm-40) REVERT: R 87 GLN cc_start: 0.9283 (mt0) cc_final: 0.8992 (mt0) REVERT: R 92 LYS cc_start: 0.9149 (mmpt) cc_final: 0.8385 (mmmt) REVERT: R 95 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: R 108 ASN cc_start: 0.9341 (t0) cc_final: 0.8987 (t0) REVERT: R 176 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8804 (tm-30) REVERT: R 182 HIS cc_start: 0.8870 (t70) cc_final: 0.8660 (t70) REVERT: S 8 ASN cc_start: 0.8801 (t0) cc_final: 0.8426 (t0) REVERT: S 14 GLU cc_start: 0.8833 (tt0) cc_final: 0.8620 (tt0) REVERT: S 92 LYS cc_start: 0.8958 (mmpt) cc_final: 0.8125 (mmmt) REVERT: S 95 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8090 (pm20) REVERT: T 8 ASN cc_start: 0.8771 (t0) cc_final: 0.8402 (t0) REVERT: T 14 GLU cc_start: 0.8810 (tt0) cc_final: 0.8602 (tt0) REVERT: T 92 LYS cc_start: 0.8982 (mmpt) cc_final: 0.8123 (mmmt) REVERT: T 95 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: T 103 MET cc_start: 0.8758 (ttm) cc_final: 0.8532 (ttm) REVERT: T 109 GLN cc_start: 0.8965 (tp40) cc_final: 0.8728 (mm-40) REVERT: U 31 TYR cc_start: 0.8884 (m-10) cc_final: 0.8406 (m-10) REVERT: U 46 GLU cc_start: 0.8156 (pp20) cc_final: 0.7948 (pp20) REVERT: U 61 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7751 (mt-10) REVERT: U 80 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8359 (mm-40) REVERT: U 92 LYS cc_start: 0.9003 (mmpt) cc_final: 0.8701 (mmmt) REVERT: U 101 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8857 (tt) REVERT: U 104 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8108 (mm-30) REVERT: U 108 ASN cc_start: 0.9260 (t0) cc_final: 0.8890 (t0) REVERT: U 140 LYS cc_start: 0.9247 (mttm) cc_final: 0.8938 (mmtm) REVERT: U 176 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8653 (tm-30) REVERT: V 61 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7703 (mt-10) REVERT: V 80 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8872 (mm-40) REVERT: V 87 GLN cc_start: 0.9330 (mt0) cc_final: 0.9070 (mt0) REVERT: V 92 LYS cc_start: 0.9159 (mmpt) cc_final: 0.8414 (mmmt) REVERT: V 95 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8115 (pm20) REVERT: V 101 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9095 (tt) REVERT: V 109 GLN cc_start: 0.8987 (tp40) cc_final: 0.8779 (tp40) REVERT: V 123 ASP cc_start: 0.9080 (t0) cc_final: 0.8841 (t0) REVERT: V 132 SER cc_start: 0.9600 (OUTLIER) cc_final: 0.9395 (p) REVERT: V 140 LYS cc_start: 0.9226 (mttm) cc_final: 0.9019 (mmtm) REVERT: V 176 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8833 (tm-30) REVERT: V 182 HIS cc_start: 0.8809 (t70) cc_final: 0.8585 (t70) REVERT: W 61 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7844 (mt-10) REVERT: W 80 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8749 (mm-40) REVERT: W 87 GLN cc_start: 0.9251 (mt0) cc_final: 0.9000 (mt0) REVERT: W 92 LYS cc_start: 0.9177 (mmpt) cc_final: 0.8737 (mmmt) REVERT: W 101 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9059 (tt) REVERT: W 123 ASP cc_start: 0.9115 (t0) cc_final: 0.8842 (t0) REVERT: W 140 LYS cc_start: 0.9206 (mttm) cc_final: 0.8916 (mmtm) REVERT: W 176 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8760 (tm-30) REVERT: B 61 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7730 (mt-10) REVERT: B 80 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8613 (mm-40) REVERT: B 92 LYS cc_start: 0.9115 (mmpt) cc_final: 0.8423 (mmmt) REVERT: B 106 ASN cc_start: 0.9417 (t0) cc_final: 0.9211 (t0) REVERT: B 108 ASN cc_start: 0.9259 (t0) cc_final: 0.8828 (t0) REVERT: B 109 GLN cc_start: 0.8719 (tp40) cc_final: 0.8395 (tp40) REVERT: B 113 ASP cc_start: 0.8433 (m-30) cc_final: 0.8172 (m-30) REVERT: B 128 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8517 (t0) REVERT: B 176 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8722 (tm-30) REVERT: D 46 GLU cc_start: 0.8240 (pp20) cc_final: 0.7983 (pp20) REVERT: D 61 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7786 (mt-10) REVERT: D 80 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8587 (mm-40) REVERT: D 101 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9053 (tt) REVERT: D 109 GLN cc_start: 0.9023 (tp40) cc_final: 0.8318 (mm-40) REVERT: D 113 ASP cc_start: 0.8567 (m-30) cc_final: 0.8183 (m-30) REVERT: D 123 ASP cc_start: 0.8985 (t0) cc_final: 0.8739 (t0) REVERT: D 132 SER cc_start: 0.9578 (OUTLIER) cc_final: 0.9343 (p) REVERT: D 140 LYS cc_start: 0.9235 (mttm) cc_final: 0.8956 (mmtm) REVERT: D 176 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8561 (tm-30) REVERT: F 61 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7726 (mt-10) REVERT: F 80 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8488 (mm-40) REVERT: F 92 LYS cc_start: 0.8925 (mmpt) cc_final: 0.8637 (mmmt) REVERT: F 101 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8904 (tt) REVERT: F 108 ASN cc_start: 0.9180 (t0) cc_final: 0.8831 (t0) REVERT: F 140 LYS cc_start: 0.9249 (mttm) cc_final: 0.9003 (mmtm) REVERT: F 176 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8783 (tm-30) outliers start: 456 outliers final: 190 residues processed: 1756 average time/residue: 1.5165 time to fit residues: 3159.3596 Evaluate side-chains 1643 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1421 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 12 GLU Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 88 ASP Chi-restraints excluded: chain Z residue 95 GLU Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 127 CYS Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 121 ARG Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain H residue 12 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 121 ARG Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain J residue 12 GLU Chi-restraints excluded: chain J residue 33 SER Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 127 CYS Chi-restraints excluded: chain K residue 12 GLU Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 121 ARG Chi-restraints excluded: chain K residue 127 CYS Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain L residue 12 GLU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 64 GLU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain M residue 12 GLU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 101 LEU Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 121 ARG Chi-restraints excluded: chain M residue 127 CYS Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 121 ARG Chi-restraints excluded: chain N residue 127 CYS Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 89 GLU Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 121 ARG Chi-restraints excluded: chain O residue 127 CYS Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 121 ARG Chi-restraints excluded: chain P residue 127 CYS Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 169 SER Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 121 ARG Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 88 ASP Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 12 GLU Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 121 ARG Chi-restraints excluded: chain S residue 127 CYS Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain T residue 12 GLU Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 86 SER Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain T residue 89 GLU Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 121 ARG Chi-restraints excluded: chain T residue 127 CYS Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 12 GLU Chi-restraints excluded: chain U residue 33 SER Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 121 ARG Chi-restraints excluded: chain U residue 127 CYS Chi-restraints excluded: chain V residue 12 GLU Chi-restraints excluded: chain V residue 33 SER Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 127 CYS Chi-restraints excluded: chain V residue 132 SER Chi-restraints excluded: chain W residue 12 GLU Chi-restraints excluded: chain W residue 33 SER Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 101 LEU Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 121 ARG Chi-restraints excluded: chain W residue 127 CYS Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain F residue 12 GLU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 127 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 4.9990 chunk 309 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 319 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 238 optimal weight: 0.9980 chunk 370 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 83 GLN Z 87 GLN Z 182 HIS ** Z 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 87 GLN ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN E 87 GLN E 182 HIS ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN G 87 GLN G 94 GLN ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN H 87 GLN ** H 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN I 87 GLN ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN J 22 ASN J 83 GLN ** J 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 GLN K 87 GLN K 182 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN L 87 GLN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 4 GLN M 182 HIS ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN N 94 GLN N 147 ASN ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 GLN O 147 ASN ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 182 HIS ** P 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 GLN Q 22 ASN Q 83 GLN Q 87 GLN Q 182 HIS ** Q 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 4 GLN R 8 ASN R 83 GLN R 87 GLN S 83 GLN S 94 GLN S 147 ASN ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN T 94 GLN T 147 ASN ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 4 GLN U 87 GLN ** U 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN V 87 GLN ** V 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 4 GLN W 83 GLN ** W 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN B 22 ASN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN D 87 GLN D 182 HIS ** D 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN ** F 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 34944 Z= 0.177 Angle : 0.502 5.618 46944 Z= 0.272 Chirality : 0.034 0.127 5040 Planarity : 0.003 0.023 6240 Dihedral : 8.539 62.838 5101 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.08 % Allowed : 25.58 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 4176 helix: 0.98 (0.09), residues: 3432 sheet: None (None), residues: 0 loop : -1.90 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 90 HIS 0.007 0.001 HIS Z 182 PHE 0.007 0.001 PHE E 36 TYR 0.014 0.001 TYR P 173 ARG 0.006 0.000 ARG I 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1769 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1622 time to evaluate : 4.172 Fit side-chains revert: symmetry clash REVERT: Z 12 GLU cc_start: 0.8442 (mp0) cc_final: 0.8099 (mp0) REVERT: Z 46 GLU cc_start: 0.8247 (pp20) cc_final: 0.7999 (pp20) REVERT: Z 57 GLU cc_start: 0.4305 (OUTLIER) cc_final: 0.3893 (mt-10) REVERT: Z 61 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7653 (mt-10) REVERT: Z 87 GLN cc_start: 0.9237 (mt0) cc_final: 0.8969 (mt0) REVERT: Z 138 GLU cc_start: 0.8365 (tp30) cc_final: 0.7986 (tp30) REVERT: Z 176 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8635 (tm-30) REVERT: Z 181 LYS cc_start: 0.8954 (tptp) cc_final: 0.8743 (tptp) REVERT: A 12 GLU cc_start: 0.8307 (mp0) cc_final: 0.7936 (mp0) REVERT: A 57 GLU cc_start: 0.4054 (OUTLIER) cc_final: 0.3438 (mt-10) REVERT: A 61 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7707 (mt-10) REVERT: A 80 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8639 (mm-40) REVERT: A 109 GLN cc_start: 0.8918 (tp40) cc_final: 0.8139 (tp40) REVERT: A 113 ASP cc_start: 0.8463 (m-30) cc_final: 0.7813 (m-30) REVERT: A 128 ASP cc_start: 0.8874 (t70) cc_final: 0.8507 (t0) REVERT: A 132 SER cc_start: 0.9605 (t) cc_final: 0.9382 (p) REVERT: A 140 LYS cc_start: 0.9357 (tppp) cc_final: 0.8953 (mmtm) REVERT: A 176 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8414 (tm-30) REVERT: C 12 GLU cc_start: 0.8459 (mp0) cc_final: 0.8239 (mp0) REVERT: C 57 GLU cc_start: 0.4316 (OUTLIER) cc_final: 0.3666 (mt-10) REVERT: C 61 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7716 (mt-10) REVERT: C 80 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8760 (mm-40) REVERT: C 87 GLN cc_start: 0.9222 (mt0) cc_final: 0.8991 (mt0) REVERT: C 95 GLU cc_start: 0.8276 (mp0) cc_final: 0.8048 (mp0) REVERT: C 113 ASP cc_start: 0.8489 (m-30) cc_final: 0.8277 (m-30) REVERT: C 132 SER cc_start: 0.9683 (t) cc_final: 0.9442 (p) REVERT: C 138 GLU cc_start: 0.8528 (tp30) cc_final: 0.8090 (mm-30) REVERT: C 176 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8473 (tm-30) REVERT: E 12 GLU cc_start: 0.8370 (mp0) cc_final: 0.8114 (mp0) REVERT: E 46 GLU cc_start: 0.8144 (pp20) cc_final: 0.7836 (pp20) REVERT: E 57 GLU cc_start: 0.4430 (OUTLIER) cc_final: 0.3928 (mt-10) REVERT: E 61 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7673 (mt-10) REVERT: E 72 ASP cc_start: 0.8756 (m-30) cc_final: 0.8415 (m-30) REVERT: E 104 GLU cc_start: 0.8560 (tp30) cc_final: 0.8247 (tp30) REVERT: E 138 GLU cc_start: 0.8371 (tp30) cc_final: 0.7978 (tp30) REVERT: E 176 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8548 (tm-30) REVERT: E 181 LYS cc_start: 0.9028 (tptp) cc_final: 0.8803 (tptp) REVERT: G 12 GLU cc_start: 0.8516 (mp0) cc_final: 0.8166 (mp0) REVERT: G 46 GLU cc_start: 0.8220 (pp20) cc_final: 0.7897 (pp20) REVERT: G 57 GLU cc_start: 0.4651 (OUTLIER) cc_final: 0.4115 (mt-10) REVERT: G 87 GLN cc_start: 0.9329 (mt0) cc_final: 0.9053 (mt0) REVERT: H 12 GLU cc_start: 0.8351 (mp0) cc_final: 0.7882 (mp0) REVERT: H 57 GLU cc_start: 0.3736 (OUTLIER) cc_final: 0.3189 (mt-10) REVERT: H 61 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7456 (mt-10) REVERT: H 80 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8435 (mm-40) REVERT: H 104 GLU cc_start: 0.8710 (tp30) cc_final: 0.8380 (tp30) REVERT: H 138 GLU cc_start: 0.8372 (tp30) cc_final: 0.7983 (tp30) REVERT: H 176 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8168 (tm-30) REVERT: I 12 GLU cc_start: 0.8375 (mp0) cc_final: 0.7959 (mp0) REVERT: I 57 GLU cc_start: 0.4130 (OUTLIER) cc_final: 0.3413 (mt-10) REVERT: I 61 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7646 (mt-10) REVERT: I 80 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8653 (mm-40) REVERT: I 95 GLU cc_start: 0.8369 (mp0) cc_final: 0.8083 (mp0) REVERT: I 113 ASP cc_start: 0.8616 (m-30) cc_final: 0.8410 (m-30) REVERT: I 176 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8415 (tm-30) REVERT: J 12 GLU cc_start: 0.8335 (mp0) cc_final: 0.7897 (mp0) REVERT: J 57 GLU cc_start: 0.4380 (OUTLIER) cc_final: 0.3735 (tt0) REVERT: J 61 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7732 (mt-10) REVERT: J 80 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8762 (mm-40) REVERT: J 87 GLN cc_start: 0.9237 (mt0) cc_final: 0.8943 (mt0) REVERT: J 95 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: J 104 GLU cc_start: 0.8573 (tp30) cc_final: 0.8281 (tp30) REVERT: J 128 ASP cc_start: 0.8918 (t0) cc_final: 0.8579 (t0) REVERT: J 176 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8378 (tm-30) REVERT: K 8 ASN cc_start: 0.9067 (t0) cc_final: 0.8858 (t0) REVERT: K 12 GLU cc_start: 0.8484 (mp0) cc_final: 0.8267 (mp0) REVERT: K 57 GLU cc_start: 0.4362 (OUTLIER) cc_final: 0.4117 (mt-10) REVERT: K 61 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7618 (mt-10) REVERT: K 80 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8830 (mm-40) REVERT: K 87 GLN cc_start: 0.9269 (mt0) cc_final: 0.9060 (mt0) REVERT: K 109 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8493 (tp40) REVERT: K 132 SER cc_start: 0.9630 (t) cc_final: 0.9427 (p) REVERT: K 138 GLU cc_start: 0.8391 (tp30) cc_final: 0.7989 (mm-30) REVERT: K 176 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8378 (tm-30) REVERT: L 8 ASN cc_start: 0.9025 (t0) cc_final: 0.8571 (t0) REVERT: L 12 GLU cc_start: 0.8451 (mp0) cc_final: 0.8237 (mp0) REVERT: L 46 GLU cc_start: 0.8130 (pp20) cc_final: 0.7893 (pp20) REVERT: L 57 GLU cc_start: 0.4372 (OUTLIER) cc_final: 0.4128 (tt0) REVERT: L 61 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7652 (mt-10) REVERT: L 80 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8692 (mm-40) REVERT: L 87 GLN cc_start: 0.9241 (mt0) cc_final: 0.9014 (mt0) REVERT: L 95 GLU cc_start: 0.8379 (mp0) cc_final: 0.8031 (pm20) REVERT: L 176 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8737 (tm-30) REVERT: L 181 LYS cc_start: 0.9089 (tptp) cc_final: 0.8867 (tptp) REVERT: M 57 GLU cc_start: 0.4198 (OUTLIER) cc_final: 0.3456 (mt-10) REVERT: M 61 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7648 (mt-10) REVERT: M 80 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8628 (mm-40) REVERT: M 109 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8476 (tp40) REVERT: M 138 GLU cc_start: 0.8451 (tp30) cc_final: 0.8092 (mm-30) REVERT: M 140 LYS cc_start: 0.9329 (tppp) cc_final: 0.8932 (mmtm) REVERT: M 176 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8256 (tm-30) REVERT: N 8 ASN cc_start: 0.8995 (t0) cc_final: 0.8066 (t0) REVERT: N 57 GLU cc_start: 0.5610 (OUTLIER) cc_final: 0.5233 (mt-10) REVERT: N 68 GLU cc_start: 0.8341 (pt0) cc_final: 0.8121 (pp20) REVERT: N 72 ASP cc_start: 0.8778 (m-30) cc_final: 0.8426 (m-30) REVERT: N 80 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8679 (mm-40) REVERT: N 84 LYS cc_start: 0.9443 (OUTLIER) cc_final: 0.9234 (ptmm) REVERT: N 92 LYS cc_start: 0.8935 (mmpt) cc_final: 0.8523 (mmmt) REVERT: N 109 GLN cc_start: 0.8850 (tp40) cc_final: 0.8367 (tp40) REVERT: O 8 ASN cc_start: 0.8941 (t0) cc_final: 0.8079 (t0) REVERT: O 10 SER cc_start: 0.8635 (p) cc_final: 0.8409 (p) REVERT: O 41 ASP cc_start: 0.8045 (p0) cc_final: 0.7728 (p0) REVERT: O 57 GLU cc_start: 0.5624 (OUTLIER) cc_final: 0.5319 (mt-10) REVERT: O 72 ASP cc_start: 0.8757 (m-30) cc_final: 0.8470 (m-30) REVERT: O 80 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8771 (mm-40) REVERT: O 84 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9206 (ptmm) REVERT: O 92 LYS cc_start: 0.8943 (mmpt) cc_final: 0.8552 (mmmt) REVERT: O 109 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8404 (tp40) REVERT: P 57 GLU cc_start: 0.4105 (OUTLIER) cc_final: 0.3473 (mt-10) REVERT: P 61 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7574 (mt-10) REVERT: P 80 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8630 (mm-40) REVERT: P 132 SER cc_start: 0.9611 (t) cc_final: 0.9314 (p) REVERT: P 138 GLU cc_start: 0.8394 (tp30) cc_final: 0.8055 (mm-30) REVERT: P 176 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8467 (tm-30) REVERT: Q 57 GLU cc_start: 0.4438 (OUTLIER) cc_final: 0.3878 (mt-10) REVERT: Q 61 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7375 (mt-10) REVERT: Q 72 ASP cc_start: 0.8646 (m-30) cc_final: 0.8339 (m-30) REVERT: Q 80 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8716 (mm-40) REVERT: Q 176 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8313 (tm-30) REVERT: R 12 GLU cc_start: 0.8271 (mp0) cc_final: 0.7812 (mp0) REVERT: R 61 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7563 (mt-10) REVERT: R 72 ASP cc_start: 0.8590 (m-30) cc_final: 0.8329 (m-30) REVERT: R 80 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8753 (mm-40) REVERT: R 87 GLN cc_start: 0.9303 (mt0) cc_final: 0.9031 (mt0) REVERT: R 138 GLU cc_start: 0.8380 (tp30) cc_final: 0.7959 (tp30) REVERT: R 176 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8728 (tm-30) REVERT: S 8 ASN cc_start: 0.9005 (t0) cc_final: 0.8120 (t0) REVERT: S 57 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.5385 (mt-10) REVERT: S 80 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8551 (mm-40) REVERT: S 92 LYS cc_start: 0.8924 (mmpt) cc_final: 0.8512 (mmmt) REVERT: S 109 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8402 (tp40) REVERT: T 8 ASN cc_start: 0.8968 (t0) cc_final: 0.8113 (t0) REVERT: T 41 ASP cc_start: 0.8141 (p0) cc_final: 0.7774 (p0) REVERT: T 57 GLU cc_start: 0.5787 (OUTLIER) cc_final: 0.5328 (mt-10) REVERT: T 80 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8623 (mm-40) REVERT: T 92 LYS cc_start: 0.8951 (mmpt) cc_final: 0.8534 (mmmt) REVERT: T 109 GLN cc_start: 0.8861 (tp40) cc_final: 0.8440 (tp40) REVERT: T 128 ASP cc_start: 0.8960 (t70) cc_final: 0.8754 (t0) REVERT: U 12 GLU cc_start: 0.8332 (mp0) cc_final: 0.7804 (mp0) REVERT: U 57 GLU cc_start: 0.4233 (OUTLIER) cc_final: 0.3599 (mt-10) REVERT: U 61 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7768 (mt-10) REVERT: U 80 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8561 (mm-40) REVERT: U 95 GLU cc_start: 0.8406 (mp0) cc_final: 0.8133 (mp0) REVERT: U 128 ASP cc_start: 0.8913 (t0) cc_final: 0.8597 (t0) REVERT: U 138 GLU cc_start: 0.8544 (tp30) cc_final: 0.8284 (tp30) REVERT: U 176 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8423 (tm-30) REVERT: V 12 GLU cc_start: 0.8464 (mp0) cc_final: 0.8259 (mp0) REVERT: V 57 GLU cc_start: 0.4395 (OUTLIER) cc_final: 0.3839 (mt-10) REVERT: V 87 GLN cc_start: 0.9302 (mt0) cc_final: 0.9070 (mt0) REVERT: V 132 SER cc_start: 0.9658 (t) cc_final: 0.9437 (p) REVERT: V 138 GLU cc_start: 0.8404 (tp30) cc_final: 0.8032 (mm-30) REVERT: V 176 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8424 (tm-30) REVERT: W 8 ASN cc_start: 0.9022 (t0) cc_final: 0.8559 (t0) REVERT: W 12 GLU cc_start: 0.8473 (mp0) cc_final: 0.8256 (mp0) REVERT: W 46 GLU cc_start: 0.8184 (pp20) cc_final: 0.7903 (pp20) REVERT: W 57 GLU cc_start: 0.4382 (OUTLIER) cc_final: 0.3664 (mt-10) REVERT: W 61 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7674 (mt-10) REVERT: W 72 ASP cc_start: 0.8732 (m-30) cc_final: 0.8405 (m-30) REVERT: W 80 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8743 (mm-40) REVERT: W 87 GLN cc_start: 0.9252 (mt0) cc_final: 0.9008 (mt0) REVERT: W 95 GLU cc_start: 0.8255 (mp0) cc_final: 0.8012 (mp0) REVERT: W 109 GLN cc_start: 0.8990 (tp40) cc_final: 0.8541 (tp40) REVERT: W 113 ASP cc_start: 0.8534 (m-30) cc_final: 0.7905 (m-30) REVERT: W 138 GLU cc_start: 0.8480 (tp30) cc_final: 0.8027 (mm-30) REVERT: W 176 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8770 (tm-30) REVERT: W 181 LYS cc_start: 0.9104 (tptp) cc_final: 0.8845 (tptp) REVERT: B 57 GLU cc_start: 0.4422 (OUTLIER) cc_final: 0.3542 (mt-10) REVERT: B 61 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7781 (mt-10) REVERT: B 80 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8709 (mm-40) REVERT: B 95 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: B 104 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8070 (mm-30) REVERT: B 128 ASP cc_start: 0.8875 (t70) cc_final: 0.8479 (t0) REVERT: B 138 GLU cc_start: 0.8580 (tp30) cc_final: 0.8088 (tp30) REVERT: B 140 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8930 (mtpp) REVERT: B 176 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8529 (tm-30) REVERT: D 8 ASN cc_start: 0.9117 (t0) cc_final: 0.8721 (t0) REVERT: D 57 GLU cc_start: 0.4379 (OUTLIER) cc_final: 0.3789 (mt-10) REVERT: D 61 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7571 (mt-10) REVERT: D 80 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8676 (mm-40) REVERT: D 95 GLU cc_start: 0.8333 (mp0) cc_final: 0.8121 (mp0) REVERT: D 109 GLN cc_start: 0.8989 (tp40) cc_final: 0.8264 (tp40) REVERT: D 113 ASP cc_start: 0.8428 (m-30) cc_final: 0.7789 (m-30) REVERT: D 132 SER cc_start: 0.9674 (t) cc_final: 0.9418 (p) REVERT: D 138 GLU cc_start: 0.8399 (tp30) cc_final: 0.7980 (mm-30) REVERT: D 176 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8233 (tm-30) REVERT: F 12 GLU cc_start: 0.8264 (mp0) cc_final: 0.7786 (mp0) REVERT: F 57 GLU cc_start: 0.4126 (OUTLIER) cc_final: 0.3665 (mt-10) REVERT: F 61 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7615 (mt-10) REVERT: F 80 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8542 (mm-40) REVERT: F 84 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9114 (pttp) REVERT: F 95 GLU cc_start: 0.8416 (mp0) cc_final: 0.8158 (mp0) REVERT: F 108 ASN cc_start: 0.9234 (t0) cc_final: 0.8672 (t0) REVERT: F 109 GLN cc_start: 0.8931 (tp40) cc_final: 0.8537 (tp40) REVERT: F 113 ASP cc_start: 0.8681 (m-30) cc_final: 0.8305 (m-30) REVERT: F 138 GLU cc_start: 0.8429 (tp30) cc_final: 0.8098 (mm-30) REVERT: F 176 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8427 (tm-30) outliers start: 147 outliers final: 77 residues processed: 1690 average time/residue: 1.6002 time to fit residues: 3191.8482 Evaluate side-chains 1601 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1496 time to evaluate : 4.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 88 ASP Chi-restraints excluded: chain Z residue 127 CYS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 127 CYS Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 127 CYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain L residue 188 SER Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 127 CYS Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 127 CYS Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain N residue 188 SER Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 84 LYS Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 127 CYS Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain P residue 127 CYS Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 88 ASP Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 127 CYS Chi-restraints excluded: chain S residue 188 SER Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain T residue 127 CYS Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain U residue 57 GLU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 127 CYS Chi-restraints excluded: chain V residue 57 GLU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain V residue 127 CYS Chi-restraints excluded: chain V residue 188 SER Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 127 CYS Chi-restraints excluded: chain W residue 188 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 127 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 0.6980 chunk 114 optimal weight: 8.9990 chunk 308 optimal weight: 4.9990 chunk 252 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 371 optimal weight: 0.7980 chunk 400 optimal weight: 2.9990 chunk 330 optimal weight: 10.0000 chunk 368 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 297 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 182 HIS ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 GLN ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN C 182 HIS ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS H 4 GLN H 94 GLN ** H 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN I 94 GLN I 182 HIS ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN J 87 GLN J 182 HIS ** J 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 182 HIS L 182 HIS M 4 GLN M 87 GLN ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 ASN ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 ASN ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 GLN P 109 GLN ** P 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 GLN Q 83 GLN Q 182 HIS R 4 GLN ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 182 HIS ** S 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 147 ASN ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 4 GLN U 94 GLN ** U 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 4 GLN ** V 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 4 GLN W 83 GLN W 87 GLN W 182 HIS ** W 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN B 87 GLN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN D 94 GLN D 182 HIS ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 34944 Z= 0.247 Angle : 0.530 6.253 46944 Z= 0.286 Chirality : 0.034 0.131 5040 Planarity : 0.003 0.025 6240 Dihedral : 5.834 57.926 4724 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 5.47 % Allowed : 30.58 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.13), residues: 4176 helix: 2.07 (0.09), residues: 3432 sheet: None (None), residues: 0 loop : -1.67 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 90 HIS 0.009 0.001 HIS Z 182 PHE 0.010 0.001 PHE G 129 TYR 0.009 0.001 TYR N 134 ARG 0.005 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1739 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1542 time to evaluate : 4.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 12 GLU cc_start: 0.8370 (mp0) cc_final: 0.8112 (mp0) REVERT: Z 46 GLU cc_start: 0.8223 (pp20) cc_final: 0.7978 (pp20) REVERT: Z 57 GLU cc_start: 0.4482 (OUTLIER) cc_final: 0.4250 (tt0) REVERT: Z 61 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7864 (mt-10) REVERT: Z 80 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8696 (mm-40) REVERT: Z 87 GLN cc_start: 0.9273 (mt0) cc_final: 0.9017 (mt0) REVERT: Z 176 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8618 (tm-30) REVERT: A 57 GLU cc_start: 0.4283 (OUTLIER) cc_final: 0.3735 (mt-10) REVERT: A 61 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7878 (mt-10) REVERT: A 80 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8714 (mm-40) REVERT: A 92 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8539 (mmmt) REVERT: A 104 GLU cc_start: 0.8571 (tp30) cc_final: 0.8134 (tp30) REVERT: A 121 ARG cc_start: 0.8571 (mmm-85) cc_final: 0.7604 (mmm-85) REVERT: A 128 ASP cc_start: 0.9032 (t70) cc_final: 0.8704 (t0) REVERT: A 138 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8042 (tp30) REVERT: A 140 LYS cc_start: 0.9382 (tppp) cc_final: 0.9037 (mmtp) REVERT: A 176 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8395 (tm-30) REVERT: C 12 GLU cc_start: 0.8305 (mp0) cc_final: 0.8068 (mp0) REVERT: C 57 GLU cc_start: 0.4365 (OUTLIER) cc_final: 0.3833 (mt-10) REVERT: C 61 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7867 (mt-10) REVERT: C 80 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8811 (mm-40) REVERT: C 87 GLN cc_start: 0.9268 (mt0) cc_final: 0.9005 (mt0) REVERT: C 95 GLU cc_start: 0.8381 (mp0) cc_final: 0.8101 (mp0) REVERT: C 104 GLU cc_start: 0.8759 (tp30) cc_final: 0.8290 (tp30) REVERT: C 121 ARG cc_start: 0.9137 (tpp-160) cc_final: 0.8847 (tpp80) REVERT: C 138 GLU cc_start: 0.8539 (tp30) cc_final: 0.8263 (tp30) REVERT: C 176 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8514 (tm-30) REVERT: E 46 GLU cc_start: 0.8170 (pp20) cc_final: 0.7960 (pp20) REVERT: E 57 GLU cc_start: 0.4555 (OUTLIER) cc_final: 0.4317 (tt0) REVERT: E 61 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7890 (mt-10) REVERT: E 87 GLN cc_start: 0.9272 (mt0) cc_final: 0.8956 (mt0) REVERT: E 92 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8789 (mmmt) REVERT: E 176 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8593 (tm-30) REVERT: G 46 GLU cc_start: 0.8248 (pp20) cc_final: 0.8016 (pp20) REVERT: G 87 GLN cc_start: 0.9331 (mt0) cc_final: 0.8993 (mt0) REVERT: G 92 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8733 (mmmt) REVERT: G 121 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8633 (tpp-160) REVERT: H 57 GLU cc_start: 0.4468 (OUTLIER) cc_final: 0.3764 (mt-10) REVERT: H 61 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7780 (mt-10) REVERT: H 87 GLN cc_start: 0.9166 (mt0) cc_final: 0.8921 (mt0) REVERT: H 92 LYS cc_start: 0.8905 (mmmt) cc_final: 0.8668 (mmmt) REVERT: H 104 GLU cc_start: 0.8718 (tp30) cc_final: 0.8475 (tp30) REVERT: H 176 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8383 (tm-30) REVERT: I 57 GLU cc_start: 0.4586 (OUTLIER) cc_final: 0.4100 (mt-10) REVERT: I 61 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7749 (mt-10) REVERT: I 80 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8726 (mm-40) REVERT: I 87 GLN cc_start: 0.9207 (mt0) cc_final: 0.8917 (mt0) REVERT: I 95 GLU cc_start: 0.8390 (mp0) cc_final: 0.8159 (mp0) REVERT: I 105 LYS cc_start: 0.9154 (mtpm) cc_final: 0.8952 (mttm) REVERT: I 121 ARG cc_start: 0.8665 (mmm-85) cc_final: 0.7993 (mmm-85) REVERT: I 176 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8508 (tm-30) REVERT: J 57 GLU cc_start: 0.4529 (OUTLIER) cc_final: 0.4095 (mt-10) REVERT: J 61 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7843 (mt-10) REVERT: J 80 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8821 (mm-40) REVERT: J 87 GLN cc_start: 0.9310 (mt0) cc_final: 0.8986 (mt0) REVERT: J 92 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8589 (mmmt) REVERT: J 95 GLU cc_start: 0.8267 (pm20) cc_final: 0.7933 (pm20) REVERT: J 138 GLU cc_start: 0.8688 (tp30) cc_final: 0.8258 (tp30) REVERT: J 176 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8475 (tm-30) REVERT: K 8 ASN cc_start: 0.9030 (t0) cc_final: 0.8507 (t0) REVERT: K 12 GLU cc_start: 0.8382 (mp0) cc_final: 0.8114 (mp0) REVERT: K 61 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7828 (mt-10) REVERT: K 80 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8805 (mm-40) REVERT: K 87 GLN cc_start: 0.9270 (mt0) cc_final: 0.8995 (mt0) REVERT: K 109 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8472 (tp40) REVERT: K 113 ASP cc_start: 0.8521 (m-30) cc_final: 0.8319 (m-30) REVERT: K 121 ARG cc_start: 0.9141 (tpp-160) cc_final: 0.8923 (tpp80) REVERT: K 138 GLU cc_start: 0.8362 (tp30) cc_final: 0.8159 (mm-30) REVERT: K 176 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8608 (tm-30) REVERT: L 8 ASN cc_start: 0.8899 (t0) cc_final: 0.8687 (t0) REVERT: L 12 GLU cc_start: 0.8350 (mp0) cc_final: 0.8067 (mp0) REVERT: L 57 GLU cc_start: 0.4546 (OUTLIER) cc_final: 0.4319 (tt0) REVERT: L 61 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7829 (mt-10) REVERT: L 80 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8747 (mm-40) REVERT: L 87 GLN cc_start: 0.9251 (mt0) cc_final: 0.8999 (mt0) REVERT: L 95 GLU cc_start: 0.8439 (mp0) cc_final: 0.8237 (mp0) REVERT: L 109 GLN cc_start: 0.8825 (tp40) cc_final: 0.8558 (tp40) REVERT: L 121 ARG cc_start: 0.9141 (tpp-160) cc_final: 0.8884 (tpp80) REVERT: L 138 GLU cc_start: 0.8344 (tp30) cc_final: 0.8133 (mm-30) REVERT: L 176 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8699 (tm-30) REVERT: M 57 GLU cc_start: 0.4454 (OUTLIER) cc_final: 0.4118 (mt-10) REVERT: M 61 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7845 (mt-10) REVERT: M 80 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8713 (mm-40) REVERT: M 87 GLN cc_start: 0.9172 (mt0) cc_final: 0.8960 (mt0) REVERT: M 95 GLU cc_start: 0.8411 (mp0) cc_final: 0.8164 (pm20) REVERT: M 109 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8498 (tp40) REVERT: M 140 LYS cc_start: 0.9361 (tppp) cc_final: 0.9003 (mmtp) REVERT: M 176 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8673 (tm-30) REVERT: N 57 GLU cc_start: 0.4751 (OUTLIER) cc_final: 0.4228 (mt-10) REVERT: N 68 GLU cc_start: 0.8429 (pt0) cc_final: 0.8156 (pp20) REVERT: N 80 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8803 (mm-40) REVERT: N 104 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8518 (mm-30) REVERT: N 109 GLN cc_start: 0.8953 (tp40) cc_final: 0.8468 (tp40) REVERT: N 138 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8252 (tp30) REVERT: O 80 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8759 (mm-40) REVERT: O 92 LYS cc_start: 0.8969 (mmpt) cc_final: 0.8764 (mmmt) REVERT: O 109 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8401 (tp40) REVERT: P 57 GLU cc_start: 0.4509 (OUTLIER) cc_final: 0.4216 (tt0) REVERT: P 61 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7740 (mt-10) REVERT: P 80 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8732 (mm-40) REVERT: P 87 GLN cc_start: 0.9175 (mt0) cc_final: 0.8963 (mt0) REVERT: P 95 GLU cc_start: 0.8417 (mp0) cc_final: 0.8155 (pm20) REVERT: Q 57 GLU cc_start: 0.4624 (OUTLIER) cc_final: 0.3908 (tt0) REVERT: Q 61 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7735 (mt-10) REVERT: Q 80 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8764 (mm-40) REVERT: Q 87 GLN cc_start: 0.9226 (mt0) cc_final: 0.8974 (mt0) REVERT: Q 92 LYS cc_start: 0.8938 (mmmt) cc_final: 0.8730 (mmmt) REVERT: Q 176 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8443 (tm-30) REVERT: R 61 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7797 (mt-10) REVERT: R 80 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8738 (mm-40) REVERT: R 87 GLN cc_start: 0.9303 (mt0) cc_final: 0.9012 (mt0) REVERT: R 176 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8690 (tm-30) REVERT: S 57 GLU cc_start: 0.4526 (OUTLIER) cc_final: 0.3863 (mt-10) REVERT: S 80 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8744 (mm-40) REVERT: S 104 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8582 (mm-30) REVERT: S 109 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8381 (tp40) REVERT: S 138 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8286 (tp30) REVERT: T 80 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8761 (mm-40) REVERT: T 92 LYS cc_start: 0.8977 (mmpt) cc_final: 0.8758 (mmmt) REVERT: T 109 GLN cc_start: 0.8988 (tp40) cc_final: 0.8539 (tp40) REVERT: T 128 ASP cc_start: 0.8956 (t70) cc_final: 0.8658 (t0) REVERT: U 57 GLU cc_start: 0.4436 (OUTLIER) cc_final: 0.3712 (tt0) REVERT: U 61 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7839 (mt-10) REVERT: U 80 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8698 (mm-40) REVERT: U 84 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9194 (pttp) REVERT: U 95 GLU cc_start: 0.8379 (mp0) cc_final: 0.8162 (mp0) REVERT: U 104 GLU cc_start: 0.8610 (tp30) cc_final: 0.8331 (tp30) REVERT: U 121 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.7837 (mmm-85) REVERT: U 137 LYS cc_start: 0.9253 (mtpm) cc_final: 0.8988 (mtmm) REVERT: U 138 GLU cc_start: 0.8495 (tp30) cc_final: 0.8241 (tp30) REVERT: U 176 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8506 (tm-30) REVERT: V 12 GLU cc_start: 0.8382 (mp0) cc_final: 0.8083 (mp0) REVERT: V 57 GLU cc_start: 0.4584 (OUTLIER) cc_final: 0.4219 (mt-10) REVERT: V 80 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8712 (mm-40) REVERT: V 87 GLN cc_start: 0.9306 (mt0) cc_final: 0.8996 (mt0) REVERT: V 92 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8699 (mmmt) REVERT: V 104 GLU cc_start: 0.8612 (tp30) cc_final: 0.8101 (tp30) REVERT: V 121 ARG cc_start: 0.9157 (tpp-160) cc_final: 0.8897 (tpp80) REVERT: V 176 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8486 (tm-30) REVERT: W 8 ASN cc_start: 0.8832 (t0) cc_final: 0.8612 (t0) REVERT: W 12 GLU cc_start: 0.8369 (mp0) cc_final: 0.8087 (mp0) REVERT: W 46 GLU cc_start: 0.8199 (pp20) cc_final: 0.7850 (pp20) REVERT: W 57 GLU cc_start: 0.4453 (OUTLIER) cc_final: 0.3916 (mt-10) REVERT: W 61 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7831 (mt-10) REVERT: W 80 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8776 (mm-40) REVERT: W 87 GLN cc_start: 0.9282 (mt0) cc_final: 0.8995 (mt0) REVERT: W 95 GLU cc_start: 0.8392 (mp0) cc_final: 0.8112 (mp0) REVERT: W 104 GLU cc_start: 0.8716 (tp30) cc_final: 0.8240 (tp30) REVERT: W 121 ARG cc_start: 0.9108 (tpp-160) cc_final: 0.8835 (tpp80) REVERT: W 138 GLU cc_start: 0.8383 (tp30) cc_final: 0.8119 (tp30) REVERT: W 140 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8812 (mmtm) REVERT: W 176 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8669 (tm-30) REVERT: B 12 GLU cc_start: 0.8182 (mp0) cc_final: 0.7969 (mp0) REVERT: B 57 GLU cc_start: 0.4338 (OUTLIER) cc_final: 0.3673 (mt-10) REVERT: B 61 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7848 (mt-10) REVERT: B 80 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8754 (mm-40) REVERT: B 92 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8658 (mmmt) REVERT: B 95 GLU cc_start: 0.8263 (pm20) cc_final: 0.7945 (pm20) REVERT: B 121 ARG cc_start: 0.8666 (mmm-85) cc_final: 0.8290 (mmm-85) REVERT: B 128 ASP cc_start: 0.8937 (t70) cc_final: 0.8560 (t0) REVERT: B 138 GLU cc_start: 0.8577 (tp30) cc_final: 0.8227 (tp30) REVERT: B 140 LYS cc_start: 0.9216 (mmmm) cc_final: 0.9008 (mtpp) REVERT: B 176 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8525 (tm-30) REVERT: D 57 GLU cc_start: 0.4529 (OUTLIER) cc_final: 0.4244 (tt0) REVERT: D 61 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7797 (mt-10) REVERT: D 80 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8768 (mm-40) REVERT: D 87 GLN cc_start: 0.9193 (mt0) cc_final: 0.8943 (mt0) REVERT: D 92 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8769 (mmmt) REVERT: D 95 GLU cc_start: 0.8350 (mp0) cc_final: 0.8023 (mp0) REVERT: D 176 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8641 (tm-30) REVERT: F 57 GLU cc_start: 0.4589 (OUTLIER) cc_final: 0.3816 (tt0) REVERT: F 61 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7890 (mt-10) REVERT: F 80 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8665 (mm-40) REVERT: F 87 GLN cc_start: 0.9125 (mt0) cc_final: 0.8858 (mt0) REVERT: F 95 GLU cc_start: 0.8380 (mp0) cc_final: 0.8153 (mp0) REVERT: F 104 GLU cc_start: 0.8627 (tp30) cc_final: 0.8352 (tp30) REVERT: F 121 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.7648 (mmm-85) REVERT: F 137 LYS cc_start: 0.9262 (mtpm) cc_final: 0.9024 (mtmm) REVERT: F 176 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8469 (tm-30) outliers start: 197 outliers final: 109 residues processed: 1606 average time/residue: 1.6348 time to fit residues: 3087.1409 Evaluate side-chains 1605 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1476 time to evaluate : 4.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 88 ASP Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 127 CYS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 127 CYS Chi-restraints excluded: chain J residue 188 SER Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 127 CYS Chi-restraints excluded: chain K residue 190 GLN Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 127 CYS Chi-restraints excluded: chain M residue 188 SER Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 127 CYS Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain N residue 140 LYS Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain N residue 188 SER Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 127 CYS Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 127 CYS Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 188 SER Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 88 ASP Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 127 CYS Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 140 LYS Chi-restraints excluded: chain S residue 188 SER Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain T residue 127 CYS Chi-restraints excluded: chain T residue 140 LYS Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain U residue 57 GLU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 84 LYS Chi-restraints excluded: chain U residue 188 SER Chi-restraints excluded: chain V residue 57 GLU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 127 CYS Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 127 CYS Chi-restraints excluded: chain W residue 188 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 139 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 7.9990 chunk 279 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 249 optimal weight: 0.9990 chunk 372 optimal weight: 1.9990 chunk 394 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 353 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 182 HIS ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN E 182 HIS G 4 GLN ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN I 4 GLN J 4 GLN ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 182 HIS L 4 GLN N 94 GLN ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 GLN Q 4 GLN R 4 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN R 182 HIS S 94 GLN ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 94 GLN ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 4 GLN ** V 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 4 GLN W 182 HIS W 190 GLN B 4 GLN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 34944 Z= 0.241 Angle : 0.526 6.188 46944 Z= 0.283 Chirality : 0.034 0.108 5040 Planarity : 0.003 0.039 6240 Dihedral : 5.162 53.143 4710 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 5.22 % Allowed : 31.64 % Favored : 63.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.13), residues: 4176 helix: 2.39 (0.09), residues: 3456 sheet: None (None), residues: 0 loop : -1.15 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 90 HIS 0.007 0.001 HIS Z 182 PHE 0.007 0.001 PHE T 36 TYR 0.009 0.001 TYR S 31 ARG 0.008 0.000 ARG P 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1703 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1515 time to evaluate : 4.017 Fit side-chains revert: symmetry clash REVERT: Z 46 GLU cc_start: 0.8220 (pp20) cc_final: 0.7889 (pp20) REVERT: Z 57 GLU cc_start: 0.4347 (OUTLIER) cc_final: 0.3949 (mt-10) REVERT: Z 61 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7823 (mt-10) REVERT: Z 80 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8822 (mm-40) REVERT: Z 87 GLN cc_start: 0.9291 (mt0) cc_final: 0.8978 (mt0) REVERT: Z 92 LYS cc_start: 0.8929 (mmmt) cc_final: 0.8469 (mmmt) REVERT: Z 176 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8601 (tm-30) REVERT: Z 181 LYS cc_start: 0.9001 (tptp) cc_final: 0.8717 (tptp) REVERT: A 57 GLU cc_start: 0.4437 (OUTLIER) cc_final: 0.4071 (mt-10) REVERT: A 61 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7918 (mt-10) REVERT: A 80 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8787 (mm-40) REVERT: A 84 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.9172 (pttp) REVERT: A 140 LYS cc_start: 0.9377 (tppp) cc_final: 0.9038 (mmtp) REVERT: C 12 GLU cc_start: 0.8313 (mp0) cc_final: 0.8087 (mp0) REVERT: C 57 GLU cc_start: 0.4358 (OUTLIER) cc_final: 0.4032 (mt-10) REVERT: C 61 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7935 (mt-10) REVERT: C 80 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8795 (mm-40) REVERT: C 87 GLN cc_start: 0.9238 (mt0) cc_final: 0.8984 (mt0) REVERT: C 92 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8664 (mmmt) REVERT: C 95 GLU cc_start: 0.8417 (mp0) cc_final: 0.8136 (mp0) REVERT: C 121 ARG cc_start: 0.9101 (tpp-160) cc_final: 0.8843 (tpp80) REVERT: E 46 GLU cc_start: 0.8172 (pp20) cc_final: 0.7885 (pp20) REVERT: E 57 GLU cc_start: 0.4414 (OUTLIER) cc_final: 0.3958 (mt-10) REVERT: E 61 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7866 (mt-10) REVERT: E 87 GLN cc_start: 0.9309 (mt0) cc_final: 0.9031 (mt0) REVERT: E 104 GLU cc_start: 0.8724 (tp30) cc_final: 0.8351 (tp30) REVERT: E 176 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8583 (tm-30) REVERT: E 177 ARG cc_start: 0.9411 (OUTLIER) cc_final: 0.9131 (mmm160) REVERT: E 181 LYS cc_start: 0.9003 (tptp) cc_final: 0.8766 (tptp) REVERT: G 46 GLU cc_start: 0.8247 (pp20) cc_final: 0.8019 (pp20) REVERT: G 87 GLN cc_start: 0.9250 (mt0) cc_final: 0.8964 (mt0) REVERT: G 92 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8491 (mmmt) REVERT: H 57 GLU cc_start: 0.4487 (OUTLIER) cc_final: 0.4159 (tt0) REVERT: H 61 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7808 (mt-10) REVERT: H 87 GLN cc_start: 0.9199 (mt0) cc_final: 0.8938 (mt0) REVERT: H 121 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.8188 (mmm-85) REVERT: I 57 GLU cc_start: 0.4495 (OUTLIER) cc_final: 0.4201 (tt0) REVERT: I 61 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7826 (mt-10) REVERT: I 80 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8775 (mm-40) REVERT: I 87 GLN cc_start: 0.9247 (mt0) cc_final: 0.8994 (mt0) REVERT: I 92 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8671 (mmmt) REVERT: I 95 GLU cc_start: 0.8407 (mp0) cc_final: 0.8158 (mp0) REVERT: I 109 GLN cc_start: 0.9023 (tp40) cc_final: 0.8251 (tp40) REVERT: I 121 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8210 (mmm-85) REVERT: J 57 GLU cc_start: 0.4486 (OUTLIER) cc_final: 0.4245 (tt0) REVERT: J 80 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8739 (mm-40) REVERT: J 87 GLN cc_start: 0.9289 (mt0) cc_final: 0.9017 (mt0) REVERT: J 92 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8578 (mmmt) REVERT: J 95 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: J 176 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8679 (tm-30) REVERT: K 10 SER cc_start: 0.8471 (p) cc_final: 0.7903 (p) REVERT: K 61 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7830 (mt-10) REVERT: K 80 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8786 (mm-40) REVERT: K 84 LYS cc_start: 0.9485 (OUTLIER) cc_final: 0.9243 (pttp) REVERT: K 87 GLN cc_start: 0.9245 (mt0) cc_final: 0.8974 (mt0) REVERT: K 109 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8402 (tp40) REVERT: K 176 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8571 (tm-30) REVERT: L 8 ASN cc_start: 0.8901 (t0) cc_final: 0.8669 (t0) REVERT: L 46 GLU cc_start: 0.8139 (pp20) cc_final: 0.7930 (pp20) REVERT: L 57 GLU cc_start: 0.4458 (OUTLIER) cc_final: 0.4218 (tt0) REVERT: L 61 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7843 (mt-10) REVERT: L 80 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8799 (mm-40) REVERT: L 87 GLN cc_start: 0.9236 (mt0) cc_final: 0.8967 (mt0) REVERT: L 95 GLU cc_start: 0.8405 (mp0) cc_final: 0.8194 (mp0) REVERT: L 176 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8684 (tm-30) REVERT: L 181 LYS cc_start: 0.9079 (tptp) cc_final: 0.8876 (tptp) REVERT: M 57 GLU cc_start: 0.4522 (OUTLIER) cc_final: 0.4028 (mt-10) REVERT: M 61 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7908 (mt-10) REVERT: M 80 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8726 (mm-40) REVERT: M 87 GLN cc_start: 0.9170 (mt0) cc_final: 0.8920 (mt0) REVERT: M 92 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8645 (mmmt) REVERT: M 95 GLU cc_start: 0.8355 (mp0) cc_final: 0.8070 (pm20) REVERT: M 109 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8470 (tp40) REVERT: M 140 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9020 (mmtp) REVERT: M 176 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8456 (tm-30) REVERT: N 80 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8807 (mm-40) REVERT: N 92 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8680 (mmmt) REVERT: N 95 GLU cc_start: 0.8355 (mp0) cc_final: 0.8097 (mp0) REVERT: N 140 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8796 (mmtm) REVERT: O 80 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8745 (mm-40) REVERT: O 92 LYS cc_start: 0.8860 (mmpt) cc_final: 0.8644 (mmmt) REVERT: O 104 GLU cc_start: 0.8537 (tp30) cc_final: 0.8255 (tp30) REVERT: O 109 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8366 (tp40) REVERT: O 138 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8270 (tp30) REVERT: P 57 GLU cc_start: 0.4458 (OUTLIER) cc_final: 0.3849 (mt-10) REVERT: P 61 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7880 (mt-10) REVERT: P 80 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8779 (mm-40) REVERT: P 87 GLN cc_start: 0.9195 (mt0) cc_final: 0.8939 (mt0) REVERT: P 92 LYS cc_start: 0.8850 (mmmt) cc_final: 0.8628 (mmmt) REVERT: P 95 GLU cc_start: 0.8382 (mp0) cc_final: 0.8067 (pm20) REVERT: P 176 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8539 (tm-30) REVERT: Q 57 GLU cc_start: 0.4579 (OUTLIER) cc_final: 0.4132 (mt-10) REVERT: Q 80 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8801 (mm-40) REVERT: Q 87 GLN cc_start: 0.9272 (mt0) cc_final: 0.8952 (mt0) REVERT: Q 176 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8473 (tm-30) REVERT: R 61 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7816 (mt-10) REVERT: R 80 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8767 (mm-40) REVERT: R 87 GLN cc_start: 0.9287 (mt0) cc_final: 0.9034 (mt0) REVERT: R 92 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8652 (mmmt) REVERT: R 104 GLU cc_start: 0.8727 (tp30) cc_final: 0.8331 (tp30) REVERT: R 137 LYS cc_start: 0.9214 (mtpm) cc_final: 0.8943 (mtmm) REVERT: R 176 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8689 (tm-30) REVERT: S 80 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8716 (mm-40) REVERT: S 92 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8664 (mmmt) REVERT: S 95 GLU cc_start: 0.8368 (mp0) cc_final: 0.8093 (mp0) REVERT: S 109 GLN cc_start: 0.8737 (mm-40) cc_final: 0.7891 (tp40) REVERT: S 113 ASP cc_start: 0.8452 (m-30) cc_final: 0.7856 (m-30) REVERT: S 138 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8263 (mm-30) REVERT: S 140 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8785 (mmtm) REVERT: T 80 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8738 (mm-40) REVERT: T 92 LYS cc_start: 0.8868 (mmpt) cc_final: 0.8652 (mmmt) REVERT: T 109 GLN cc_start: 0.8983 (tp40) cc_final: 0.8545 (tp40) REVERT: T 128 ASP cc_start: 0.8974 (t70) cc_final: 0.8667 (OUTLIER) REVERT: T 140 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8786 (mmtm) REVERT: U 57 GLU cc_start: 0.4514 (OUTLIER) cc_final: 0.4191 (tt0) REVERT: U 61 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7908 (mt-10) REVERT: U 80 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8748 (mm-40) REVERT: U 92 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8692 (mmmt) REVERT: U 95 GLU cc_start: 0.8401 (mp0) cc_final: 0.8159 (mp0) REVERT: U 121 ARG cc_start: 0.8524 (mmm-85) cc_final: 0.8283 (mmm-85) REVERT: U 137 LYS cc_start: 0.9242 (mtpm) cc_final: 0.8972 (mtmm) REVERT: V 10 SER cc_start: 0.8505 (p) cc_final: 0.7915 (p) REVERT: V 80 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8814 (mm-40) REVERT: V 87 GLN cc_start: 0.9232 (mt0) cc_final: 0.8981 (mt0) REVERT: V 92 LYS cc_start: 0.8871 (mmmt) cc_final: 0.8472 (mmmt) REVERT: V 138 GLU cc_start: 0.8709 (tp30) cc_final: 0.8394 (tp30) REVERT: W 10 SER cc_start: 0.8431 (p) cc_final: 0.7924 (p) REVERT: W 57 GLU cc_start: 0.4436 (OUTLIER) cc_final: 0.4199 (tt0) REVERT: W 61 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7876 (mt-10) REVERT: W 80 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8763 (mm-40) REVERT: W 87 GLN cc_start: 0.9257 (mt0) cc_final: 0.8996 (mt0) REVERT: W 92 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8718 (mmmt) REVERT: W 95 GLU cc_start: 0.8414 (mp0) cc_final: 0.8146 (mp0) REVERT: W 176 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8708 (tm-30) REVERT: B 57 GLU cc_start: 0.4488 (OUTLIER) cc_final: 0.4226 (tt0) REVERT: B 61 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7930 (mt-10) REVERT: B 80 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8761 (mm-40) REVERT: B 92 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8469 (mmmt) REVERT: B 95 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: B 121 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.8316 (mmm-85) REVERT: B 128 ASP cc_start: 0.8985 (t70) cc_final: 0.8593 (t0) REVERT: B 140 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8969 (mmtm) REVERT: D 57 GLU cc_start: 0.4473 (OUTLIER) cc_final: 0.4119 (mt-10) REVERT: D 61 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7911 (mt-10) REVERT: D 80 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8779 (mm-40) REVERT: D 87 GLN cc_start: 0.9185 (mt0) cc_final: 0.8938 (mt0) REVERT: D 92 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8641 (mmmt) REVERT: D 95 GLU cc_start: 0.8374 (mp0) cc_final: 0.8045 (mp0) REVERT: D 104 GLU cc_start: 0.8696 (tp30) cc_final: 0.8247 (tp30) REVERT: D 176 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8437 (tm-30) REVERT: F 57 GLU cc_start: 0.4518 (OUTLIER) cc_final: 0.4236 (tt0) REVERT: F 61 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7894 (mt-10) REVERT: F 80 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8718 (mm-40) REVERT: F 87 GLN cc_start: 0.9187 (mt0) cc_final: 0.8960 (mt0) REVERT: F 95 GLU cc_start: 0.8359 (mp0) cc_final: 0.8128 (mp0) REVERT: F 121 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8278 (mmm-85) REVERT: F 137 LYS cc_start: 0.9236 (mtpm) cc_final: 0.9004 (mtmm) outliers start: 188 outliers final: 76 residues processed: 1582 average time/residue: 1.6608 time to fit residues: 3078.8538 Evaluate side-chains 1561 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1461 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 190 GLN Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 140 LYS Chi-restraints excluded: chain M residue 190 GLN Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 127 CYS Chi-restraints excluded: chain N residue 140 LYS Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain N residue 188 SER Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 127 CYS Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain R residue 88 ASP Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 127 CYS Chi-restraints excluded: chain S residue 140 LYS Chi-restraints excluded: chain S residue 188 SER Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain T residue 127 CYS Chi-restraints excluded: chain T residue 140 LYS Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain U residue 57 GLU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 127 CYS Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 188 SER Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 188 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 188 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 293 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 336 optimal weight: 8.9990 chunk 272 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 353 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 4 GLN Z 182 HIS ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 GLN C 8 ASN C 83 GLN E 4 GLN E 80 GLN G 8 ASN G 80 GLN G 94 GLN H 8 ASN H 83 GLN H 94 GLN J 4 GLN J 8 ASN J 94 GLN K 4 GLN L 4 GLN L 94 GLN M 8 ASN N 4 GLN N 182 HIS ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN O 182 HIS ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 GLN Q 8 ASN R 4 GLN R 8 ASN R 83 GLN S 4 GLN ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 4 GLN ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 4 GLN V 94 GLN W 4 GLN W 83 GLN B 94 GLN B 190 GLN D 4 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34944 Z= 0.184 Angle : 0.517 6.597 46944 Z= 0.282 Chirality : 0.033 0.138 5040 Planarity : 0.003 0.036 6240 Dihedral : 3.986 43.708 4688 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.42 % Allowed : 31.69 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.13), residues: 4176 helix: 2.69 (0.09), residues: 3456 sheet: None (None), residues: 0 loop : -0.89 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 90 HIS 0.005 0.000 HIS O 182 PHE 0.005 0.001 PHE R 36 TYR 0.010 0.001 TYR P 173 ARG 0.008 0.000 ARG R 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1686 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1527 time to evaluate : 4.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 46 GLU cc_start: 0.8146 (pp20) cc_final: 0.7830 (pp20) REVERT: Z 57 GLU cc_start: 0.4249 (OUTLIER) cc_final: 0.3643 (tt0) REVERT: Z 58 GLU cc_start: 0.6197 (mm-30) cc_final: 0.5992 (mm-30) REVERT: Z 80 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8857 (mm-40) REVERT: Z 87 GLN cc_start: 0.9270 (mt0) cc_final: 0.8976 (mt0) REVERT: Z 104 GLU cc_start: 0.8597 (tp30) cc_final: 0.8200 (tp30) REVERT: Z 138 GLU cc_start: 0.8540 (mm-30) cc_final: 0.7989 (tp30) REVERT: Z 176 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8647 (tm-30) REVERT: Z 181 LYS cc_start: 0.8993 (tptp) cc_final: 0.8757 (tptp) REVERT: A 57 GLU cc_start: 0.4300 (OUTLIER) cc_final: 0.4064 (mt-10) REVERT: A 61 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7884 (mt-10) REVERT: A 80 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8753 (mm-40) REVERT: A 109 GLN cc_start: 0.8997 (tp40) cc_final: 0.8462 (tp40) REVERT: A 140 LYS cc_start: 0.9371 (tppp) cc_final: 0.9024 (mmtm) REVERT: A 176 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8522 (tm-30) REVERT: C 12 GLU cc_start: 0.8390 (mp0) cc_final: 0.8174 (mp0) REVERT: C 61 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7881 (mt-10) REVERT: C 80 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8749 (mm-40) REVERT: C 87 GLN cc_start: 0.9258 (mt0) cc_final: 0.8973 (mt0) REVERT: C 92 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8542 (mmmt) REVERT: C 95 GLU cc_start: 0.8422 (mp0) cc_final: 0.8190 (mp0) REVERT: E 46 GLU cc_start: 0.8127 (pp20) cc_final: 0.7858 (pp20) REVERT: E 58 GLU cc_start: 0.6474 (mm-30) cc_final: 0.6259 (mm-30) REVERT: E 87 GLN cc_start: 0.9285 (mt0) cc_final: 0.9021 (mt0) REVERT: E 92 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8638 (mmmt) REVERT: E 95 GLU cc_start: 0.8380 (mp0) cc_final: 0.8133 (pm20) REVERT: E 176 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8609 (tm-30) REVERT: E 177 ARG cc_start: 0.9359 (OUTLIER) cc_final: 0.9128 (mmm160) REVERT: G 87 GLN cc_start: 0.9242 (mt0) cc_final: 0.8960 (mt0) REVERT: G 92 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8574 (mmmt) REVERT: G 95 GLU cc_start: 0.8342 (mp0) cc_final: 0.8078 (pm20) REVERT: G 104 GLU cc_start: 0.8560 (tp30) cc_final: 0.8169 (tp30) REVERT: G 138 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8104 (tp30) REVERT: G 176 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8599 (tm-30) REVERT: H 57 GLU cc_start: 0.4418 (OUTLIER) cc_final: 0.3975 (mt-10) REVERT: H 58 GLU cc_start: 0.6506 (mm-30) cc_final: 0.6292 (mm-30) REVERT: H 87 GLN cc_start: 0.9196 (mt0) cc_final: 0.8926 (mt0) REVERT: H 121 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.8308 (mmm-85) REVERT: H 176 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8459 (tm-30) REVERT: I 57 GLU cc_start: 0.4384 (OUTLIER) cc_final: 0.3992 (mt-10) REVERT: I 61 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7782 (mt-10) REVERT: I 80 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8780 (mm-40) REVERT: I 87 GLN cc_start: 0.9232 (mt0) cc_final: 0.8973 (mt0) REVERT: I 95 GLU cc_start: 0.8443 (mp0) cc_final: 0.8241 (mp0) REVERT: I 109 GLN cc_start: 0.8999 (tp40) cc_final: 0.8234 (tp40) REVERT: I 176 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8522 (tm-30) REVERT: J 57 GLU cc_start: 0.4432 (OUTLIER) cc_final: 0.4068 (mt-10) REVERT: J 80 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8757 (mm-40) REVERT: J 87 GLN cc_start: 0.9315 (mt0) cc_final: 0.9001 (mt0) REVERT: J 92 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8522 (mmmt) REVERT: J 95 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: J 176 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8471 (tm-30) REVERT: K 61 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7805 (mt-10) REVERT: K 80 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8772 (mm-40) REVERT: K 87 GLN cc_start: 0.9185 (mt0) cc_final: 0.8923 (mt0) REVERT: K 92 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8670 (mmmt) REVERT: K 95 GLU cc_start: 0.8357 (mp0) cc_final: 0.8095 (pm20) REVERT: K 104 GLU cc_start: 0.8522 (tp30) cc_final: 0.8100 (tp30) REVERT: K 109 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8337 (tp40) REVERT: K 113 ASP cc_start: 0.8480 (m-30) cc_final: 0.8222 (m-30) REVERT: K 138 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8097 (tp30) REVERT: K 176 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8394 (tm-30) REVERT: L 46 GLU cc_start: 0.8074 (pp20) cc_final: 0.7801 (pp20) REVERT: L 57 GLU cc_start: 0.4452 (OUTLIER) cc_final: 0.4015 (mt-10) REVERT: L 68 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8126 (pp20) REVERT: L 80 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8774 (mm-40) REVERT: L 87 GLN cc_start: 0.9181 (mt0) cc_final: 0.8923 (mt0) REVERT: L 95 GLU cc_start: 0.8408 (mp0) cc_final: 0.8176 (mp0) REVERT: L 104 GLU cc_start: 0.8529 (tp30) cc_final: 0.7935 (tp30) REVERT: L 138 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7766 (tp30) REVERT: L 145 MET cc_start: 0.8625 (mtp) cc_final: 0.8225 (mtm) REVERT: L 176 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8712 (tm-30) REVERT: L 181 LYS cc_start: 0.9073 (tptp) cc_final: 0.8801 (tptp) REVERT: M 58 GLU cc_start: 0.6454 (mm-30) cc_final: 0.6244 (mm-30) REVERT: M 61 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7773 (mt-10) REVERT: M 80 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8748 (mm-40) REVERT: M 87 GLN cc_start: 0.9197 (mt0) cc_final: 0.8949 (mt0) REVERT: M 109 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8451 (tp40) REVERT: M 140 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9054 (mmtp) REVERT: N 68 GLU cc_start: 0.8480 (pt0) cc_final: 0.8208 (pp20) REVERT: N 80 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8836 (mm-40) REVERT: N 92 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8624 (mmmt) REVERT: N 95 GLU cc_start: 0.8376 (mp0) cc_final: 0.8050 (mp0) REVERT: N 104 GLU cc_start: 0.8519 (tp30) cc_final: 0.8278 (tp30) REVERT: N 138 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8209 (tp30) REVERT: N 140 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8864 (mmtm) REVERT: O 80 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8806 (mm-40) REVERT: O 95 GLU cc_start: 0.8346 (mp0) cc_final: 0.8048 (pm20) REVERT: O 140 LYS cc_start: 0.9208 (ttmm) cc_final: 0.8965 (mttm) REVERT: P 61 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7760 (mt-10) REVERT: P 80 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8751 (mm-40) REVERT: P 87 GLN cc_start: 0.9190 (mt0) cc_final: 0.8912 (mt0) REVERT: Q 80 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8763 (mm-40) REVERT: Q 87 GLN cc_start: 0.9257 (mt0) cc_final: 0.9005 (mt0) REVERT: Q 92 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8652 (mmmt) REVERT: Q 95 GLU cc_start: 0.8390 (mp0) cc_final: 0.8102 (pm20) REVERT: R 80 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8747 (mm-40) REVERT: R 87 GLN cc_start: 0.9292 (mt0) cc_final: 0.9019 (mt0) REVERT: R 137 LYS cc_start: 0.9212 (mtpm) cc_final: 0.8962 (mtmm) REVERT: R 176 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8663 (tm-30) REVERT: S 80 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8788 (mm-40) REVERT: S 92 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8635 (mmmt) REVERT: S 95 GLU cc_start: 0.8388 (mp0) cc_final: 0.8058 (mp0) REVERT: S 104 GLU cc_start: 0.8592 (tp30) cc_final: 0.8134 (tp30) REVERT: S 109 GLN cc_start: 0.8731 (mm-40) cc_final: 0.7902 (tp40) REVERT: S 113 ASP cc_start: 0.8459 (m-30) cc_final: 0.7860 (m-30) REVERT: S 136 ASP cc_start: 0.8408 (p0) cc_final: 0.8207 (t70) REVERT: S 138 GLU cc_start: 0.8553 (mm-30) cc_final: 0.7907 (tp30) REVERT: S 140 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8679 (mmtm) REVERT: T 80 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8778 (mm-40) REVERT: T 95 GLU cc_start: 0.8393 (mp0) cc_final: 0.8061 (pm20) REVERT: T 104 GLU cc_start: 0.8492 (tp30) cc_final: 0.8206 (tp30) REVERT: T 138 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8369 (tp30) REVERT: T 140 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8860 (mmtm) REVERT: U 46 GLU cc_start: 0.8123 (pp20) cc_final: 0.7882 (pp20) REVERT: U 58 GLU cc_start: 0.6503 (mm-30) cc_final: 0.6291 (mm-30) REVERT: U 61 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7825 (mt-10) REVERT: U 80 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8773 (mm-40) REVERT: U 92 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8632 (mmmt) REVERT: U 95 GLU cc_start: 0.8428 (mp0) cc_final: 0.8164 (mp0) REVERT: U 109 GLN cc_start: 0.9011 (tp40) cc_final: 0.8607 (tp40) REVERT: U 113 ASP cc_start: 0.8639 (m-30) cc_final: 0.8357 (m-30) REVERT: U 121 ARG cc_start: 0.8573 (mmm-85) cc_final: 0.8357 (mmm-85) REVERT: U 137 LYS cc_start: 0.9268 (mtpm) cc_final: 0.9044 (mtmm) REVERT: V 80 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8800 (mm-40) REVERT: V 87 GLN cc_start: 0.9221 (mt0) cc_final: 0.8962 (mt0) REVERT: V 92 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8562 (mmmt) REVERT: V 95 GLU cc_start: 0.8318 (mp0) cc_final: 0.8028 (pm20) REVERT: V 109 GLN cc_start: 0.8970 (tp40) cc_final: 0.8487 (tp40) REVERT: V 176 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8542 (tm-30) REVERT: W 57 GLU cc_start: 0.4424 (OUTLIER) cc_final: 0.4083 (mt-10) REVERT: W 80 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8758 (mm-40) REVERT: W 87 GLN cc_start: 0.9271 (mt0) cc_final: 0.8985 (mt0) REVERT: W 92 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8620 (mmmt) REVERT: W 95 GLU cc_start: 0.8436 (mp0) cc_final: 0.8164 (mp0) REVERT: W 104 GLU cc_start: 0.8607 (tp30) cc_final: 0.8365 (tp30) REVERT: W 138 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7887 (tp30) REVERT: W 176 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8662 (tm-30) REVERT: B 57 GLU cc_start: 0.4364 (OUTLIER) cc_final: 0.3814 (mt-10) REVERT: B 58 GLU cc_start: 0.6537 (mm-30) cc_final: 0.6334 (mm-30) REVERT: B 61 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7824 (mt-10) REVERT: B 80 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8757 (mm-40) REVERT: B 92 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8365 (mmmt) REVERT: B 95 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: B 121 ARG cc_start: 0.8655 (mmm-85) cc_final: 0.8435 (mmm-85) REVERT: B 128 ASP cc_start: 0.8939 (t70) cc_final: 0.8644 (OUTLIER) REVERT: B 140 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8969 (mmtm) REVERT: B 176 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8533 (tm-30) REVERT: D 58 GLU cc_start: 0.6459 (mm-30) cc_final: 0.6253 (mm-30) REVERT: D 61 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7769 (mt-10) REVERT: D 80 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8752 (mm-40) REVERT: D 87 GLN cc_start: 0.9202 (mt0) cc_final: 0.8979 (mt0) REVERT: D 95 GLU cc_start: 0.8366 (mp0) cc_final: 0.8093 (mp0) REVERT: D 109 GLN cc_start: 0.9034 (tp40) cc_final: 0.8582 (tp40) REVERT: F 57 GLU cc_start: 0.4400 (OUTLIER) cc_final: 0.3829 (mt-10) REVERT: F 58 GLU cc_start: 0.6437 (mm-30) cc_final: 0.6226 (mm-30) REVERT: F 61 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7786 (mt-10) REVERT: F 80 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8735 (mm-40) REVERT: F 87 GLN cc_start: 0.9196 (mt0) cc_final: 0.8923 (mt0) REVERT: F 95 GLU cc_start: 0.8393 (mp0) cc_final: 0.8164 (mp0) REVERT: F 176 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8491 (tm-30) outliers start: 159 outliers final: 65 residues processed: 1607 average time/residue: 1.6464 time to fit residues: 3105.4407 Evaluate side-chains 1530 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1449 time to evaluate : 4.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 127 CYS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 127 CYS Chi-restraints excluded: chain J residue 190 GLN Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 127 CYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 127 CYS Chi-restraints excluded: chain M residue 140 LYS Chi-restraints excluded: chain N residue 127 CYS Chi-restraints excluded: chain N residue 140 LYS Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain N residue 188 SER Chi-restraints excluded: chain O residue 127 CYS Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 127 CYS Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 127 CYS Chi-restraints excluded: chain S residue 140 LYS Chi-restraints excluded: chain S residue 188 SER Chi-restraints excluded: chain T residue 127 CYS Chi-restraints excluded: chain T residue 140 LYS Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 127 CYS Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 127 CYS Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 127 CYS Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 190 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 6.9990 chunk 355 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 394 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 4 GLN Z 94 GLN ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 ASN C 94 GLN C 147 ASN C 148 HIS ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN H 83 GLN H 94 GLN I 4 GLN ** I 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN L 4 GLN L 94 GLN L 147 ASN M 94 GLN M 147 ASN N 4 GLN N 182 HIS ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 182 HIS ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN P 147 ASN P 148 HIS ** Q 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 4 GLN R 94 GLN S 147 ASN S 182 HIS ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 4 GLN T 94 GLN ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 4 GLN V 147 ASN V 148 HIS W 4 GLN W 94 GLN W 147 ASN B 4 GLN B 94 GLN B 147 ASN D 4 GLN D 147 ASN D 148 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 34944 Z= 0.278 Angle : 0.572 6.587 46944 Z= 0.307 Chirality : 0.035 0.124 5040 Planarity : 0.003 0.024 6240 Dihedral : 3.937 36.995 4662 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.39 % Allowed : 30.64 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.13), residues: 4176 helix: 2.92 (0.09), residues: 3456 sheet: None (None), residues: 0 loop : -0.69 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 90 HIS 0.006 0.001 HIS S 182 PHE 0.008 0.001 PHE S 36 TYR 0.010 0.001 TYR Z 173 ARG 0.005 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1589 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1431 time to evaluate : 4.004 Fit side-chains revert: symmetry clash REVERT: Z 46 GLU cc_start: 0.8235 (pp20) cc_final: 0.7846 (pp20) REVERT: Z 80 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8845 (mm-40) REVERT: Z 87 GLN cc_start: 0.9244 (mt0) cc_final: 0.8942 (mt0) REVERT: Z 176 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8591 (tm-30) REVERT: Z 181 LYS cc_start: 0.9017 (tptp) cc_final: 0.8719 (tptp) REVERT: A 57 GLU cc_start: 0.4407 (OUTLIER) cc_final: 0.4153 (tt0) REVERT: A 58 GLU cc_start: 0.6460 (mm-30) cc_final: 0.6237 (mm-30) REVERT: A 61 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7947 (mt-10) REVERT: A 80 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8786 (mm-40) REVERT: A 140 LYS cc_start: 0.9373 (tppp) cc_final: 0.9014 (mmtm) REVERT: C 61 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7928 (mt-10) REVERT: C 80 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8807 (mm-40) REVERT: C 87 GLN cc_start: 0.9248 (mt0) cc_final: 0.8956 (mt0) REVERT: C 95 GLU cc_start: 0.8403 (mp0) cc_final: 0.8166 (mp0) REVERT: E 87 GLN cc_start: 0.9300 (mt0) cc_final: 0.9004 (mt0) REVERT: E 176 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8599 (tm-30) REVERT: G 87 GLN cc_start: 0.9250 (mt0) cc_final: 0.8958 (mt0) REVERT: G 92 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8542 (mmmt) REVERT: G 95 GLU cc_start: 0.8398 (mp0) cc_final: 0.8030 (pm20) REVERT: G 104 GLU cc_start: 0.8599 (tp30) cc_final: 0.8216 (tp30) REVERT: G 138 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8267 (tp30) REVERT: H 57 GLU cc_start: 0.4433 (OUTLIER) cc_final: 0.3698 (mt-10) REVERT: H 87 GLN cc_start: 0.9223 (mt0) cc_final: 0.8963 (mt0) REVERT: I 57 GLU cc_start: 0.4485 (OUTLIER) cc_final: 0.3919 (mt-10) REVERT: I 58 GLU cc_start: 0.6225 (mm-30) cc_final: 0.6007 (mm-30) REVERT: I 61 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7921 (mt-10) REVERT: I 80 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8754 (mm-40) REVERT: I 87 GLN cc_start: 0.9222 (mt0) cc_final: 0.8916 (mt0) REVERT: I 95 GLU cc_start: 0.8419 (mp0) cc_final: 0.8197 (mp0) REVERT: I 109 GLN cc_start: 0.8971 (tp40) cc_final: 0.8532 (tp40) REVERT: I 113 ASP cc_start: 0.8500 (m-30) cc_final: 0.7914 (m-30) REVERT: J 57 GLU cc_start: 0.4483 (OUTLIER) cc_final: 0.3768 (mt-10) REVERT: J 80 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8773 (mm-40) REVERT: J 87 GLN cc_start: 0.9257 (mt0) cc_final: 0.8943 (mt0) REVERT: K 58 GLU cc_start: 0.6190 (mm-30) cc_final: 0.5986 (mm-30) REVERT: K 61 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7892 (mt-10) REVERT: K 80 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8791 (mm-40) REVERT: K 87 GLN cc_start: 0.9214 (mt0) cc_final: 0.8947 (mt0) REVERT: K 104 GLU cc_start: 0.8587 (tp30) cc_final: 0.8040 (tp30) REVERT: K 109 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8467 (tp40) REVERT: K 138 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8144 (tp30) REVERT: K 176 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8578 (tm-30) REVERT: L 46 GLU cc_start: 0.8202 (pp20) cc_final: 0.7929 (pp20) REVERT: L 80 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8766 (mm-40) REVERT: L 87 GLN cc_start: 0.9216 (mt0) cc_final: 0.8958 (mt0) REVERT: L 109 GLN cc_start: 0.9029 (tp40) cc_final: 0.8521 (tp40) REVERT: L 176 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8611 (tm-30) REVERT: L 181 LYS cc_start: 0.9076 (tptp) cc_final: 0.8806 (tptp) REVERT: M 46 GLU cc_start: 0.8333 (pp20) cc_final: 0.8090 (pp20) REVERT: M 61 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7932 (mt-10) REVERT: M 80 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8800 (mm-40) REVERT: M 87 GLN cc_start: 0.9214 (mt0) cc_final: 0.8947 (mt0) REVERT: M 95 GLU cc_start: 0.8461 (mp0) cc_final: 0.8182 (pm20) REVERT: M 109 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8413 (tp40) REVERT: M 140 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9044 (mmtp) REVERT: N 92 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8541 (mmmt) REVERT: N 95 GLU cc_start: 0.8460 (mp0) cc_final: 0.8023 (mp0) REVERT: N 104 GLU cc_start: 0.8675 (tp30) cc_final: 0.8425 (tp30) REVERT: N 109 GLN cc_start: 0.9061 (tp40) cc_final: 0.8577 (tp40) REVERT: N 119 SER cc_start: 0.9253 (m) cc_final: 0.8876 (t) REVERT: N 138 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8258 (tp30) REVERT: N 140 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8919 (mmtm) REVERT: O 80 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8790 (mm-40) REVERT: O 104 GLU cc_start: 0.8535 (tp30) cc_final: 0.8294 (tp30) REVERT: O 109 GLN cc_start: 0.9108 (tp40) cc_final: 0.8706 (tp40) REVERT: O 113 ASP cc_start: 0.8567 (m-30) cc_final: 0.8314 (m-30) REVERT: O 119 SER cc_start: 0.9252 (m) cc_final: 0.8873 (t) REVERT: O 140 LYS cc_start: 0.9236 (ttmm) cc_final: 0.8931 (mmtm) REVERT: P 61 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7925 (mt-10) REVERT: P 80 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8757 (mm-40) REVERT: P 87 GLN cc_start: 0.9231 (mt0) cc_final: 0.8942 (mt0) REVERT: P 95 GLU cc_start: 0.8445 (mp0) cc_final: 0.8188 (pm20) REVERT: P 109 GLN cc_start: 0.9157 (tp40) cc_final: 0.8723 (tp40) REVERT: Q 46 GLU cc_start: 0.8278 (pp20) cc_final: 0.8023 (pp20) REVERT: Q 80 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8774 (mm-40) REVERT: Q 87 GLN cc_start: 0.9295 (mt0) cc_final: 0.9014 (mt0) REVERT: R 80 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8766 (mm-40) REVERT: R 87 GLN cc_start: 0.9276 (mt0) cc_final: 0.8976 (mt0) REVERT: R 137 LYS cc_start: 0.9242 (mtpm) cc_final: 0.9032 (mtmm) REVERT: R 176 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8585 (tm-30) REVERT: S 68 GLU cc_start: 0.8140 (pp20) cc_final: 0.7661 (pp20) REVERT: S 72 ASP cc_start: 0.8606 (m-30) cc_final: 0.8252 (m-30) REVERT: S 80 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8809 (mm-40) REVERT: S 87 GLN cc_start: 0.9435 (pt0) cc_final: 0.9222 (pt0) REVERT: S 92 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8547 (mmmt) REVERT: S 95 GLU cc_start: 0.8391 (mp0) cc_final: 0.7963 (mp0) REVERT: S 119 SER cc_start: 0.9265 (m) cc_final: 0.8890 (t) REVERT: S 140 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8879 (mmtp) REVERT: T 104 GLU cc_start: 0.8469 (tp30) cc_final: 0.8185 (tp30) REVERT: T 119 SER cc_start: 0.9277 (m) cc_final: 0.8904 (t) REVERT: T 121 ARG cc_start: 0.8912 (tpp80) cc_final: 0.8706 (tpp80) REVERT: T 138 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8234 (tp30) REVERT: T 140 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8952 (mmtm) REVERT: U 61 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7969 (mt-10) REVERT: U 80 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8768 (mm-40) REVERT: U 95 GLU cc_start: 0.8425 (mp0) cc_final: 0.8181 (mp0) REVERT: V 80 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8849 (mm-40) REVERT: V 87 GLN cc_start: 0.9263 (mt0) cc_final: 0.8967 (mt0) REVERT: W 80 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8777 (mm-40) REVERT: W 87 GLN cc_start: 0.9255 (mt0) cc_final: 0.8968 (mt0) REVERT: W 95 GLU cc_start: 0.8426 (mp0) cc_final: 0.8159 (mp0) REVERT: W 176 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8578 (tm-30) REVERT: B 57 GLU cc_start: 0.4573 (OUTLIER) cc_final: 0.4269 (tt0) REVERT: B 61 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7925 (mt-10) REVERT: B 80 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8738 (mm-40) REVERT: B 138 GLU cc_start: 0.8728 (tp30) cc_final: 0.8513 (tp30) REVERT: D 46 GLU cc_start: 0.8296 (pp20) cc_final: 0.8043 (pp20) REVERT: D 61 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7930 (mt-10) REVERT: D 80 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8772 (mm-40) REVERT: D 84 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9215 (pttp) REVERT: D 87 GLN cc_start: 0.9234 (mt0) cc_final: 0.8937 (mt0) REVERT: D 95 GLU cc_start: 0.8399 (mp0) cc_final: 0.8145 (mp0) REVERT: F 57 GLU cc_start: 0.4614 (OUTLIER) cc_final: 0.4326 (tt0) REVERT: F 61 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7943 (mt-10) REVERT: F 80 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8779 (mm-40) REVERT: F 87 GLN cc_start: 0.9202 (mt0) cc_final: 0.8922 (mt0) REVERT: F 95 GLU cc_start: 0.8411 (mp0) cc_final: 0.8194 (mp0) outliers start: 158 outliers final: 106 residues processed: 1493 average time/residue: 1.6566 time to fit residues: 2900.1162 Evaluate side-chains 1527 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1410 time to evaluate : 4.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 127 CYS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 190 GLN Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 127 CYS Chi-restraints excluded: chain J residue 190 GLN Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 127 CYS Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain M residue 84 LYS Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 127 CYS Chi-restraints excluded: chain M residue 140 LYS Chi-restraints excluded: chain M residue 190 GLN Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 127 CYS Chi-restraints excluded: chain N residue 140 LYS Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain N residue 188 SER Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 127 CYS Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 127 CYS Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 127 CYS Chi-restraints excluded: chain S residue 140 LYS Chi-restraints excluded: chain S residue 188 SER Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 127 CYS Chi-restraints excluded: chain T residue 140 LYS Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 127 CYS Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 127 CYS Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 127 CYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 190 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 chunk 288 optimal weight: 0.6980 chunk 223 optimal weight: 0.9980 chunk 332 optimal weight: 0.8980 chunk 220 optimal weight: 0.6980 chunk 393 optimal weight: 0.8980 chunk 246 optimal weight: 10.0000 chunk 239 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 94 GLN ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 GLN C 94 GLN E 94 GLN H 4 GLN H 83 GLN H 94 GLN I 4 GLN I 94 GLN J 94 GLN J 148 HIS L 4 GLN L 94 GLN M 94 GLN N 4 GLN N 94 GLN N 182 HIS ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 GLN O 182 HIS ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN P 94 GLN ** Q 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 GLN R 4 GLN R 94 GLN S 4 GLN S 182 HIS ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 94 GLN T 182 HIS ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 GLN V 4 GLN V 8 ASN W 4 GLN W 8 ASN W 94 GLN W 148 HIS B 4 GLN B 94 GLN D 4 GLN D 8 ASN F 94 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34944 Z= 0.193 Angle : 0.564 6.497 46944 Z= 0.306 Chirality : 0.034 0.122 5040 Planarity : 0.003 0.024 6240 Dihedral : 3.828 28.835 4660 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.89 % Allowed : 32.22 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.13), residues: 4176 helix: 3.21 (0.09), residues: 3408 sheet: None (None), residues: 0 loop : -0.34 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 90 HIS 0.006 0.000 HIS T 182 PHE 0.005 0.001 PHE O 69 TYR 0.013 0.001 TYR Z 173 ARG 0.006 0.000 ARG Z 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1619 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1479 time to evaluate : 4.611 Fit side-chains revert: symmetry clash REVERT: Z 46 GLU cc_start: 0.8146 (pp20) cc_final: 0.7749 (pp20) REVERT: Z 80 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8862 (mm-40) REVERT: Z 87 GLN cc_start: 0.9201 (mt0) cc_final: 0.8914 (mt0) REVERT: Z 145 MET cc_start: 0.8645 (mtp) cc_final: 0.8272 (mtm) REVERT: Z 176 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8571 (tm-30) REVERT: Z 181 LYS cc_start: 0.9052 (tptp) cc_final: 0.8770 (tptp) REVERT: A 57 GLU cc_start: 0.4144 (OUTLIER) cc_final: 0.3678 (mt-10) REVERT: A 61 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 80 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8713 (mm-40) REVERT: A 109 GLN cc_start: 0.9042 (tp40) cc_final: 0.8508 (tp40) REVERT: A 140 LYS cc_start: 0.9365 (tppp) cc_final: 0.9040 (mmtm) REVERT: A 176 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8593 (tm-30) REVERT: C 80 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8772 (mm-40) REVERT: C 87 GLN cc_start: 0.9187 (mt0) cc_final: 0.8892 (mt0) REVERT: C 95 GLU cc_start: 0.8396 (mp0) cc_final: 0.8165 (mp0) REVERT: E 87 GLN cc_start: 0.9247 (mt0) cc_final: 0.8954 (mt0) REVERT: E 95 GLU cc_start: 0.8401 (mp0) cc_final: 0.8169 (pm20) REVERT: E 145 MET cc_start: 0.8620 (mtp) cc_final: 0.8146 (mtm) REVERT: E 176 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8623 (tm-30) REVERT: G 87 GLN cc_start: 0.9222 (mt0) cc_final: 0.8929 (mt0) REVERT: G 104 GLU cc_start: 0.8539 (tp30) cc_final: 0.8064 (tp30) REVERT: G 138 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8049 (tp30) REVERT: G 176 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8632 (tm-30) REVERT: H 57 GLU cc_start: 0.4071 (OUTLIER) cc_final: 0.3730 (mt-10) REVERT: H 68 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8089 (pp20) REVERT: H 87 GLN cc_start: 0.9195 (mt0) cc_final: 0.8934 (mt0) REVERT: H 109 GLN cc_start: 0.8973 (tp40) cc_final: 0.8764 (tp40) REVERT: H 176 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8699 (tm-30) REVERT: I 57 GLU cc_start: 0.4233 (OUTLIER) cc_final: 0.3667 (mt-10) REVERT: I 61 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7840 (mt-10) REVERT: I 80 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8830 (mm-40) REVERT: I 87 GLN cc_start: 0.9186 (mt0) cc_final: 0.8885 (mt0) REVERT: I 95 GLU cc_start: 0.8421 (mp0) cc_final: 0.8150 (mp0) REVERT: I 109 GLN cc_start: 0.8982 (tp40) cc_final: 0.8549 (tp40) REVERT: I 113 ASP cc_start: 0.8527 (m-30) cc_final: 0.7956 (m-30) REVERT: I 176 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8621 (tm-30) REVERT: J 57 GLU cc_start: 0.4205 (OUTLIER) cc_final: 0.3762 (mt-10) REVERT: J 80 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8771 (mm-40) REVERT: J 87 GLN cc_start: 0.9193 (mt0) cc_final: 0.8887 (mt0) REVERT: J 109 GLN cc_start: 0.9005 (tp40) cc_final: 0.8616 (tp40) REVERT: J 113 ASP cc_start: 0.8535 (m-30) cc_final: 0.8278 (m-30) REVERT: J 176 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8440 (tm-30) REVERT: K 80 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8767 (mm-40) REVERT: K 87 GLN cc_start: 0.9175 (mt0) cc_final: 0.8896 (mt0) REVERT: K 95 GLU cc_start: 0.8398 (mp0) cc_final: 0.8157 (pm20) REVERT: K 104 GLU cc_start: 0.8546 (tp30) cc_final: 0.8053 (tp30) REVERT: K 138 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8185 (tp30) REVERT: K 145 MET cc_start: 0.8639 (mtp) cc_final: 0.8227 (mtm) REVERT: K 176 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8596 (tm-30) REVERT: L 46 GLU cc_start: 0.8084 (pp20) cc_final: 0.7767 (pp20) REVERT: L 68 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8088 (pp20) REVERT: L 80 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8771 (mm-40) REVERT: L 87 GLN cc_start: 0.9185 (mt0) cc_final: 0.8924 (mt0) REVERT: L 95 GLU cc_start: 0.8425 (mp0) cc_final: 0.8160 (pm20) REVERT: L 109 GLN cc_start: 0.9011 (tp40) cc_final: 0.8574 (tp40) REVERT: L 145 MET cc_start: 0.8558 (mtp) cc_final: 0.8193 (mtm) REVERT: L 176 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8593 (tm-30) REVERT: L 181 LYS cc_start: 0.9099 (tptp) cc_final: 0.8774 (tptp) REVERT: M 61 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7858 (mt-10) REVERT: M 80 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8798 (mm-40) REVERT: M 87 GLN cc_start: 0.9205 (mt0) cc_final: 0.8903 (mt0) REVERT: M 95 GLU cc_start: 0.8413 (mp0) cc_final: 0.8149 (pm20) REVERT: M 104 GLU cc_start: 0.8525 (tp30) cc_final: 0.8042 (tp30) REVERT: M 109 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8436 (tp40) REVERT: M 138 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8038 (tp30) REVERT: M 140 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.9031 (mmtm) REVERT: M 176 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8470 (tm-30) REVERT: N 68 GLU cc_start: 0.8458 (pt0) cc_final: 0.8155 (pp20) REVERT: N 92 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8555 (mmmt) REVERT: N 95 GLU cc_start: 0.8432 (mp0) cc_final: 0.8028 (mp0) REVERT: N 104 GLU cc_start: 0.8602 (tp30) cc_final: 0.8091 (tp30) REVERT: N 109 GLN cc_start: 0.8978 (tp40) cc_final: 0.8515 (tp40) REVERT: N 113 ASP cc_start: 0.8568 (m-30) cc_final: 0.8254 (m-30) REVERT: N 119 SER cc_start: 0.9239 (m) cc_final: 0.8854 (t) REVERT: N 138 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7904 (tp30) REVERT: N 140 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8930 (mmtm) REVERT: O 95 GLU cc_start: 0.8421 (mp0) cc_final: 0.8212 (pm20) REVERT: O 109 GLN cc_start: 0.9051 (tp40) cc_final: 0.8550 (tp40) REVERT: O 119 SER cc_start: 0.9256 (m) cc_final: 0.8882 (t) REVERT: P 61 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7883 (mt-10) REVERT: P 80 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8756 (mm-40) REVERT: P 84 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9233 (pttp) REVERT: P 87 GLN cc_start: 0.9208 (mt0) cc_final: 0.8899 (mt0) REVERT: P 95 GLU cc_start: 0.8420 (mp0) cc_final: 0.8132 (pm20) REVERT: P 104 GLU cc_start: 0.8565 (tp30) cc_final: 0.8090 (tp30) REVERT: P 109 GLN cc_start: 0.9119 (tp40) cc_final: 0.8705 (tp40) REVERT: P 138 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7996 (tp30) REVERT: P 176 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8496 (tm-30) REVERT: Q 80 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8765 (mm-40) REVERT: Q 87 GLN cc_start: 0.9274 (mt0) cc_final: 0.8980 (mt0) REVERT: Q 95 GLU cc_start: 0.8405 (mp0) cc_final: 0.8149 (pm20) REVERT: Q 145 MET cc_start: 0.8661 (mtp) cc_final: 0.8266 (mtm) REVERT: Q 176 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8357 (tm-30) REVERT: R 80 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8752 (mm-40) REVERT: R 87 GLN cc_start: 0.9208 (mt0) cc_final: 0.8910 (mt0) REVERT: R 137 LYS cc_start: 0.9227 (mtpm) cc_final: 0.8968 (mttt) REVERT: R 145 MET cc_start: 0.8627 (mtp) cc_final: 0.8210 (mtm) REVERT: R 176 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8606 (tm-30) REVERT: S 80 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8804 (mm-40) REVERT: S 87 GLN cc_start: 0.9473 (pt0) cc_final: 0.9226 (pt0) REVERT: S 92 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8501 (mmmt) REVERT: S 95 GLU cc_start: 0.8452 (mp0) cc_final: 0.8029 (mp0) REVERT: S 109 GLN cc_start: 0.9081 (tp40) cc_final: 0.8594 (tp40) REVERT: S 119 SER cc_start: 0.9260 (m) cc_final: 0.8882 (t) REVERT: S 140 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8792 (mmtm) REVERT: T 87 GLN cc_start: 0.9422 (pt0) cc_final: 0.9158 (pt0) REVERT: T 95 GLU cc_start: 0.8460 (mp0) cc_final: 0.8203 (pm20) REVERT: T 104 GLU cc_start: 0.8418 (tp30) cc_final: 0.8007 (tp30) REVERT: T 109 GLN cc_start: 0.9075 (tp40) cc_final: 0.8803 (tp40) REVERT: T 119 SER cc_start: 0.9256 (m) cc_final: 0.8882 (t) REVERT: T 138 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8070 (tp30) REVERT: T 140 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8933 (mmtm) REVERT: U 80 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8822 (mm-40) REVERT: U 95 GLU cc_start: 0.8377 (mp0) cc_final: 0.8160 (mp0) REVERT: U 109 GLN cc_start: 0.9050 (tp40) cc_final: 0.8656 (tp40) REVERT: U 113 ASP cc_start: 0.8627 (m-30) cc_final: 0.8349 (m-30) REVERT: U 121 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.7954 (mmm-85) REVERT: V 80 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8841 (mm-40) REVERT: V 87 GLN cc_start: 0.9228 (mt0) cc_final: 0.8957 (mt0) REVERT: V 144 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8784 (ttpp) REVERT: V 176 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8609 (tm-30) REVERT: W 80 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8752 (mm-40) REVERT: W 87 GLN cc_start: 0.9203 (mt0) cc_final: 0.8894 (mt0) REVERT: W 95 GLU cc_start: 0.8395 (mp0) cc_final: 0.8171 (mp0) REVERT: W 104 GLU cc_start: 0.8587 (tp30) cc_final: 0.8094 (tp30) REVERT: W 109 GLN cc_start: 0.8948 (tp40) cc_final: 0.8462 (tp40) REVERT: W 138 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7965 (tp30) REVERT: W 176 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8648 (tm-30) REVERT: B 80 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8798 (mm-40) REVERT: B 109 GLN cc_start: 0.9054 (tp40) cc_final: 0.8621 (tp40) REVERT: B 176 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8592 (tm-30) REVERT: D 58 GLU cc_start: 0.6418 (mm-30) cc_final: 0.6206 (mm-30) REVERT: D 61 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7801 (mt-10) REVERT: D 80 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8772 (mm-40) REVERT: D 87 GLN cc_start: 0.9218 (mt0) cc_final: 0.8914 (mt0) REVERT: D 95 GLU cc_start: 0.8407 (mp0) cc_final: 0.8144 (mp0) REVERT: D 109 GLN cc_start: 0.9035 (tp40) cc_final: 0.8429 (tp40) REVERT: D 144 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8787 (ttpp) REVERT: D 176 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8307 (tm-30) REVERT: F 57 GLU cc_start: 0.4241 (OUTLIER) cc_final: 0.3872 (mt-10) REVERT: F 61 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7834 (mt-10) REVERT: F 80 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8723 (mm-40) REVERT: F 87 GLN cc_start: 0.9210 (mt0) cc_final: 0.8906 (mt0) REVERT: F 95 GLU cc_start: 0.8410 (mp0) cc_final: 0.8209 (mp0) REVERT: F 109 GLN cc_start: 0.8988 (tp40) cc_final: 0.8330 (tp40) REVERT: F 137 LYS cc_start: 0.9245 (mtpm) cc_final: 0.8998 (mtmm) outliers start: 140 outliers final: 78 residues processed: 1533 average time/residue: 1.6569 time to fit residues: 2976.4467 Evaluate side-chains 1473 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1381 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 88 ASP Chi-restraints excluded: chain Z residue 127 CYS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 190 GLN Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 127 CYS Chi-restraints excluded: chain J residue 190 GLN Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 127 CYS Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 84 LYS Chi-restraints excluded: chain M residue 127 CYS Chi-restraints excluded: chain M residue 140 LYS Chi-restraints excluded: chain M residue 190 GLN Chi-restraints excluded: chain N residue 127 CYS Chi-restraints excluded: chain N residue 140 LYS Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain N residue 188 SER Chi-restraints excluded: chain O residue 84 LYS Chi-restraints excluded: chain O residue 127 CYS Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 84 LYS Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 127 CYS Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 127 CYS Chi-restraints excluded: chain S residue 140 LYS Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 127 CYS Chi-restraints excluded: chain T residue 140 LYS Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 127 CYS Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 127 CYS Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 127 CYS Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 190 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 chunk 267 optimal weight: 0.9980 chunk 194 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 309 optimal weight: 0.0980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 94 GLN ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN E 8 ASN E 80 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN E 148 HIS G 80 GLN G 94 GLN G 147 ASN H 80 GLN H 83 GLN H 94 GLN ** I 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 GLN J 147 ASN K 94 GLN K 147 ASN K 148 HIS L 4 GLN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 HIS M 94 GLN N 4 GLN N 94 GLN ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 GLN O 147 ASN ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN P 147 ASN ** Q 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 GLN Q 147 ASN Q 148 HIS R 4 GLN R 94 GLN R 148 HIS ** S 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 4 GLN T 94 GLN T 147 ASN ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 94 GLN V 147 ASN W 4 GLN ** W 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN D 4 GLN D 94 GLN D 147 ASN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34944 Z= 0.246 Angle : 0.595 6.671 46944 Z= 0.321 Chirality : 0.035 0.147 5040 Planarity : 0.003 0.028 6240 Dihedral : 3.797 25.244 4660 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.97 % Allowed : 32.75 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.13), residues: 4176 helix: 3.25 (0.09), residues: 3408 sheet: None (None), residues: 0 loop : -0.24 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP S 90 HIS 0.002 0.000 HIS A 125 PHE 0.007 0.001 PHE O 36 TYR 0.014 0.001 TYR Z 173 ARG 0.006 0.000 ARG H 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1510 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1367 time to evaluate : 3.167 Fit side-chains revert: symmetry clash REVERT: Z 46 GLU cc_start: 0.8181 (pp20) cc_final: 0.7773 (pp20) REVERT: Z 80 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8888 (mm-40) REVERT: Z 87 GLN cc_start: 0.9194 (mt0) cc_final: 0.8896 (mt0) REVERT: Z 104 GLU cc_start: 0.8637 (tp30) cc_final: 0.8297 (tp30) REVERT: Z 145 MET cc_start: 0.8735 (mtp) cc_final: 0.8358 (mtm) REVERT: Z 176 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8542 (tm-30) REVERT: Z 181 LYS cc_start: 0.9107 (tptp) cc_final: 0.8727 (tptp) REVERT: A 57 GLU cc_start: 0.4095 (OUTLIER) cc_final: 0.3558 (mt-10) REVERT: A 80 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8804 (mm-40) REVERT: A 104 GLU cc_start: 0.8572 (tp30) cc_final: 0.8362 (tp30) REVERT: A 138 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8182 (tp30) REVERT: A 140 LYS cc_start: 0.9369 (tppp) cc_final: 0.9037 (mmtm) REVERT: C 80 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8775 (mm-40) REVERT: C 87 GLN cc_start: 0.9184 (mt0) cc_final: 0.8881 (mt0) REVERT: C 95 GLU cc_start: 0.8367 (mp0) cc_final: 0.8156 (mp0) REVERT: C 104 GLU cc_start: 0.8629 (tp30) cc_final: 0.8265 (tp30) REVERT: C 109 GLN cc_start: 0.8846 (tp40) cc_final: 0.8601 (tp40) REVERT: C 138 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8354 (tp30) REVERT: C 145 MET cc_start: 0.8877 (mtp) cc_final: 0.8666 (mtm) REVERT: C 176 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8734 (tm-30) REVERT: E 87 GLN cc_start: 0.9244 (mt0) cc_final: 0.8931 (mt0) REVERT: E 95 GLU cc_start: 0.8433 (mp0) cc_final: 0.8150 (pm20) REVERT: E 176 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8587 (tm-30) REVERT: G 87 GLN cc_start: 0.9220 (mt0) cc_final: 0.8931 (mt0) REVERT: G 95 GLU cc_start: 0.8443 (mp0) cc_final: 0.8198 (pm20) REVERT: G 104 GLU cc_start: 0.8589 (tp30) cc_final: 0.8270 (tp30) REVERT: G 138 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8339 (tp30) REVERT: H 57 GLU cc_start: 0.4329 (OUTLIER) cc_final: 0.3791 (mt-10) REVERT: H 68 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8095 (pp20) REVERT: H 87 GLN cc_start: 0.9208 (mt0) cc_final: 0.8930 (mt0) REVERT: I 57 GLU cc_start: 0.4482 (OUTLIER) cc_final: 0.4212 (mt-10) REVERT: I 80 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8771 (mm-40) REVERT: I 87 GLN cc_start: 0.9178 (mt0) cc_final: 0.8858 (mt0) REVERT: I 95 GLU cc_start: 0.8403 (mp0) cc_final: 0.8168 (mp0) REVERT: J 57 GLU cc_start: 0.4429 (OUTLIER) cc_final: 0.3886 (mt-10) REVERT: J 80 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8778 (mm-40) REVERT: J 87 GLN cc_start: 0.9180 (mt0) cc_final: 0.8867 (mt0) REVERT: J 145 MET cc_start: 0.8865 (mtp) cc_final: 0.8615 (mtm) REVERT: K 31 TYR cc_start: 0.8934 (m-10) cc_final: 0.8621 (m-10) REVERT: K 80 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8805 (mm-40) REVERT: K 87 GLN cc_start: 0.9170 (mt0) cc_final: 0.8899 (mt0) REVERT: K 95 GLU cc_start: 0.8390 (mp0) cc_final: 0.8119 (pm20) REVERT: K 104 GLU cc_start: 0.8551 (tp30) cc_final: 0.8225 (tp30) REVERT: K 109 GLN cc_start: 0.9082 (tp40) cc_final: 0.8583 (tp40) REVERT: K 176 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8578 (tm-30) REVERT: L 46 GLU cc_start: 0.8149 (pp20) cc_final: 0.7879 (pp20) REVERT: L 68 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8090 (pp20) REVERT: L 80 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8785 (mm-40) REVERT: L 87 GLN cc_start: 0.9173 (mt0) cc_final: 0.8897 (mt0) REVERT: L 104 GLU cc_start: 0.8500 (tp30) cc_final: 0.8167 (tp30) REVERT: L 138 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8234 (tp30) REVERT: L 176 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8546 (tm-30) REVERT: M 61 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7957 (mt-10) REVERT: M 80 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8803 (mm-40) REVERT: M 87 GLN cc_start: 0.9223 (mt0) cc_final: 0.8910 (mt0) REVERT: M 95 GLU cc_start: 0.8428 (mp0) cc_final: 0.8176 (pm20) REVERT: M 104 GLU cc_start: 0.8523 (tp30) cc_final: 0.8017 (tp30) REVERT: M 138 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8095 (tp30) REVERT: M 140 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9034 (mmtm) REVERT: N 95 GLU cc_start: 0.8451 (mp0) cc_final: 0.8119 (mp0) REVERT: N 104 GLU cc_start: 0.8631 (tp30) cc_final: 0.8338 (tp30) REVERT: N 119 SER cc_start: 0.9195 (m) cc_final: 0.8708 (p) REVERT: N 138 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8277 (tp30) REVERT: N 140 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8928 (mmtm) REVERT: O 95 GLU cc_start: 0.8447 (mp0) cc_final: 0.8188 (pm20) REVERT: O 103 MET cc_start: 0.8760 (ttm) cc_final: 0.8538 (ttm) REVERT: O 109 GLN cc_start: 0.9093 (tp40) cc_final: 0.8688 (tp40) REVERT: O 119 SER cc_start: 0.9221 (m) cc_final: 0.8863 (t) REVERT: P 61 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7931 (mt-10) REVERT: P 80 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8786 (mm-40) REVERT: P 87 GLN cc_start: 0.9242 (mt0) cc_final: 0.8930 (mt0) REVERT: P 95 GLU cc_start: 0.8431 (mp0) cc_final: 0.8153 (pm20) REVERT: P 104 GLU cc_start: 0.8591 (tp30) cc_final: 0.8128 (tp30) REVERT: P 109 GLN cc_start: 0.9138 (tp40) cc_final: 0.8695 (tp40) REVERT: P 138 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8024 (tp30) REVERT: Q 80 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8777 (mm-40) REVERT: Q 87 GLN cc_start: 0.9264 (mt0) cc_final: 0.8956 (mt0) REVERT: Q 95 GLU cc_start: 0.8448 (mp0) cc_final: 0.8173 (pm20) REVERT: R 80 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8781 (mm-40) REVERT: R 87 GLN cc_start: 0.9214 (mt0) cc_final: 0.8933 (mt0) REVERT: R 176 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8575 (tm-30) REVERT: S 87 GLN cc_start: 0.9461 (pt0) cc_final: 0.9152 (pt0) REVERT: S 92 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8557 (mmmt) REVERT: S 95 GLU cc_start: 0.8425 (mp0) cc_final: 0.8121 (mp0) REVERT: S 104 GLU cc_start: 0.8649 (tp30) cc_final: 0.8235 (tp30) REVERT: S 109 GLN cc_start: 0.9096 (tp40) cc_final: 0.8616 (tp40) REVERT: S 119 SER cc_start: 0.9228 (m) cc_final: 0.8860 (t) REVERT: S 138 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8143 (tp30) REVERT: S 140 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8912 (mmtm) REVERT: T 87 GLN cc_start: 0.9419 (pt0) cc_final: 0.9156 (pt0) REVERT: T 95 GLU cc_start: 0.8470 (mp0) cc_final: 0.8186 (pm20) REVERT: T 104 GLU cc_start: 0.8462 (tp30) cc_final: 0.8189 (tp30) REVERT: T 119 SER cc_start: 0.9237 (m) cc_final: 0.8875 (t) REVERT: T 138 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8246 (tp30) REVERT: T 140 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8975 (mmtm) REVERT: U 80 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8795 (mm-40) REVERT: U 95 GLU cc_start: 0.8424 (mp0) cc_final: 0.8193 (mp0) REVERT: U 137 LYS cc_start: 0.9172 (mtpm) cc_final: 0.8968 (mtmm) REVERT: V 80 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8856 (mm-40) REVERT: V 87 GLN cc_start: 0.9217 (mt0) cc_final: 0.8933 (mt0) REVERT: V 92 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8444 (mtmm) REVERT: V 95 GLU cc_start: 0.8289 (pm20) cc_final: 0.7899 (pm20) REVERT: V 109 GLN cc_start: 0.9040 (tp40) cc_final: 0.8556 (tp40) REVERT: V 144 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8822 (ttpp) REVERT: W 31 TYR cc_start: 0.8962 (m-10) cc_final: 0.8739 (m-10) REVERT: W 80 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8785 (mm-40) REVERT: W 87 GLN cc_start: 0.9202 (mt0) cc_final: 0.8909 (mt0) REVERT: W 95 GLU cc_start: 0.8389 (mp0) cc_final: 0.8179 (mp0) REVERT: W 104 GLU cc_start: 0.8590 (tp30) cc_final: 0.8181 (tp30) REVERT: W 138 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8105 (tp30) REVERT: W 145 MET cc_start: 0.8871 (mtp) cc_final: 0.8626 (mtm) REVERT: W 176 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8584 (tm-30) REVERT: B 80 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8746 (mm-40) REVERT: D 61 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7932 (mt-10) REVERT: D 80 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8791 (mm-40) REVERT: D 87 GLN cc_start: 0.9215 (mt0) cc_final: 0.8857 (mt0) REVERT: D 88 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8172 (m-30) REVERT: D 95 GLU cc_start: 0.8418 (mp0) cc_final: 0.8154 (mp0) REVERT: D 144 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8800 (ttpp) REVERT: F 57 GLU cc_start: 0.4477 (OUTLIER) cc_final: 0.3973 (mt-10) REVERT: F 61 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7944 (mt-10) REVERT: F 80 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8756 (mm-40) REVERT: F 87 GLN cc_start: 0.9219 (mt0) cc_final: 0.8882 (mt0) REVERT: F 88 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8154 (m-30) REVERT: F 95 GLU cc_start: 0.8386 (mp0) cc_final: 0.8167 (mp0) REVERT: F 137 LYS cc_start: 0.9214 (mtpm) cc_final: 0.8937 (mttt) outliers start: 143 outliers final: 97 residues processed: 1429 average time/residue: 1.6343 time to fit residues: 2726.8768 Evaluate side-chains 1477 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1365 time to evaluate : 4.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 88 ASP Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 127 CYS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 190 GLN Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 127 CYS Chi-restraints excluded: chain J residue 190 GLN Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 127 CYS Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 127 CYS Chi-restraints excluded: chain M residue 140 LYS Chi-restraints excluded: chain M residue 190 GLN Chi-restraints excluded: chain N residue 140 LYS Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 84 LYS Chi-restraints excluded: chain O residue 94 GLN Chi-restraints excluded: chain P residue 94 GLN Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 127 CYS Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 94 GLN Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 140 LYS Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 94 GLN Chi-restraints excluded: chain T residue 140 LYS Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 127 CYS Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 127 CYS Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 127 CYS Chi-restraints excluded: chain W residue 188 SER Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 190 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 3.9990 chunk 376 optimal weight: 0.8980 chunk 343 optimal weight: 3.9990 chunk 366 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 331 optimal weight: 9.9990 chunk 346 optimal weight: 6.9990 chunk 365 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 94 GLN ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN H 83 GLN H 94 GLN ** I 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN J 94 GLN K 94 GLN L 4 GLN L 94 GLN M 94 GLN N 4 GLN ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 GLN ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN Q 94 GLN R 94 GLN ** S 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 4 GLN T 94 GLN ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 4 GLN ** U 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 94 GLN ** W 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS D 94 GLN F 4 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 34944 Z= 0.318 Angle : 0.652 7.004 46944 Z= 0.348 Chirality : 0.037 0.143 5040 Planarity : 0.003 0.029 6240 Dihedral : 3.791 11.685 4656 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.17 % Allowed : 32.94 % Favored : 62.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.13), residues: 4176 helix: 3.12 (0.09), residues: 3432 sheet: None (None), residues: 0 loop : -0.99 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP N 90 HIS 0.003 0.001 HIS A 125 PHE 0.009 0.001 PHE R 36 TYR 0.018 0.001 TYR T 173 ARG 0.006 0.000 ARG U 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1522 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1372 time to evaluate : 4.081 Fit side-chains revert: symmetry clash REVERT: Z 46 GLU cc_start: 0.8275 (pp20) cc_final: 0.7841 (pp20) REVERT: Z 80 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8868 (mm-40) REVERT: Z 87 GLN cc_start: 0.9219 (mt0) cc_final: 0.8921 (mt0) REVERT: Z 176 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8609 (tm-30) REVERT: Z 181 LYS cc_start: 0.9106 (tptp) cc_final: 0.8709 (tptp) REVERT: A 57 GLU cc_start: 0.4354 (OUTLIER) cc_final: 0.3938 (mt-10) REVERT: A 80 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8756 (mm-40) REVERT: A 104 GLU cc_start: 0.8607 (tp30) cc_final: 0.8274 (tp30) REVERT: A 138 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8185 (tp30) REVERT: A 140 LYS cc_start: 0.9374 (tppp) cc_final: 0.9029 (mmtm) REVERT: C 80 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8782 (mm-40) REVERT: C 87 GLN cc_start: 0.9191 (mt0) cc_final: 0.8874 (mt0) REVERT: C 95 GLU cc_start: 0.8371 (mp0) cc_final: 0.8159 (mp0) REVERT: C 104 GLU cc_start: 0.8647 (tp30) cc_final: 0.8253 (tp30) REVERT: C 109 GLN cc_start: 0.8874 (tp40) cc_final: 0.8627 (tp40) REVERT: C 138 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8183 (tp30) REVERT: E 87 GLN cc_start: 0.9227 (mt0) cc_final: 0.8911 (mt0) REVERT: E 95 GLU cc_start: 0.8447 (mp0) cc_final: 0.8186 (pm20) REVERT: E 145 MET cc_start: 0.8896 (mtp) cc_final: 0.8656 (mtm) REVERT: E 176 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8554 (tm-30) REVERT: G 87 GLN cc_start: 0.9201 (mt0) cc_final: 0.8885 (mt0) REVERT: G 95 GLU cc_start: 0.8464 (mp0) cc_final: 0.8192 (pm20) REVERT: G 104 GLU cc_start: 0.8628 (tp30) cc_final: 0.8254 (tp30) REVERT: G 138 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8359 (tp30) REVERT: H 57 GLU cc_start: 0.4376 (OUTLIER) cc_final: 0.4139 (mt-10) REVERT: H 68 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8104 (pp20) REVERT: H 87 GLN cc_start: 0.9231 (mt0) cc_final: 0.8953 (mt0) REVERT: H 176 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8702 (tm-30) REVERT: I 57 GLU cc_start: 0.4494 (OUTLIER) cc_final: 0.4207 (mt-10) REVERT: I 80 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8796 (mm-40) REVERT: I 87 GLN cc_start: 0.9187 (mt0) cc_final: 0.8870 (mt0) REVERT: I 95 GLU cc_start: 0.8404 (mp0) cc_final: 0.8182 (mp0) REVERT: J 57 GLU cc_start: 0.4391 (OUTLIER) cc_final: 0.3954 (mt-10) REVERT: J 80 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8798 (mm-40) REVERT: J 87 GLN cc_start: 0.9203 (mt0) cc_final: 0.8885 (mt0) REVERT: J 176 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8382 (tm-30) REVERT: K 80 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8812 (mm-40) REVERT: K 87 GLN cc_start: 0.9194 (mt0) cc_final: 0.8899 (mt0) REVERT: K 95 GLU cc_start: 0.8432 (mp0) cc_final: 0.8183 (pm20) REVERT: K 109 GLN cc_start: 0.9110 (tp40) cc_final: 0.8645 (tp40) REVERT: K 145 MET cc_start: 0.8895 (mtp) cc_final: 0.8669 (mtm) REVERT: K 176 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8542 (tm-30) REVERT: L 68 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8117 (pp20) REVERT: L 80 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8790 (mm-40) REVERT: L 87 GLN cc_start: 0.9193 (mt0) cc_final: 0.8920 (mt0) REVERT: L 104 GLU cc_start: 0.8547 (tp30) cc_final: 0.8119 (tp30) REVERT: L 109 GLN cc_start: 0.9088 (tp40) cc_final: 0.8630 (tp40) REVERT: L 138 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8331 (tp30) REVERT: L 176 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8539 (tm-30) REVERT: M 61 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7960 (mt-10) REVERT: M 80 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8809 (mm-40) REVERT: M 87 GLN cc_start: 0.9193 (mt0) cc_final: 0.8894 (mt0) REVERT: M 104 GLU cc_start: 0.8546 (tp30) cc_final: 0.8141 (tp30) REVERT: M 109 GLN cc_start: 0.9111 (tp40) cc_final: 0.8666 (tp40) REVERT: M 138 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8270 (tp30) REVERT: M 140 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.9048 (mmtp) REVERT: N 95 GLU cc_start: 0.8499 (mp0) cc_final: 0.8228 (mp0) REVERT: N 104 GLU cc_start: 0.8676 (tp30) cc_final: 0.8398 (tp30) REVERT: N 109 GLN cc_start: 0.9069 (tp40) cc_final: 0.8570 (tp40) REVERT: N 119 SER cc_start: 0.9200 (m) cc_final: 0.8838 (t) REVERT: N 140 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8958 (mmtm) REVERT: O 95 GLU cc_start: 0.8402 (mp0) cc_final: 0.8162 (pm20) REVERT: O 109 GLN cc_start: 0.9110 (tp40) cc_final: 0.8717 (tp40) REVERT: O 113 ASP cc_start: 0.8554 (m-30) cc_final: 0.8291 (m-30) REVERT: O 119 SER cc_start: 0.9219 (m) cc_final: 0.8872 (t) REVERT: O 138 GLU cc_start: 0.8834 (tp30) cc_final: 0.8382 (mm-30) REVERT: P 61 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7955 (mt-10) REVERT: P 84 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9195 (pttp) REVERT: P 87 GLN cc_start: 0.9230 (mt0) cc_final: 0.8923 (mt0) REVERT: P 95 GLU cc_start: 0.8456 (mp0) cc_final: 0.8176 (pm20) REVERT: P 104 GLU cc_start: 0.8590 (tp30) cc_final: 0.8119 (tp30) REVERT: P 109 GLN cc_start: 0.9162 (tp40) cc_final: 0.8720 (tp40) REVERT: P 138 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8183 (tp30) REVERT: Q 80 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8793 (mm-40) REVERT: Q 87 GLN cc_start: 0.9254 (mt0) cc_final: 0.8945 (mt0) REVERT: Q 95 GLU cc_start: 0.8474 (mp0) cc_final: 0.8197 (pm20) REVERT: Q 145 MET cc_start: 0.8890 (mtp) cc_final: 0.8641 (mtm) REVERT: R 80 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8793 (mm-40) REVERT: R 87 GLN cc_start: 0.9202 (mt0) cc_final: 0.8877 (mt0) REVERT: R 176 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8543 (tm-30) REVERT: S 87 GLN cc_start: 0.9452 (pt0) cc_final: 0.9159 (pt0) REVERT: S 92 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8516 (mmmt) REVERT: S 95 GLU cc_start: 0.8436 (mp0) cc_final: 0.8104 (mp0) REVERT: S 104 GLU cc_start: 0.8585 (tp30) cc_final: 0.8270 (tp30) REVERT: S 109 GLN cc_start: 0.9112 (tp40) cc_final: 0.8772 (tp40) REVERT: S 119 SER cc_start: 0.9222 (m) cc_final: 0.8862 (t) REVERT: S 140 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8946 (mmtm) REVERT: T 87 GLN cc_start: 0.9415 (pt0) cc_final: 0.9156 (pt0) REVERT: T 95 GLU cc_start: 0.8483 (mp0) cc_final: 0.8173 (pm20) REVERT: T 104 GLU cc_start: 0.8494 (tp30) cc_final: 0.8204 (tp30) REVERT: T 119 SER cc_start: 0.9119 (m) cc_final: 0.8736 (t) REVERT: T 138 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8280 (tp30) REVERT: T 140 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8986 (mmtm) REVERT: U 80 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8808 (mm-40) REVERT: U 84 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9221 (pttp) REVERT: U 95 GLU cc_start: 0.8410 (mp0) cc_final: 0.8194 (mp0) REVERT: U 137 LYS cc_start: 0.9177 (mtpm) cc_final: 0.8963 (mttt) REVERT: U 138 GLU cc_start: 0.8814 (tp30) cc_final: 0.8607 (tp30) REVERT: V 80 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8863 (mm-40) REVERT: V 87 GLN cc_start: 0.9191 (mt0) cc_final: 0.8873 (mt0) REVERT: V 144 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8825 (ttpp) REVERT: W 31 TYR cc_start: 0.9000 (m-10) cc_final: 0.8712 (m-10) REVERT: W 80 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8795 (mm-40) REVERT: W 87 GLN cc_start: 0.9198 (mt0) cc_final: 0.8882 (mt0) REVERT: W 95 GLU cc_start: 0.8391 (mp0) cc_final: 0.8187 (mp0) REVERT: W 104 GLU cc_start: 0.8604 (tp30) cc_final: 0.8186 (tp30) REVERT: W 138 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8300 (tp30) REVERT: W 176 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8555 (tm-30) REVERT: B 80 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8782 (mm-40) REVERT: D 61 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7971 (mt-10) REVERT: D 80 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8790 (mm-40) REVERT: D 87 GLN cc_start: 0.9217 (mt0) cc_final: 0.8884 (mt0) REVERT: D 88 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8149 (m-30) REVERT: D 95 GLU cc_start: 0.8414 (mp0) cc_final: 0.8144 (mp0) REVERT: D 144 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8842 (ttpp) REVERT: F 57 GLU cc_start: 0.4531 (OUTLIER) cc_final: 0.3846 (mt-10) REVERT: F 61 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7974 (mt-10) REVERT: F 80 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8781 (mm-40) REVERT: F 87 GLN cc_start: 0.9220 (mt0) cc_final: 0.8884 (mt0) REVERT: F 88 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8152 (m-30) REVERT: F 95 GLU cc_start: 0.8400 (mp0) cc_final: 0.8159 (mp0) REVERT: F 113 ASP cc_start: 0.8396 (m-30) cc_final: 0.8156 (m-30) REVERT: F 137 LYS cc_start: 0.9174 (mtpm) cc_final: 0.8953 (mttt) outliers start: 150 outliers final: 104 residues processed: 1434 average time/residue: 1.6931 time to fit residues: 2835.7786 Evaluate side-chains 1464 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1343 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 94 GLN Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 127 CYS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 190 GLN Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 127 CYS Chi-restraints excluded: chain J residue 190 GLN Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 127 CYS Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 127 CYS Chi-restraints excluded: chain M residue 140 LYS Chi-restraints excluded: chain M residue 190 GLN Chi-restraints excluded: chain N residue 140 LYS Chi-restraints excluded: chain P residue 84 LYS Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 94 GLN Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 127 CYS Chi-restraints excluded: chain P residue 188 SER Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 140 LYS Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 94 GLN Chi-restraints excluded: chain T residue 140 LYS Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 84 LYS Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 127 CYS Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 94 GLN Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 127 CYS Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 127 CYS Chi-restraints excluded: chain W residue 188 SER Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 190 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 0.6980 chunk 387 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 269 optimal weight: 0.9990 chunk 406 optimal weight: 6.9990 chunk 374 optimal weight: 5.9990 chunk 323 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: