Starting phenix.real_space_refine on Mon Mar 11 03:52:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/03_2024/7rfh_24442_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/03_2024/7rfh_24442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/03_2024/7rfh_24442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/03_2024/7rfh_24442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/03_2024/7rfh_24442_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/03_2024/7rfh_24442_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.279 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 S 169 5.16 5 C 17265 2.51 5 N 4717 2.21 5 O 5339 1.98 5 H 27603 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG -10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 43": "OD1" <-> "OD2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 216": "OD1" <-> "OD2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 470": "OD1" <-> "OD2" Residue "B ARG -10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 43": "OD1" <-> "OD2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 216": "OD1" <-> "OD2" Residue "B ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 470": "OD1" <-> "OD2" Residue "C GLU -19": "OE1" <-> "OE2" Residue "C ARG -10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 214": "OD1" <-> "OD2" Residue "C ASP 216": "OD1" <-> "OD2" Residue "C ASP 226": "OD1" <-> "OD2" Residue "C ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 470": "OD1" <-> "OD2" Residue "D GLU -19": "OE1" <-> "OE2" Residue "D ARG -10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 164": "OD1" <-> "OD2" Residue "D GLU 177": "OE1" <-> "OE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D ASP 216": "OD1" <-> "OD2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 470": "OD1" <-> "OD2" Residue "E GLU -19": "OE1" <-> "OE2" Residue "E ARG -10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 34": "OD1" <-> "OD2" Residue "E ASP 43": "OD1" <-> "OD2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 216": "OD1" <-> "OD2" Residue "E ASP 226": "OD1" <-> "OD2" Residue "E ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 254": "OE1" <-> "OE2" Residue "E ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 470": "OD1" <-> "OD2" Residue "F GLU -19": "OE1" <-> "OE2" Residue "F ARG -10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F GLU 199": "OE1" <-> "OE2" Residue "F ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 216": "OD1" <-> "OD2" Residue "F ASP 226": "OD1" <-> "OD2" Residue "F ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 470": "OD1" <-> "OD2" Residue "G ARG -10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 34": "OD1" <-> "OD2" Residue "G PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 43": "OD1" <-> "OD2" Residue "G ASP 77": "OD1" <-> "OD2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G GLU 196": "OE1" <-> "OE2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "G ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 216": "OD1" <-> "OD2" Residue "G ASP 226": "OD1" <-> "OD2" Residue "G ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 254": "OE1" <-> "OE2" Residue "G ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 470": "OD1" <-> "OD2" Residue "H GLU -19": "OE1" <-> "OE2" Residue "H ARG -10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 43": "OD1" <-> "OD2" Residue "H ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H ASP 164": "OD1" <-> "OD2" Residue "H GLU 196": "OE1" <-> "OE2" Residue "H GLU 199": "OE1" <-> "OE2" Residue "H ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 216": "OD1" <-> "OD2" Residue "H ASP 226": "OD1" <-> "OD2" Residue "H ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 254": "OE1" <-> "OE2" Residue "H ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 470": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 55141 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 6823 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain breaks: 5 Chain: "B" Number of atoms: 6823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 6823 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain breaks: 5 Chain: "C" Number of atoms: 6823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 6823 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain breaks: 5 Chain: "D" Number of atoms: 6823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 6823 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain breaks: 5 Chain: "E" Number of atoms: 6823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 6823 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain breaks: 5 Chain: "F" Number of atoms: 6823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 6823 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain breaks: 5 Chain: "G" Number of atoms: 6845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 6845 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 17, 'TRANS': 432} Chain breaks: 5 Chain: "H" Number of atoms: 6862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 6862 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 5 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.37, per 1000 atoms: 0.35 Number of scatterers: 55141 At special positions: 0 Unit cell: (142.8, 142.8, 156.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 169 16.00 P 48 15.00 O 5339 8.00 N 4717 7.00 C 17265 6.00 H 27603 1.00 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: 32.60 Conformation dependent library (CDL) restraints added in 4.2 seconds 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6502 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 153 helices and 36 sheets defined 36.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.72 Creating SS restraints... Processing helix chain 'A' and resid -17 through -6 Processing helix chain 'A' and resid 4 through 7 No H-bonds generated for 'chain 'A' and resid 4 through 7' Processing helix chain 'A' and resid 20 through 26 removed outlier: 3.789A pdb=" N ALA A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.661A pdb=" N LEU A 131 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 136 No H-bonds generated for 'chain 'A' and resid 133 through 136' Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 224 through 227 No H-bonds generated for 'chain 'A' and resid 224 through 227' Processing helix chain 'A' and resid 254 through 265 removed outlier: 3.986A pdb=" N LYS A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR A 258 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 263 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 343 through 356 removed outlier: 4.291A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 453 through 470 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'B' and resid -17 through -6 Processing helix chain 'B' and resid 4 through 7 No H-bonds generated for 'chain 'B' and resid 4 through 7' Processing helix chain 'B' and resid 20 through 26 removed outlier: 3.658A pdb=" N ALA B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 127 through 129 No H-bonds generated for 'chain 'B' and resid 127 through 129' Processing helix chain 'B' and resid 133 through 136 No H-bonds generated for 'chain 'B' and resid 133 through 136' Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 224 through 227 No H-bonds generated for 'chain 'B' and resid 224 through 227' Processing helix chain 'B' and resid 254 through 265 removed outlier: 3.928A pdb=" N LYS B 257 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR B 258 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 343 through 356 removed outlier: 4.112A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 453 through 470 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 495 through 499 Processing helix chain 'C' and resid -17 through -6 removed outlier: 3.801A pdb=" N ALA C -6 " --> pdb=" O ARG C -10 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 7 No H-bonds generated for 'chain 'C' and resid 4 through 7' Processing helix chain 'C' and resid 20 through 26 removed outlier: 3.689A pdb=" N ALA C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 133 through 136 No H-bonds generated for 'chain 'C' and resid 133 through 136' Processing helix chain 'C' and resid 160 through 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 224 through 227 No H-bonds generated for 'chain 'C' and resid 224 through 227' Processing helix chain 'C' and resid 254 through 265 removed outlier: 3.974A pdb=" N LYS C 257 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR C 258 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 263 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 343 through 356 removed outlier: 4.294A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 453 through 470 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 484 Processing helix chain 'C' and resid 495 through 499 Processing helix chain 'D' and resid -17 through -6 Processing helix chain 'D' and resid 4 through 7 No H-bonds generated for 'chain 'D' and resid 4 through 7' Processing helix chain 'D' and resid 20 through 25 removed outlier: 3.596A pdb=" N ALA D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.649A pdb=" N LEU D 131 " --> pdb=" O GLY D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 136 No H-bonds generated for 'chain 'D' and resid 133 through 136' Processing helix chain 'D' and resid 160 through 163 No H-bonds generated for 'chain 'D' and resid 160 through 163' Processing helix chain 'D' and resid 194 through 204 removed outlier: 3.672A pdb=" N GLN D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 227 No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 254 through 265 removed outlier: 3.955A pdb=" N LYS D 257 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR D 258 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 263 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 343 through 356 removed outlier: 4.306A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 379 Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 453 through 470 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 476 through 484 Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'E' and resid -17 through -6 removed outlier: 3.549A pdb=" N GLN E -7 " --> pdb=" O ALA E -11 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA E -6 " --> pdb=" O ARG E -10 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 20 through 25 removed outlier: 3.709A pdb=" N ALA E 25 " --> pdb=" O GLN E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 127 through 131 removed outlier: 3.607A pdb=" N LEU E 131 " --> pdb=" O GLY E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 136 No H-bonds generated for 'chain 'E' and resid 133 through 136' Processing helix chain 'E' and resid 160 through 163 No H-bonds generated for 'chain 'E' and resid 160 through 163' Processing helix chain 'E' and resid 194 through 204 removed outlier: 3.582A pdb=" N GLU E 199 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 227 No H-bonds generated for 'chain 'E' and resid 224 through 227' Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.953A pdb=" N LYS E 257 " --> pdb=" O GLU E 254 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR E 258 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 Processing helix chain 'E' and resid 343 through 356 removed outlier: 4.287A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 453 through 470 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 484 Processing helix chain 'F' and resid -17 through -6 removed outlier: 3.885A pdb=" N ALA F -6 " --> pdb=" O ARG F -10 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 7 No H-bonds generated for 'chain 'F' and resid 4 through 7' Processing helix chain 'F' and resid 20 through 23 No H-bonds generated for 'chain 'F' and resid 20 through 23' Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 97 through 108 Processing helix chain 'F' and resid 133 through 136 No H-bonds generated for 'chain 'F' and resid 133 through 136' Processing helix chain 'F' and resid 160 through 163 No H-bonds generated for 'chain 'F' and resid 160 through 163' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 224 through 227 No H-bonds generated for 'chain 'F' and resid 224 through 227' Processing helix chain 'F' and resid 254 through 265 removed outlier: 3.973A pdb=" N LYS F 257 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR F 258 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 263 " --> pdb=" O LEU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 Processing helix chain 'F' and resid 343 through 356 removed outlier: 4.140A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 379 Processing helix chain 'F' and resid 388 through 390 No H-bonds generated for 'chain 'F' and resid 388 through 390' Processing helix chain 'F' and resid 453 through 470 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 476 through 484 Processing helix chain 'F' and resid 495 through 497 No H-bonds generated for 'chain 'F' and resid 495 through 497' Processing helix chain 'G' and resid -17 through -6 removed outlier: 3.979A pdb=" N ALA G -6 " --> pdb=" O ARG G -10 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 25 removed outlier: 3.780A pdb=" N ALA G 25 " --> pdb=" O GLN G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 84 Processing helix chain 'G' and resid 97 through 108 Processing helix chain 'G' and resid 127 through 131 removed outlier: 3.613A pdb=" N LEU G 131 " --> pdb=" O GLY G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 136 No H-bonds generated for 'chain 'G' and resid 133 through 136' Processing helix chain 'G' and resid 160 through 163 No H-bonds generated for 'chain 'G' and resid 160 through 163' Processing helix chain 'G' and resid 194 through 204 removed outlier: 3.990A pdb=" N GLU G 199 " --> pdb=" O LYS G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 227 No H-bonds generated for 'chain 'G' and resid 224 through 227' Processing helix chain 'G' and resid 254 through 266 removed outlier: 4.000A pdb=" N LYS G 257 " --> pdb=" O GLU G 254 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR G 258 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU G 263 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 Processing helix chain 'G' and resid 343 through 356 removed outlier: 4.310A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 388 through 390 No H-bonds generated for 'chain 'G' and resid 388 through 390' Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 476 through 484 Processing helix chain 'H' and resid -17 through -6 removed outlier: 3.502A pdb=" N GLN H -7 " --> pdb=" O ALA H -11 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA H -6 " --> pdb=" O ARG H -10 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 7 No H-bonds generated for 'chain 'H' and resid 4 through 7' Processing helix chain 'H' and resid 20 through 26 removed outlier: 3.722A pdb=" N ALA H 25 " --> pdb=" O GLN H 21 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER H 26 " --> pdb=" O GLN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 84 Processing helix chain 'H' and resid 97 through 109 Processing helix chain 'H' and resid 128 through 131 No H-bonds generated for 'chain 'H' and resid 128 through 131' Processing helix chain 'H' and resid 133 through 136 No H-bonds generated for 'chain 'H' and resid 133 through 136' Processing helix chain 'H' and resid 160 through 163 No H-bonds generated for 'chain 'H' and resid 160 through 163' Processing helix chain 'H' and resid 194 through 204 removed outlier: 3.520A pdb=" N GLN H 202 " --> pdb=" O ASN H 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 227 No H-bonds generated for 'chain 'H' and resid 224 through 227' Processing helix chain 'H' and resid 254 through 265 removed outlier: 3.910A pdb=" N LYS H 257 " --> pdb=" O GLU H 254 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR H 258 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 Processing helix chain 'H' and resid 343 through 356 removed outlier: 4.250A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 388 through 390 No H-bonds generated for 'chain 'H' and resid 388 through 390' Processing helix chain 'H' and resid 453 through 470 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 484 Processing helix chain 'H' and resid 495 through 499 removed outlier: 3.744A pdb=" N ILE H 499 " --> pdb=" O SER H 496 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.533A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.609A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 208 through 212 Processing sheet with id= E, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= F, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.574A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.698A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 208 through 212 Processing sheet with id= I, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= J, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.539A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.647A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 208 through 213 removed outlier: 5.542A pdb=" N ASN C 213 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU C 218 " --> pdb=" O ASN C 213 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.561A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 142 through 144 removed outlier: 3.664A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.626A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 208 through 212 Processing sheet with id= R, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= S, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.534A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.645A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 142 through 144 removed outlier: 4.501A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 208 through 212 Processing sheet with id= W, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= X, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.500A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.682A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 321 through 323 Processing sheet with id= AA, first strand: chain 'F' and resid 208 through 213 removed outlier: 5.386A pdb=" N ASN F 213 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU F 218 " --> pdb=" O ASN F 213 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AC, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.497A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET G 385 " --> pdb=" O ALA G 363 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 208 through 210 Processing sheet with id= AE, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.582A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AG, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.534A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.684A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'H' and resid 321 through 323 Processing sheet with id= AJ, first strand: chain 'H' and resid 208 through 212 removed outlier: 3.605A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 1929 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: 17.07 Time building geometry restraints manager: 34.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 27555 1.09 - 1.27: 4588 1.27 - 1.46: 7881 1.46 - 1.64: 15243 1.64 - 1.82: 290 Bond restraints: 55557 Sorted by residual: bond pdb=" N SER H 237 " pdb=" H SER H 237 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" CE1 TYR E 282 " pdb=" HE1 TYR E 282 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N VAL G 373 " pdb=" H VAL G 373 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N LYS F 238 " pdb=" H LYS F 238 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N LEU B 174 " pdb=" H LEU B 174 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 55552 not shown) Histogram of bond angle deviations from ideal: 93.75 - 101.60: 165 101.60 - 109.45: 39364 109.45 - 117.30: 33151 117.30 - 125.15: 26674 125.15 - 133.00: 1241 Bond angle restraints: 100595 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 120.19 19.68 1.00e+00 1.00e+00 3.87e+02 angle pdb=" PB ATP G 602 " pdb=" O3B ATP G 602 " pdb=" PG ATP G 602 " ideal model delta sigma weight residual 139.87 120.24 19.63 1.00e+00 1.00e+00 3.85e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 120.63 19.24 1.00e+00 1.00e+00 3.70e+02 angle pdb=" PA ATP D 601 " pdb=" O3A ATP D 601 " pdb=" PB ATP D 601 " ideal model delta sigma weight residual 136.83 117.78 19.05 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 ... (remaining 100590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 22923 17.83 - 35.66: 1854 35.66 - 53.49: 831 53.49 - 71.31: 527 71.31 - 89.14: 107 Dihedral angle restraints: 26242 sinusoidal: 14873 harmonic: 11369 Sorted by residual: dihedral pdb=" C VAL E 503 " pdb=" N VAL E 503 " pdb=" CA VAL E 503 " pdb=" CB VAL E 503 " ideal model delta harmonic sigma weight residual -122.00 -137.80 15.80 0 2.50e+00 1.60e-01 3.99e+01 dihedral pdb=" C VAL D 503 " pdb=" N VAL D 503 " pdb=" CA VAL D 503 " pdb=" CB VAL D 503 " ideal model delta harmonic sigma weight residual -122.00 -137.68 15.68 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" N VAL E 503 " pdb=" C VAL E 503 " pdb=" CA VAL E 503 " pdb=" CB VAL E 503 " ideal model delta harmonic sigma weight residual 123.40 138.09 -14.69 0 2.50e+00 1.60e-01 3.45e+01 ... (remaining 26239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3698 0.120 - 0.239: 641 0.239 - 0.359: 93 0.359 - 0.479: 24 0.479 - 0.599: 3 Chirality restraints: 4459 Sorted by residual: chirality pdb=" CA VAL E 503 " pdb=" N VAL E 503 " pdb=" C VAL E 503 " pdb=" CB VAL E 503 " both_signs ideal model delta sigma weight residual False 2.44 1.84 0.60 2.00e-01 2.50e+01 8.96e+00 chirality pdb=" CA VAL D 503 " pdb=" N VAL D 503 " pdb=" C VAL D 503 " pdb=" CB VAL D 503 " both_signs ideal model delta sigma weight residual False 2.44 1.85 0.59 2.00e-01 2.50e+01 8.75e+00 chirality pdb=" CG LEU E 18 " pdb=" CB LEU E 18 " pdb=" CD1 LEU E 18 " pdb=" CD2 LEU E 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.74e+00 ... (remaining 4456 not shown) Planarity restraints: 8174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 139 " -0.190 2.00e-02 2.50e+03 8.17e-02 2.00e+02 pdb=" CG PHE B 139 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 139 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE B 139 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 PHE B 139 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE B 139 " 0.036 2.00e-02 2.50e+03 pdb=" CZ PHE B 139 " -0.036 2.00e-02 2.50e+03 pdb=" HD1 PHE B 139 " 0.073 2.00e-02 2.50e+03 pdb=" HD2 PHE B 139 " 0.038 2.00e-02 2.50e+03 pdb=" HE1 PHE B 139 " 0.016 2.00e-02 2.50e+03 pdb=" HE2 PHE B 139 " 0.056 2.00e-02 2.50e+03 pdb=" HZ PHE B 139 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 139 " -0.197 2.00e-02 2.50e+03 8.15e-02 1.99e+02 pdb=" CG PHE C 139 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE C 139 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 PHE C 139 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 PHE C 139 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE C 139 " 0.036 2.00e-02 2.50e+03 pdb=" CZ PHE C 139 " -0.032 2.00e-02 2.50e+03 pdb=" HD1 PHE C 139 " 0.072 2.00e-02 2.50e+03 pdb=" HD2 PHE C 139 " 0.048 2.00e-02 2.50e+03 pdb=" HE1 PHE C 139 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE C 139 " 0.036 2.00e-02 2.50e+03 pdb=" HZ PHE C 139 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 161 " 0.022 9.50e-02 1.11e+02 9.11e-02 1.86e+02 pdb=" NE ARG A 161 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 161 " -0.058 2.00e-02 2.50e+03 pdb=" NH1 ARG A 161 " -0.091 2.00e-02 2.50e+03 pdb=" NH2 ARG A 161 " -0.021 2.00e-02 2.50e+03 pdb="HH11 ARG A 161 " 0.044 2.00e-02 2.50e+03 pdb="HH12 ARG A 161 " 0.136 2.00e-02 2.50e+03 pdb="HH21 ARG A 161 " 0.153 2.00e-02 2.50e+03 pdb="HH22 ARG A 161 " -0.132 2.00e-02 2.50e+03 ... (remaining 8171 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 2167 2.06 - 2.70: 76337 2.70 - 3.33: 165235 3.33 - 3.97: 213201 3.97 - 4.60: 320999 Nonbonded interactions: 777939 Sorted by model distance: nonbonded pdb=" OE1 GLU B 146 " pdb=" H GLU B 146 " model vdw 1.426 1.850 nonbonded pdb=" H GLY H 128 " pdb=" H ASP H 129 " model vdw 1.480 2.100 nonbonded pdb=" HG3 LYS F 134 " pdb=" HZ3 LYS F 134 " model vdw 1.496 2.270 nonbonded pdb=" HB2 CYS B 95 " pdb=" HD2 PHE B 99 " model vdw 1.500 2.270 nonbonded pdb=" H GLY F 128 " pdb=" H ASP F 129 " model vdw 1.500 2.100 ... (remaining 777934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = (chain 'G' and (resid -20 through 149 or resid 154 through 504 or resid 601 thro \ ugh 602)) selection = (chain 'H' and (resid -20 through 149 or resid 154 through 504 or resid 601 thro \ ugh 602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.650 Extract box with map and model: 9.040 Check model and map are aligned: 0.750 Set scattering table: 0.460 Process input model: 132.070 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.290 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 : 0.013 0.135 27954 Z= 0.837 Angle : 1.861 19.683 37896 Z= 1.279 Chirality : 0.098 0.599 4459 Planarity : 0.013 0.123 4763 Dihedral : 16.782 89.142 10622 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 1.09 % Allowed : 8.75 % Favored : 90.17 % Rotamer: Outliers : 2.73 % Allowed : 9.31 % Favored : 87.96 % Cbeta Deviations : 1.11 % 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: -3.02 (0.13), residues: 3499 helix: -2.39 (0.11), residues: 1357 sheet: -1.10 (0.26), residues: 281 loop : -1.80 (0.15), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS B 288 PHE 0.109 0.013 PHE C 139 TYR 0.132 0.019 TYR B 282 ARG 0.009 0.001 ARG G 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 786 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6868 (t0) cc_final: 0.6483 (t0) REVERT: A 102 ASN cc_start: 0.8114 (t0) cc_final: 0.7893 (t0) REVERT: A 226 ASP cc_start: 0.7466 (m-30) cc_final: 0.7181 (m-30) REVERT: A 230 ASN cc_start: 0.6804 (p0) cc_final: 0.6384 (p0) REVERT: A 253 ARG cc_start: 0.7617 (mmt90) cc_final: 0.7319 (mmm160) REVERT: A 500 GLU cc_start: 0.7850 (tm-30) cc_final: 0.6414 (tt0) REVERT: B 47 ASP cc_start: 0.6906 (t0) cc_final: 0.6541 (t0) REVERT: B 85 MET cc_start: 0.8409 (mmm) cc_final: 0.8183 (mmt) REVERT: B 109 LYS cc_start: 0.7930 (mttm) cc_final: 0.7722 (mtpt) REVERT: B 230 ASN cc_start: 0.6845 (p0) cc_final: 0.6402 (p0) REVERT: B 245 LEU cc_start: 0.8794 (mt) cc_final: 0.8565 (mt) REVERT: B 483 MET cc_start: 0.9207 (tmm) cc_final: 0.8923 (tmm) REVERT: C 42 ILE cc_start: 0.9006 (mt) cc_final: 0.8597 (mt) REVERT: C 47 ASP cc_start: 0.6905 (t0) cc_final: 0.6540 (t0) REVERT: C 94 ASN cc_start: 0.7663 (t0) cc_final: 0.7247 (t0) REVERT: C 98 GLU cc_start: 0.7349 (tp30) cc_final: 0.7039 (tp30) REVERT: C 194 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7407 (tt) REVERT: C 238 LYS cc_start: 0.7969 (mttt) cc_final: 0.7604 (mtpt) REVERT: C 245 LEU cc_start: 0.8824 (mt) cc_final: 0.8577 (mt) REVERT: C 253 ARG cc_start: 0.7560 (mmt90) cc_final: 0.7341 (mmm160) REVERT: C 455 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7631 (tmmt) REVERT: D 34 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7831 (t0) REVERT: D 47 ASP cc_start: 0.6906 (t0) cc_final: 0.6523 (t0) REVERT: D 102 ASN cc_start: 0.8110 (t0) cc_final: 0.7860 (t0) REVERT: D 109 LYS cc_start: 0.7903 (mttm) cc_final: 0.7695 (mtmm) REVERT: D 146 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: D 179 MET cc_start: 0.7182 (mpp) cc_final: 0.6455 (mpp) REVERT: D 239 ASP cc_start: 0.7805 (p0) cc_final: 0.7553 (p0) REVERT: E 47 ASP cc_start: 0.6939 (t0) cc_final: 0.6530 (t0) REVERT: E 109 LYS cc_start: 0.7873 (mttm) cc_final: 0.7629 (mtpt) REVERT: E 226 ASP cc_start: 0.7254 (m-30) cc_final: 0.6862 (m-30) REVERT: E 293 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8002 (ttmm) REVERT: F 47 ASP cc_start: 0.6935 (t0) cc_final: 0.6607 (t0) REVERT: F 102 ASN cc_start: 0.8159 (t0) cc_final: 0.7748 (t0) REVERT: F 455 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7709 (tmmt) REVERT: F 504 HIS cc_start: 0.6417 (OUTLIER) cc_final: 0.6052 (m-70) REVERT: G 42 ILE cc_start: 0.9016 (mt) cc_final: 0.8733 (mt) REVERT: G 102 ASN cc_start: 0.8076 (t0) cc_final: 0.7764 (t0) REVERT: G 483 MET cc_start: 0.9089 (tmm) cc_final: 0.8860 (tmm) REVERT: H 47 ASP cc_start: 0.6862 (t0) cc_final: 0.6527 (t0) REVERT: H 238 LYS cc_start: 0.7906 (mttt) cc_final: 0.7529 (mtmt) REVERT: H 455 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7801 (tmtt) outliers start: 79 outliers final: 28 residues processed: 843 average time/residue: 0.7914 time to fit residues: 1044.9199 Evaluate side-chains 752 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 717 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 504 HIS Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 504 HIS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 0.6980 chunk 268 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 206 optimal weight: 0.7980 chunk 321 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 466 HIS B 241 GLN B 466 HIS B 498 GLN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS D 466 HIS E 466 HIS F 22 GLN F 466 HIS F 469 GLN G 230 ASN H 230 ASN H 466 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27954 Z= 0.243 Angle : 0.677 7.134 37896 Z= 0.360 Chirality : 0.043 0.186 4459 Planarity : 0.005 0.067 4763 Dihedral : 15.089 89.804 4435 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.29 % Favored : 93.26 % Rotamer: Outliers : 2.38 % Allowed : 12.59 % Favored : 85.03 % 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: -2.42 (0.13), residues: 3499 helix: -1.35 (0.12), residues: 1372 sheet: -1.08 (0.25), residues: 331 loop : -1.89 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 125 PHE 0.014 0.002 PHE G 456 TYR 0.037 0.002 TYR F 282 ARG 0.004 0.000 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 741 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6775 (t0) cc_final: 0.6400 (t0) REVERT: A 102 ASN cc_start: 0.8065 (t0) cc_final: 0.7813 (t0) REVERT: A 155 VAL cc_start: 0.6490 (OUTLIER) cc_final: 0.6088 (t) REVERT: A 226 ASP cc_start: 0.7544 (m-30) cc_final: 0.7300 (m-30) REVERT: A 242 LYS cc_start: 0.7621 (mttt) cc_final: 0.7326 (ttmt) REVERT: A 253 ARG cc_start: 0.7739 (mmt90) cc_final: 0.7400 (mmp-170) REVERT: B 34 ASP cc_start: 0.7838 (t70) cc_final: 0.7579 (t0) REVERT: B 47 ASP cc_start: 0.6776 (t0) cc_final: 0.6371 (t0) REVERT: B 85 MET cc_start: 0.8479 (mmm) cc_final: 0.8208 (mmt) REVERT: B 109 LYS cc_start: 0.7764 (mttm) cc_final: 0.7533 (mtpt) REVERT: B 241 GLN cc_start: 0.7973 (mm110) cc_final: 0.7731 (mm110) REVERT: B 455 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7622 (tmmt) REVERT: B 483 MET cc_start: 0.9235 (tmm) cc_final: 0.9028 (tmm) REVERT: C 47 ASP cc_start: 0.6818 (t0) cc_final: 0.6453 (t0) REVERT: C 94 ASN cc_start: 0.7749 (t0) cc_final: 0.7276 (t0) REVERT: C 98 GLU cc_start: 0.7463 (tp30) cc_final: 0.7147 (tp30) REVERT: C 125 HIS cc_start: 0.6812 (t70) cc_final: 0.6427 (t70) REVERT: C 238 LYS cc_start: 0.7813 (mttt) cc_final: 0.7554 (mtpt) REVERT: C 253 ARG cc_start: 0.7700 (mmt90) cc_final: 0.7444 (mmp-170) REVERT: C 498 GLN cc_start: 0.8511 (pt0) cc_final: 0.8299 (pt0) REVERT: D 34 ASP cc_start: 0.8205 (t70) cc_final: 0.7990 (t0) REVERT: D 47 ASP cc_start: 0.6836 (t0) cc_final: 0.6462 (t0) REVERT: D 109 LYS cc_start: 0.7829 (mttm) cc_final: 0.7590 (mtpt) REVERT: D 238 LYS cc_start: 0.7923 (mttt) cc_final: 0.7595 (mtpt) REVERT: D 293 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7793 (ttmm) REVERT: D 395 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7654 (mm-30) REVERT: E 47 ASP cc_start: 0.6779 (t0) cc_final: 0.6387 (t0) REVERT: E 226 ASP cc_start: 0.7293 (m-30) cc_final: 0.7030 (m-30) REVERT: E 242 LYS cc_start: 0.7774 (mttt) cc_final: 0.7421 (ttmt) REVERT: F 34 ASP cc_start: 0.7910 (t0) cc_final: 0.7662 (t0) REVERT: F 47 ASP cc_start: 0.6925 (t0) cc_final: 0.6562 (t0) REVERT: F 98 GLU cc_start: 0.7272 (tp30) cc_final: 0.7003 (tp30) REVERT: F 105 ARG cc_start: 0.8041 (ttp-170) cc_final: 0.7809 (ttp80) REVERT: F 230 ASN cc_start: 0.7317 (m110) cc_final: 0.7090 (m110) REVERT: G 34 ASP cc_start: 0.7934 (t70) cc_final: 0.7718 (t0) REVERT: G 199 GLU cc_start: 0.7232 (tm-30) cc_final: 0.7008 (tm-30) REVERT: G 242 LYS cc_start: 0.7604 (mttt) cc_final: 0.7145 (ttmm) REVERT: G 504 HIS cc_start: 0.7466 (OUTLIER) cc_final: 0.7199 (m170) REVERT: H 34 ASP cc_start: 0.8102 (t0) cc_final: 0.7836 (t0) REVERT: H 47 ASP cc_start: 0.6830 (t0) cc_final: 0.6445 (t0) REVERT: H 109 LYS cc_start: 0.8038 (mttm) cc_final: 0.7748 (mtmt) REVERT: H 226 ASP cc_start: 0.7303 (m-30) cc_final: 0.7063 (m-30) REVERT: H 238 LYS cc_start: 0.7950 (mttt) cc_final: 0.7535 (mtmt) outliers start: 69 outliers final: 43 residues processed: 789 average time/residue: 0.7754 time to fit residues: 967.1006 Evaluate side-chains 758 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 712 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 504 HIS Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 504 HIS Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 471 ILE Chi-restraints excluded: chain G residue 504 HIS Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 457 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 0.0980 chunk 99 optimal weight: 2.9990 chunk 267 optimal weight: 0.1980 chunk 218 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 322 optimal weight: 1.9990 chunk 347 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 chunk 319 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN B 454 GLN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN F 504 HIS H 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27954 Z= 0.259 Angle : 0.602 6.717 37896 Z= 0.316 Chirality : 0.043 0.166 4459 Planarity : 0.004 0.050 4763 Dihedral : 14.446 89.872 4391 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.92 % Favored : 92.68 % Rotamer: Outliers : 2.48 % Allowed : 13.66 % Favored : 83.86 % 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: -2.03 (0.14), residues: 3499 helix: -0.76 (0.13), residues: 1334 sheet: -1.16 (0.25), residues: 351 loop : -1.84 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 92 PHE 0.010 0.001 PHE G 456 TYR 0.028 0.002 TYR G 282 ARG 0.002 0.000 ARG H 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 728 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6856 (t0) cc_final: 0.6608 (t0) REVERT: A 102 ASN cc_start: 0.8052 (t0) cc_final: 0.7837 (t0) REVERT: A 226 ASP cc_start: 0.7621 (m-30) cc_final: 0.7392 (m-30) REVERT: A 242 LYS cc_start: 0.7690 (mttt) cc_final: 0.7210 (ttmm) REVERT: A 368 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: A 500 GLU cc_start: 0.8029 (tm-30) cc_final: 0.6815 (tt0) REVERT: B 34 ASP cc_start: 0.7916 (t70) cc_final: 0.7653 (t0) REVERT: B 47 ASP cc_start: 0.6890 (t0) cc_final: 0.6655 (t0) REVERT: B 85 MET cc_start: 0.8496 (mmm) cc_final: 0.8253 (mmt) REVERT: B 242 LYS cc_start: 0.7682 (mttt) cc_final: 0.7317 (ttmt) REVERT: B 253 ARG cc_start: 0.7696 (tpp80) cc_final: 0.6962 (mmp-170) REVERT: B 283 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: B 455 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7677 (tmmt) REVERT: C 1 MET cc_start: 0.7576 (pmm) cc_final: 0.7196 (pmm) REVERT: C 47 ASP cc_start: 0.6869 (t0) cc_final: 0.6644 (t0) REVERT: C 85 MET cc_start: 0.8279 (mmm) cc_final: 0.8040 (mmt) REVERT: C 94 ASN cc_start: 0.7868 (t0) cc_final: 0.7358 (t0) REVERT: C 98 GLU cc_start: 0.7553 (tp30) cc_final: 0.7212 (tp30) REVERT: C 238 LYS cc_start: 0.7950 (mttt) cc_final: 0.7627 (mtpt) REVERT: C 253 ARG cc_start: 0.7588 (mmt90) cc_final: 0.7379 (mmp-170) REVERT: D 34 ASP cc_start: 0.8188 (t70) cc_final: 0.7950 (t0) REVERT: D 47 ASP cc_start: 0.6894 (t0) cc_final: 0.6658 (t0) REVERT: D 238 LYS cc_start: 0.7877 (mttt) cc_final: 0.7552 (mtpt) REVERT: D 395 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7759 (mm-30) REVERT: D 456 PHE cc_start: 0.8228 (t80) cc_final: 0.7984 (t80) REVERT: E 47 ASP cc_start: 0.6922 (t0) cc_final: 0.6689 (t0) REVERT: E 242 LYS cc_start: 0.7696 (mttt) cc_final: 0.7365 (ttmt) REVERT: F 34 ASP cc_start: 0.7968 (t0) cc_final: 0.7689 (t0) REVERT: F 47 ASP cc_start: 0.6982 (t0) cc_final: 0.6745 (t0) REVERT: F 132 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6717 (pp20) REVERT: G 34 ASP cc_start: 0.8072 (t70) cc_final: 0.7804 (t0) REVERT: G 242 LYS cc_start: 0.7625 (mttt) cc_final: 0.7342 (ttmt) REVERT: G 504 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.7142 (m170) REVERT: H 34 ASP cc_start: 0.8134 (t0) cc_final: 0.7877 (t0) REVERT: H 47 ASP cc_start: 0.6854 (t0) cc_final: 0.6484 (t0) REVERT: H 109 LYS cc_start: 0.7969 (mttm) cc_final: 0.7713 (mtmt) REVERT: H 154 LEU cc_start: 0.4119 (OUTLIER) cc_final: 0.3876 (tt) REVERT: H 238 LYS cc_start: 0.7988 (mttt) cc_final: 0.7616 (mtmt) outliers start: 72 outliers final: 52 residues processed: 769 average time/residue: 0.7741 time to fit residues: 943.9123 Evaluate side-chains 761 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 703 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 474 ARG Chi-restraints excluded: chain E residue 504 HIS Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 482 MET Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 504 HIS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 504 HIS Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 482 MET Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 4.9990 chunk 242 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 216 optimal weight: 0.2980 chunk 323 optimal weight: 10.0000 chunk 342 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 454 GLN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN F 454 GLN ** F 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27954 Z= 0.171 Angle : 0.545 5.306 37896 Z= 0.287 Chirality : 0.042 0.160 4459 Planarity : 0.004 0.046 4763 Dihedral : 13.676 87.054 4388 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.97 % Favored : 93.63 % Rotamer: Outliers : 2.21 % Allowed : 14.56 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3499 helix: -0.45 (0.14), residues: 1371 sheet: -1.08 (0.25), residues: 341 loop : -1.75 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.030 0.001 HIS F 504 PHE 0.011 0.001 PHE B 456 TYR 0.020 0.001 TYR E 282 ARG 0.003 0.000 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 707 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6904 (t0) cc_final: 0.6661 (t0) REVERT: A 85 MET cc_start: 0.7950 (mmm) cc_final: 0.7722 (mmt) REVERT: A 155 VAL cc_start: 0.6515 (OUTLIER) cc_final: 0.6124 (t) REVERT: A 242 LYS cc_start: 0.7714 (mttt) cc_final: 0.7235 (ttmm) REVERT: A 253 ARG cc_start: 0.7670 (mmt90) cc_final: 0.7413 (mmp-170) REVERT: A 368 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7775 (pt0) REVERT: A 500 GLU cc_start: 0.7944 (tm-30) cc_final: 0.6753 (tt0) REVERT: B 34 ASP cc_start: 0.7959 (t70) cc_final: 0.7682 (t0) REVERT: B 47 ASP cc_start: 0.6930 (t0) cc_final: 0.6671 (t0) REVERT: B 177 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.4700 (pm20) REVERT: B 242 LYS cc_start: 0.7676 (mttt) cc_final: 0.7359 (ttmt) REVERT: B 253 ARG cc_start: 0.7727 (tpp80) cc_final: 0.6958 (mmp-170) REVERT: B 292 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7940 (tm-30) REVERT: B 393 THR cc_start: 0.7702 (p) cc_final: 0.7352 (t) REVERT: B 455 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7651 (tmmt) REVERT: B 456 PHE cc_start: 0.8279 (t80) cc_final: 0.8039 (t80) REVERT: C 1 MET cc_start: 0.7517 (pmm) cc_final: 0.7133 (pmm) REVERT: C 47 ASP cc_start: 0.6932 (t0) cc_final: 0.6692 (t0) REVERT: C 85 MET cc_start: 0.8328 (mmm) cc_final: 0.8121 (mmt) REVERT: C 94 ASN cc_start: 0.7870 (t0) cc_final: 0.7386 (t0) REVERT: C 98 GLU cc_start: 0.7507 (tp30) cc_final: 0.7140 (tp30) REVERT: C 226 ASP cc_start: 0.7445 (m-30) cc_final: 0.7245 (m-30) REVERT: C 238 LYS cc_start: 0.7923 (mttt) cc_final: 0.7524 (mtpt) REVERT: C 253 ARG cc_start: 0.7552 (mmt90) cc_final: 0.7228 (mmp-170) REVERT: D 47 ASP cc_start: 0.6982 (t0) cc_final: 0.6724 (t0) REVERT: D 109 LYS cc_start: 0.7973 (mttt) cc_final: 0.7770 (mtmm) REVERT: D 203 ARG cc_start: 0.7182 (ttp-110) cc_final: 0.6864 (ttp-110) REVERT: D 238 LYS cc_start: 0.7847 (mttt) cc_final: 0.7531 (mtpt) REVERT: D 395 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7626 (mm-30) REVERT: E 47 ASP cc_start: 0.6991 (t0) cc_final: 0.6721 (t0) REVERT: E 242 LYS cc_start: 0.7674 (mttt) cc_final: 0.7399 (ttmt) REVERT: F 34 ASP cc_start: 0.7966 (t0) cc_final: 0.7669 (t0) REVERT: F 47 ASP cc_start: 0.7026 (t0) cc_final: 0.6772 (t0) REVERT: F 132 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6637 (pp20) REVERT: F 253 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7059 (mmp-170) REVERT: G 34 ASP cc_start: 0.8100 (t70) cc_final: 0.7849 (t0) REVERT: G 242 LYS cc_start: 0.7633 (mttt) cc_final: 0.7203 (ttmm) REVERT: H 34 ASP cc_start: 0.8111 (t0) cc_final: 0.7831 (t0) REVERT: H 47 ASP cc_start: 0.6909 (t0) cc_final: 0.6674 (t0) REVERT: H 109 LYS cc_start: 0.7974 (mttm) cc_final: 0.7682 (mtpt) REVERT: H 154 LEU cc_start: 0.4024 (OUTLIER) cc_final: 0.3774 (tp) REVERT: H 238 LYS cc_start: 0.7916 (mttt) cc_final: 0.7545 (mtmt) outliers start: 64 outliers final: 44 residues processed: 742 average time/residue: 0.7469 time to fit residues: 872.2098 Evaluate side-chains 735 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 685 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 2.9990 chunk 194 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN F 454 GLN H 94 ASN H 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27954 Z= 0.221 Angle : 0.537 7.194 37896 Z= 0.282 Chirality : 0.042 0.155 4459 Planarity : 0.004 0.042 4763 Dihedral : 13.312 88.682 4386 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.63 % Favored : 92.97 % Rotamer: Outliers : 2.41 % Allowed : 14.28 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3499 helix: -0.19 (0.14), residues: 1371 sheet: -1.11 (0.25), residues: 353 loop : -1.80 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.001 HIS F 504 PHE 0.017 0.001 PHE G 456 TYR 0.020 0.001 TYR G 282 ARG 0.003 0.000 ARG H 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 692 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6902 (t0) cc_final: 0.6655 (t0) REVERT: A 85 MET cc_start: 0.8047 (mmm) cc_final: 0.7823 (mmt) REVERT: A 242 LYS cc_start: 0.7693 (mttt) cc_final: 0.7226 (ttmm) REVERT: A 253 ARG cc_start: 0.7695 (mmt90) cc_final: 0.7425 (mmp-170) REVERT: A 368 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7705 (pt0) REVERT: B 34 ASP cc_start: 0.8032 (t70) cc_final: 0.7743 (t0) REVERT: B 47 ASP cc_start: 0.6920 (t0) cc_final: 0.6677 (t0) REVERT: B 85 MET cc_start: 0.8072 (mmm) cc_final: 0.7802 (mmt) REVERT: B 177 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5256 (tp30) REVERT: B 242 LYS cc_start: 0.7733 (mttt) cc_final: 0.7416 (ttmt) REVERT: B 253 ARG cc_start: 0.7801 (tpp80) cc_final: 0.7035 (mmp-170) REVERT: B 292 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7885 (tm-30) REVERT: B 455 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7646 (tmmt) REVERT: C 1 MET cc_start: 0.7527 (pmm) cc_final: 0.7261 (pmm) REVERT: C 47 ASP cc_start: 0.6832 (t0) cc_final: 0.6587 (t0) REVERT: C 85 MET cc_start: 0.8419 (mmm) cc_final: 0.8192 (mmt) REVERT: C 94 ASN cc_start: 0.7900 (t0) cc_final: 0.7459 (t0) REVERT: C 98 GLU cc_start: 0.7527 (tp30) cc_final: 0.7143 (tp30) REVERT: C 109 LYS cc_start: 0.7746 (mtmt) cc_final: 0.7477 (mttp) REVERT: C 125 HIS cc_start: 0.6856 (t70) cc_final: 0.6633 (t70) REVERT: C 253 ARG cc_start: 0.7512 (mmt90) cc_final: 0.7148 (mmp-170) REVERT: D 47 ASP cc_start: 0.6909 (t0) cc_final: 0.6648 (t0) REVERT: D 94 ASN cc_start: 0.7937 (t0) cc_final: 0.7407 (t0) REVERT: D 109 LYS cc_start: 0.7981 (mttt) cc_final: 0.7744 (mtmm) REVERT: D 242 LYS cc_start: 0.7553 (mttp) cc_final: 0.7043 (ttmm) REVERT: D 395 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7622 (mm-30) REVERT: E 47 ASP cc_start: 0.6984 (t0) cc_final: 0.6723 (t0) REVERT: E 85 MET cc_start: 0.8148 (mmm) cc_final: 0.7911 (mmt) REVERT: E 242 LYS cc_start: 0.7704 (mttt) cc_final: 0.7426 (ttmt) REVERT: F 34 ASP cc_start: 0.7990 (t0) cc_final: 0.7728 (t0) REVERT: F 47 ASP cc_start: 0.7022 (t0) cc_final: 0.6778 (t0) REVERT: F 226 ASP cc_start: 0.7461 (m-30) cc_final: 0.7236 (m-30) REVERT: F 253 ARG cc_start: 0.7870 (tpp80) cc_final: 0.7051 (mmp-170) REVERT: G 34 ASP cc_start: 0.8116 (t70) cc_final: 0.7878 (t0) REVERT: G 242 LYS cc_start: 0.7654 (mttt) cc_final: 0.7207 (ttmm) REVERT: G 456 PHE cc_start: 0.8210 (t80) cc_final: 0.8001 (t80) REVERT: H 34 ASP cc_start: 0.8054 (t0) cc_final: 0.7755 (t0) REVERT: H 47 ASP cc_start: 0.6909 (t0) cc_final: 0.6675 (t0) REVERT: H 85 MET cc_start: 0.8344 (mmm) cc_final: 0.8080 (mmt) REVERT: H 109 LYS cc_start: 0.7903 (mttm) cc_final: 0.7608 (mtpt) REVERT: H 154 LEU cc_start: 0.4259 (OUTLIER) cc_final: 0.4000 (tp) REVERT: H 238 LYS cc_start: 0.7927 (mttt) cc_final: 0.7453 (mtmt) REVERT: H 253 ARG cc_start: 0.7904 (tpp80) cc_final: 0.7033 (mmp-170) outliers start: 70 outliers final: 47 residues processed: 731 average time/residue: 0.7542 time to fit residues: 866.8265 Evaluate side-chains 720 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 669 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 454 GLN Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 1.9990 chunk 308 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 342 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN F 230 ASN F 454 GLN H 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 27954 Z= 0.300 Angle : 0.548 5.189 37896 Z= 0.290 Chirality : 0.043 0.153 4459 Planarity : 0.004 0.042 4763 Dihedral : 13.285 87.517 4383 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.89 % Favored : 92.68 % Rotamer: Outliers : 2.62 % Allowed : 14.83 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3499 helix: -0.10 (0.14), residues: 1359 sheet: -1.11 (0.26), residues: 352 loop : -1.79 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 504 PHE 0.009 0.001 PHE G 456 TYR 0.023 0.002 TYR B 282 ARG 0.003 0.000 ARG F 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 690 time to evaluate : 3.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6912 (t0) cc_final: 0.6660 (t0) REVERT: A 85 MET cc_start: 0.8133 (mmm) cc_final: 0.7901 (mmt) REVERT: A 155 VAL cc_start: 0.6594 (OUTLIER) cc_final: 0.6209 (t) REVERT: A 253 ARG cc_start: 0.7716 (mmt90) cc_final: 0.7460 (mmp-170) REVERT: A 293 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7929 (ttmm) REVERT: B 34 ASP cc_start: 0.8089 (t70) cc_final: 0.7821 (t0) REVERT: B 47 ASP cc_start: 0.6932 (t0) cc_final: 0.6693 (t0) REVERT: B 85 MET cc_start: 0.8300 (mmm) cc_final: 0.8054 (mmt) REVERT: B 177 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5355 (tp30) REVERT: B 242 LYS cc_start: 0.7749 (mttt) cc_final: 0.7424 (ttmt) REVERT: B 253 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7043 (mmp-170) REVERT: B 455 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7619 (tmmt) REVERT: B 456 PHE cc_start: 0.8334 (t80) cc_final: 0.8080 (t80) REVERT: C 1 MET cc_start: 0.7531 (pmm) cc_final: 0.7281 (pmm) REVERT: C 47 ASP cc_start: 0.6836 (t0) cc_final: 0.6586 (t0) REVERT: C 85 MET cc_start: 0.8434 (mmm) cc_final: 0.8210 (mmt) REVERT: C 94 ASN cc_start: 0.7970 (t0) cc_final: 0.7540 (t0) REVERT: C 98 GLU cc_start: 0.7529 (tp30) cc_final: 0.7143 (tp30) REVERT: C 109 LYS cc_start: 0.7741 (mtmt) cc_final: 0.7441 (mttp) REVERT: C 125 HIS cc_start: 0.6912 (t70) cc_final: 0.6664 (t70) REVERT: C 253 ARG cc_start: 0.7504 (mmt90) cc_final: 0.7131 (mmp-170) REVERT: D 47 ASP cc_start: 0.6887 (t0) cc_final: 0.6623 (t0) REVERT: D 94 ASN cc_start: 0.7966 (t0) cc_final: 0.7444 (t0) REVERT: D 109 LYS cc_start: 0.7972 (mttt) cc_final: 0.7740 (mtmm) REVERT: D 242 LYS cc_start: 0.7620 (mttp) cc_final: 0.7108 (ttmm) REVERT: D 293 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7946 (ttmm) REVERT: D 395 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7632 (mm-30) REVERT: E 47 ASP cc_start: 0.6985 (t0) cc_final: 0.6729 (t0) REVERT: E 85 MET cc_start: 0.8249 (mmm) cc_final: 0.8024 (mmt) REVERT: E 213 ASN cc_start: 0.8035 (p0) cc_final: 0.7831 (p0) REVERT: E 238 LYS cc_start: 0.7944 (mttt) cc_final: 0.7607 (mtmt) REVERT: E 293 LYS cc_start: 0.8261 (ttmm) cc_final: 0.8007 (ttmm) REVERT: F 34 ASP cc_start: 0.7992 (t0) cc_final: 0.7741 (t0) REVERT: F 47 ASP cc_start: 0.7042 (t0) cc_final: 0.6791 (t0) REVERT: F 206 LYS cc_start: 0.7755 (mmtp) cc_final: 0.7532 (mmtp) REVERT: F 253 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7054 (mmp-170) REVERT: G 34 ASP cc_start: 0.8228 (t70) cc_final: 0.7973 (t0) REVERT: G 242 LYS cc_start: 0.7640 (mttt) cc_final: 0.7223 (ttmm) REVERT: G 293 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7926 (ttmm) REVERT: H 34 ASP cc_start: 0.8145 (t0) cc_final: 0.7841 (t0) REVERT: H 47 ASP cc_start: 0.6921 (t0) cc_final: 0.6689 (t0) REVERT: H 85 MET cc_start: 0.8423 (mmm) cc_final: 0.8187 (mmt) REVERT: H 109 LYS cc_start: 0.7885 (mttm) cc_final: 0.7575 (mtpt) REVERT: H 154 LEU cc_start: 0.4194 (OUTLIER) cc_final: 0.3987 (tt) REVERT: H 238 LYS cc_start: 0.7918 (mttt) cc_final: 0.7533 (mtmt) REVERT: H 253 ARG cc_start: 0.7898 (tpp80) cc_final: 0.7043 (mmp-170) outliers start: 76 outliers final: 58 residues processed: 736 average time/residue: 0.7908 time to fit residues: 926.2912 Evaluate side-chains 739 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 677 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 470 ASP Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** F 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27954 Z= 0.273 Angle : 0.540 4.997 37896 Z= 0.285 Chirality : 0.042 0.152 4459 Planarity : 0.004 0.046 4763 Dihedral : 13.058 86.874 4377 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.89 % Favored : 92.68 % Rotamer: Outliers : 2.83 % Allowed : 14.94 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.14), residues: 3499 helix: -0.04 (0.14), residues: 1371 sheet: -1.05 (0.27), residues: 352 loop : -1.81 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 504 PHE 0.010 0.001 PHE G 456 TYR 0.023 0.001 TYR B 282 ARG 0.003 0.000 ARG B 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 695 time to evaluate : 3.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6794 (t0) cc_final: 0.6583 (t0) REVERT: A 85 MET cc_start: 0.8201 (mmm) cc_final: 0.7957 (mmt) REVERT: A 94 ASN cc_start: 0.7916 (t0) cc_final: 0.7413 (t0) REVERT: A 242 LYS cc_start: 0.7605 (mttp) cc_final: 0.7298 (mttm) REVERT: A 253 ARG cc_start: 0.7688 (mmt90) cc_final: 0.7362 (mmp-170) REVERT: A 293 LYS cc_start: 0.8189 (ttmm) cc_final: 0.7937 (ttmm) REVERT: B 34 ASP cc_start: 0.8085 (t70) cc_final: 0.7804 (t0) REVERT: B 47 ASP cc_start: 0.6854 (t0) cc_final: 0.6610 (t0) REVERT: B 85 MET cc_start: 0.8356 (mmm) cc_final: 0.8106 (mmt) REVERT: B 177 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.5246 (tp30) REVERT: B 242 LYS cc_start: 0.7748 (mttt) cc_final: 0.7426 (ttmt) REVERT: B 253 ARG cc_start: 0.7882 (tpp80) cc_final: 0.7053 (mmp-170) REVERT: B 455 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7613 (tmmt) REVERT: B 456 PHE cc_start: 0.8343 (t80) cc_final: 0.7987 (t80) REVERT: B 460 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8482 (mp) REVERT: C 1 MET cc_start: 0.7533 (pmm) cc_final: 0.7283 (pmm) REVERT: C 47 ASP cc_start: 0.6818 (t0) cc_final: 0.6576 (t0) REVERT: C 78 MET cc_start: 0.8896 (tpp) cc_final: 0.8632 (tpt) REVERT: C 85 MET cc_start: 0.8475 (mmm) cc_final: 0.8245 (mmt) REVERT: C 94 ASN cc_start: 0.7950 (t0) cc_final: 0.7518 (t0) REVERT: C 98 GLU cc_start: 0.7473 (tp30) cc_final: 0.7096 (tp30) REVERT: C 125 HIS cc_start: 0.6891 (t70) cc_final: 0.6639 (t70) REVERT: C 238 LYS cc_start: 0.8001 (mttt) cc_final: 0.7602 (mtpt) REVERT: C 253 ARG cc_start: 0.7490 (mmt90) cc_final: 0.7126 (mmp-170) REVERT: D 47 ASP cc_start: 0.6880 (t0) cc_final: 0.6614 (t0) REVERT: D 78 MET cc_start: 0.8788 (tpp) cc_final: 0.8277 (tpp) REVERT: D 94 ASN cc_start: 0.7963 (t0) cc_final: 0.7434 (t0) REVERT: D 238 LYS cc_start: 0.7903 (mttt) cc_final: 0.7409 (mtpp) REVERT: D 293 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7940 (ttmm) REVERT: D 395 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7634 (mm-30) REVERT: E 47 ASP cc_start: 0.6979 (t0) cc_final: 0.6727 (t0) REVERT: E 78 MET cc_start: 0.8861 (tpp) cc_final: 0.8564 (tpt) REVERT: E 85 MET cc_start: 0.8294 (mmm) cc_final: 0.8074 (mmt) REVERT: E 242 LYS cc_start: 0.7682 (mttp) cc_final: 0.7472 (ttmt) REVERT: E 293 LYS cc_start: 0.8255 (ttmm) cc_final: 0.8006 (ttmm) REVERT: F 34 ASP cc_start: 0.8039 (t0) cc_final: 0.7789 (t0) REVERT: F 47 ASP cc_start: 0.6928 (t0) cc_final: 0.6663 (t0) REVERT: F 94 ASN cc_start: 0.8096 (t0) cc_final: 0.7693 (t0) REVERT: F 253 ARG cc_start: 0.7889 (tpp80) cc_final: 0.7074 (mmp-170) REVERT: G 34 ASP cc_start: 0.8231 (t70) cc_final: 0.7968 (t0) REVERT: G 242 LYS cc_start: 0.7650 (mttt) cc_final: 0.7373 (ttmt) REVERT: G 293 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7921 (ttmm) REVERT: H 34 ASP cc_start: 0.8196 (t0) cc_final: 0.7886 (t0) REVERT: H 47 ASP cc_start: 0.6923 (t0) cc_final: 0.6685 (t0) REVERT: H 85 MET cc_start: 0.8447 (mmm) cc_final: 0.8224 (mmt) REVERT: H 109 LYS cc_start: 0.7849 (mttm) cc_final: 0.7541 (mtpt) REVERT: H 154 LEU cc_start: 0.4221 (OUTLIER) cc_final: 0.4009 (tt) REVERT: H 238 LYS cc_start: 0.7921 (mttt) cc_final: 0.7543 (mtmt) REVERT: H 253 ARG cc_start: 0.7907 (tpp80) cc_final: 0.7051 (mmp-170) outliers start: 82 outliers final: 67 residues processed: 751 average time/residue: 0.7530 time to fit residues: 892.0388 Evaluate side-chains 759 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 688 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 504 HIS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 470 ASP Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 216 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN F 454 GLN H 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27954 Z= 0.217 Angle : 0.527 5.339 37896 Z= 0.277 Chirality : 0.042 0.152 4459 Planarity : 0.004 0.049 4763 Dihedral : 12.770 84.825 4377 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.69 % Favored : 92.88 % Rotamer: Outliers : 2.55 % Allowed : 15.76 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3499 helix: 0.19 (0.15), residues: 1329 sheet: -1.03 (0.26), residues: 362 loop : -1.62 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 125 PHE 0.032 0.001 PHE G 456 TYR 0.025 0.001 TYR C 282 ARG 0.004 0.000 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 695 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6760 (t0) cc_final: 0.6532 (t0) REVERT: A 85 MET cc_start: 0.8231 (mmm) cc_final: 0.7999 (mmt) REVERT: A 94 ASN cc_start: 0.7910 (t0) cc_final: 0.7436 (t0) REVERT: A 155 VAL cc_start: 0.6582 (OUTLIER) cc_final: 0.6233 (t) REVERT: A 242 LYS cc_start: 0.7593 (mttp) cc_final: 0.7272 (mttm) REVERT: A 253 ARG cc_start: 0.7655 (mmt90) cc_final: 0.7301 (mmp-170) REVERT: B 34 ASP cc_start: 0.8069 (t70) cc_final: 0.7818 (t0) REVERT: B 47 ASP cc_start: 0.6835 (t0) cc_final: 0.6580 (t0) REVERT: B 85 MET cc_start: 0.8372 (mmm) cc_final: 0.8112 (mmt) REVERT: B 177 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.5456 (tp30) REVERT: B 242 LYS cc_start: 0.7747 (mttt) cc_final: 0.7425 (ttmt) REVERT: B 253 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7036 (mmp-170) REVERT: B 455 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7617 (tmmt) REVERT: B 456 PHE cc_start: 0.8337 (t80) cc_final: 0.7990 (t80) REVERT: B 460 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8472 (mp) REVERT: C 1 MET cc_start: 0.7529 (pmm) cc_final: 0.7265 (pmm) REVERT: C 47 ASP cc_start: 0.6774 (t0) cc_final: 0.6548 (t0) REVERT: C 78 MET cc_start: 0.8896 (tpp) cc_final: 0.8659 (tpt) REVERT: C 85 MET cc_start: 0.8502 (mmm) cc_final: 0.8272 (mmt) REVERT: C 94 ASN cc_start: 0.7938 (t0) cc_final: 0.7525 (t0) REVERT: C 98 GLU cc_start: 0.7464 (tp30) cc_final: 0.7073 (tp30) REVERT: C 125 HIS cc_start: 0.6917 (t70) cc_final: 0.6693 (t70) REVERT: C 238 LYS cc_start: 0.7975 (mttt) cc_final: 0.7559 (mtpt) REVERT: C 242 LYS cc_start: 0.7631 (mttp) cc_final: 0.7391 (mtpp) REVERT: C 253 ARG cc_start: 0.7527 (mmt90) cc_final: 0.7162 (mmp-170) REVERT: C 456 PHE cc_start: 0.8210 (t80) cc_final: 0.7958 (t80) REVERT: D 47 ASP cc_start: 0.6846 (t0) cc_final: 0.6559 (t0) REVERT: D 94 ASN cc_start: 0.7955 (t0) cc_final: 0.7461 (t0) REVERT: D 238 LYS cc_start: 0.7901 (mttt) cc_final: 0.7391 (mtpp) REVERT: D 293 LYS cc_start: 0.8257 (ttmm) cc_final: 0.8006 (ttmm) REVERT: D 395 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7753 (mm-30) REVERT: E 47 ASP cc_start: 0.6885 (t0) cc_final: 0.6613 (t0) REVERT: E 78 MET cc_start: 0.8904 (tpp) cc_final: 0.8694 (tpt) REVERT: E 125 HIS cc_start: 0.7480 (t70) cc_final: 0.7176 (t70) REVERT: E 242 LYS cc_start: 0.7704 (mttp) cc_final: 0.7493 (ttmt) REVERT: E 293 LYS cc_start: 0.8263 (ttmm) cc_final: 0.8010 (ttmm) REVERT: F 34 ASP cc_start: 0.8028 (t0) cc_final: 0.7784 (t0) REVERT: F 47 ASP cc_start: 0.6921 (t0) cc_final: 0.6663 (t0) REVERT: F 94 ASN cc_start: 0.8079 (t0) cc_final: 0.7675 (t0) REVERT: F 253 ARG cc_start: 0.7862 (tpp80) cc_final: 0.7045 (mmp-170) REVERT: G 34 ASP cc_start: 0.8219 (t70) cc_final: 0.7969 (t0) REVERT: G 94 ASN cc_start: 0.7909 (t0) cc_final: 0.7493 (t0) REVERT: G 242 LYS cc_start: 0.7648 (mttt) cc_final: 0.7220 (ttmm) REVERT: G 293 LYS cc_start: 0.8251 (ttmm) cc_final: 0.7984 (ttmm) REVERT: G 456 PHE cc_start: 0.8121 (t80) cc_final: 0.7879 (t80) REVERT: H 34 ASP cc_start: 0.8177 (t0) cc_final: 0.7865 (t0) REVERT: H 47 ASP cc_start: 0.6811 (t0) cc_final: 0.6565 (t0) REVERT: H 85 MET cc_start: 0.8459 (mmm) cc_final: 0.8225 (mmt) REVERT: H 109 LYS cc_start: 0.7817 (mttm) cc_final: 0.7513 (mtpt) REVERT: H 154 LEU cc_start: 0.4198 (OUTLIER) cc_final: 0.3993 (tt) REVERT: H 179 MET cc_start: 0.8297 (mpp) cc_final: 0.8066 (mmt) REVERT: H 238 LYS cc_start: 0.7934 (mttt) cc_final: 0.7547 (mtmt) outliers start: 74 outliers final: 54 residues processed: 742 average time/residue: 0.7563 time to fit residues: 887.0878 Evaluate side-chains 746 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 687 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 504 HIS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 470 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 20.0000 chunk 326 optimal weight: 4.9990 chunk 298 optimal weight: 0.8980 chunk 317 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 287 optimal weight: 5.9990 chunk 300 optimal weight: 0.7980 chunk 316 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN H 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27954 Z= 0.210 Angle : 0.525 9.071 37896 Z= 0.275 Chirality : 0.042 0.151 4459 Planarity : 0.004 0.049 4763 Dihedral : 12.471 85.266 4377 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.32 % Favored : 93.26 % Rotamer: Outliers : 2.24 % Allowed : 16.21 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 3499 helix: 0.33 (0.15), residues: 1323 sheet: -0.98 (0.27), residues: 362 loop : -1.51 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 504 PHE 0.021 0.001 PHE G 456 TYR 0.018 0.001 TYR B 282 ARG 0.003 0.000 ARG H 341 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 683 time to evaluate : 3.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7924 (t0) cc_final: 0.7481 (t0) REVERT: A 242 LYS cc_start: 0.7570 (mttp) cc_final: 0.7263 (mttm) REVERT: A 253 ARG cc_start: 0.7646 (mmt90) cc_final: 0.7319 (mmp-170) REVERT: A 293 LYS cc_start: 0.8242 (ttmm) cc_final: 0.7994 (ttmm) REVERT: A 393 THR cc_start: 0.7711 (p) cc_final: 0.7481 (t) REVERT: A 456 PHE cc_start: 0.8281 (t80) cc_final: 0.7944 (t80) REVERT: B 34 ASP cc_start: 0.8091 (t70) cc_final: 0.7875 (t0) REVERT: B 47 ASP cc_start: 0.6825 (t0) cc_final: 0.6573 (t0) REVERT: B 85 MET cc_start: 0.8397 (mmm) cc_final: 0.8154 (mmt) REVERT: B 177 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.5602 (tp30) REVERT: B 242 LYS cc_start: 0.7762 (mttt) cc_final: 0.7441 (ttmt) REVERT: B 253 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7013 (mmp-170) REVERT: B 393 THR cc_start: 0.7008 (p) cc_final: 0.6591 (t) REVERT: B 455 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7619 (tmmt) REVERT: B 456 PHE cc_start: 0.8316 (t80) cc_final: 0.8043 (t80) REVERT: C 78 MET cc_start: 0.8918 (tpp) cc_final: 0.8663 (tpt) REVERT: C 85 MET cc_start: 0.8524 (mmm) cc_final: 0.8274 (mmt) REVERT: C 94 ASN cc_start: 0.7960 (t0) cc_final: 0.7552 (t0) REVERT: C 98 GLU cc_start: 0.7441 (tp30) cc_final: 0.6832 (tp30) REVERT: C 238 LYS cc_start: 0.7963 (mttt) cc_final: 0.7568 (mtpt) REVERT: C 253 ARG cc_start: 0.7484 (mmt90) cc_final: 0.7144 (mmp-170) REVERT: D 47 ASP cc_start: 0.6834 (t0) cc_final: 0.6574 (t0) REVERT: D 94 ASN cc_start: 0.7975 (t0) cc_final: 0.7500 (t0) REVERT: D 238 LYS cc_start: 0.7882 (mttt) cc_final: 0.7522 (mtpt) REVERT: D 395 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7532 (mm-30) REVERT: D 456 PHE cc_start: 0.8228 (t80) cc_final: 0.7943 (t80) REVERT: E 47 ASP cc_start: 0.6864 (t0) cc_final: 0.6623 (t0) REVERT: E 78 MET cc_start: 0.8916 (tpp) cc_final: 0.8706 (tpt) REVERT: E 125 HIS cc_start: 0.7572 (t70) cc_final: 0.7299 (t70) REVERT: E 238 LYS cc_start: 0.7952 (mttt) cc_final: 0.7597 (mtpt) REVERT: E 293 LYS cc_start: 0.8300 (ttmm) cc_final: 0.8059 (ttmm) REVERT: F 34 ASP cc_start: 0.8030 (t0) cc_final: 0.7775 (t0) REVERT: F 78 MET cc_start: 0.8792 (tpp) cc_final: 0.8587 (tpt) REVERT: F 94 ASN cc_start: 0.8081 (t0) cc_final: 0.7688 (t0) REVERT: F 253 ARG cc_start: 0.7866 (tpp80) cc_final: 0.7030 (mmp-170) REVERT: G 34 ASP cc_start: 0.8254 (t70) cc_final: 0.7995 (t0) REVERT: G 94 ASN cc_start: 0.7928 (t0) cc_final: 0.7528 (t0) REVERT: G 242 LYS cc_start: 0.7649 (mttt) cc_final: 0.7233 (ttmm) REVERT: H 34 ASP cc_start: 0.8108 (t0) cc_final: 0.7808 (t0) REVERT: H 47 ASP cc_start: 0.6760 (t0) cc_final: 0.6524 (t0) REVERT: H 109 LYS cc_start: 0.7682 (mttm) cc_final: 0.7410 (mtpt) REVERT: H 154 LEU cc_start: 0.4160 (OUTLIER) cc_final: 0.3945 (tt) REVERT: H 238 LYS cc_start: 0.7921 (mttt) cc_final: 0.7553 (mtmt) outliers start: 65 outliers final: 54 residues processed: 726 average time/residue: 0.7651 time to fit residues: 877.7948 Evaluate side-chains 734 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 677 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 470 ASP Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 1.9990 chunk 336 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 352 optimal weight: 1.9990 chunk 324 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 216 optimal weight: 0.9980 chunk 172 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN H 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 27954 Z= 0.237 Angle : 0.532 6.493 37896 Z= 0.279 Chirality : 0.042 0.149 4459 Planarity : 0.004 0.049 4763 Dihedral : 12.443 88.992 4377 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.97 % Favored : 92.60 % Rotamer: Outliers : 2.17 % Allowed : 16.35 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.15), residues: 3499 helix: 0.36 (0.15), residues: 1322 sheet: -0.93 (0.27), residues: 362 loop : -1.47 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 504 PHE 0.045 0.001 PHE G 456 TYR 0.020 0.001 TYR B 282 ARG 0.003 0.000 ARG D 341 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 678 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.6141 (mm-30) REVERT: A 94 ASN cc_start: 0.7957 (t0) cc_final: 0.7518 (t0) REVERT: A 242 LYS cc_start: 0.7570 (mttp) cc_final: 0.7275 (mttm) REVERT: A 293 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7976 (ttmm) REVERT: A 393 THR cc_start: 0.7670 (p) cc_final: 0.7406 (t) REVERT: B 34 ASP cc_start: 0.8114 (t70) cc_final: 0.7900 (t0) REVERT: B 47 ASP cc_start: 0.6787 (t0) cc_final: 0.6531 (t0) REVERT: B 177 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.5625 (tp30) REVERT: B 242 LYS cc_start: 0.7761 (mttt) cc_final: 0.7440 (ttmt) REVERT: B 253 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7002 (mmp-170) REVERT: B 393 THR cc_start: 0.6994 (p) cc_final: 0.6605 (t) REVERT: B 455 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7624 (tmmt) REVERT: B 456 PHE cc_start: 0.8310 (t80) cc_final: 0.7956 (t80) REVERT: C 94 ASN cc_start: 0.7995 (t0) cc_final: 0.7604 (t0) REVERT: C 98 GLU cc_start: 0.7451 (tp30) cc_final: 0.6837 (tp30) REVERT: C 238 LYS cc_start: 0.7960 (mttt) cc_final: 0.7578 (mtpt) REVERT: C 253 ARG cc_start: 0.7477 (mmt90) cc_final: 0.7143 (mmp-170) REVERT: D 94 ASN cc_start: 0.8013 (t0) cc_final: 0.7523 (t0) REVERT: D 238 LYS cc_start: 0.7885 (mttt) cc_final: 0.7524 (mtpt) REVERT: D 293 LYS cc_start: 0.8311 (ttmm) cc_final: 0.8049 (ttmm) REVERT: D 395 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7574 (mm-30) REVERT: D 456 PHE cc_start: 0.8259 (t80) cc_final: 0.7978 (t80) REVERT: E 47 ASP cc_start: 0.6859 (t0) cc_final: 0.6620 (t0) REVERT: E 78 MET cc_start: 0.8913 (tpp) cc_final: 0.8609 (tpt) REVERT: E 125 HIS cc_start: 0.7602 (t70) cc_final: 0.7334 (t70) REVERT: E 179 MET cc_start: 0.7984 (mpp) cc_final: 0.7771 (mpp) REVERT: E 238 LYS cc_start: 0.7954 (mttt) cc_final: 0.7585 (mtmt) REVERT: E 293 LYS cc_start: 0.8311 (ttmm) cc_final: 0.8053 (ttmm) REVERT: F 34 ASP cc_start: 0.8017 (t0) cc_final: 0.7764 (t0) REVERT: F 78 MET cc_start: 0.8815 (tpp) cc_final: 0.8595 (tpt) REVERT: F 94 ASN cc_start: 0.8107 (t0) cc_final: 0.7710 (t0) REVERT: F 253 ARG cc_start: 0.7852 (tpp80) cc_final: 0.7022 (mmp-170) REVERT: G 34 ASP cc_start: 0.8247 (t70) cc_final: 0.7985 (t0) REVERT: G 94 ASN cc_start: 0.7970 (t0) cc_final: 0.7569 (t0) REVERT: G 242 LYS cc_start: 0.7669 (mttt) cc_final: 0.7260 (ttmm) REVERT: G 293 LYS cc_start: 0.8302 (ttmm) cc_final: 0.8039 (ttmm) REVERT: G 456 PHE cc_start: 0.8135 (t80) cc_final: 0.7864 (t80) REVERT: H 34 ASP cc_start: 0.8113 (t0) cc_final: 0.7813 (t0) REVERT: H 109 LYS cc_start: 0.7718 (mttm) cc_final: 0.7380 (mtpt) REVERT: H 154 LEU cc_start: 0.4204 (OUTLIER) cc_final: 0.3974 (tt) REVERT: H 238 LYS cc_start: 0.7929 (mttt) cc_final: 0.7547 (mtmt) REVERT: H 242 LYS cc_start: 0.8172 (mttt) cc_final: 0.7893 (mtpp) REVERT: H 253 ARG cc_start: 0.7907 (tpp80) cc_final: 0.7078 (mmp-170) outliers start: 63 outliers final: 49 residues processed: 721 average time/residue: 0.7780 time to fit residues: 891.8342 Evaluate side-chains 719 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 666 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 470 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 1.9990 chunk 299 optimal weight: 0.2980 chunk 86 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 281 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN H 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.155038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.107270 restraints weight = 99533.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.112692 restraints weight = 51149.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.116209 restraints weight = 34685.008| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27954 Z= 0.168 Angle : 0.522 9.829 37896 Z= 0.271 Chirality : 0.041 0.150 4459 Planarity : 0.004 0.049 4763 Dihedral : 11.973 87.783 4377 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.32 % Favored : 94.26 % Rotamer: Outliers : 1.69 % Allowed : 16.97 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 3499 helix: 0.51 (0.15), residues: 1323 sheet: -1.03 (0.25), residues: 418 loop : -1.30 (0.16), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS C 125 PHE 0.030 0.001 PHE G 456 TYR 0.029 0.001 TYR H 294 ARG 0.002 0.000 ARG F 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13595.65 seconds wall clock time: 236 minutes 53.02 seconds (14213.02 seconds total)