Starting phenix.real_space_refine on Fri Dec 8 05:06:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/12_2023/7rfh_24442_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/12_2023/7rfh_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_24442/12_2023/7rfh_24442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/12_2023/7rfh_24442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/12_2023/7rfh_24442_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/12_2023/7rfh_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 17.70, per 1000 atoms: 0.32 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: 32.39 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: 8.01 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: 16.83 Time building geometry restraints manager: 34.32 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: 22595 17.83 - 35.66: 1698 35.66 - 53.49: 582 53.49 - 71.31: 412 71.31 - 89.14: 107 Dihedral angle restraints: 25394 sinusoidal: 14025 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 25391 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: 1.270 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: 0.640 Extract box with map and model: 8.230 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 129.780 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.260 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:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.900 ------------------------------------------------------------------------------- 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 : 3.071 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 outliers start: 79 outliers final: 28 residues processed: 843 average time/residue: 0.7770 time to fit residues: 1024.4940 Evaluate side-chains 743 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 715 time to evaluate : 3.088 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 28 outliers final: 1 residues processed: 28 average time/residue: 0.5368 time to fit residues: 31.1609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 148 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 277 optimal weight: 5.9990 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: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS B 241 GLN B 454 GLN B 466 HIS B 498 GLN C 94 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN H 466 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 27954 Z= 0.249 Angle : 0.703 7.417 37896 Z= 0.377 Chirality : 0.045 0.194 4459 Planarity : 0.005 0.070 4763 Dihedral : 14.762 89.860 4355 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.72 % Favored : 92.88 % Rotamer: Outliers : 1.55 % Allowed : 13.11 % Favored : 85.34 % 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: -2.45 (0.13), residues: 3499 helix: -1.40 (0.12), residues: 1371 sheet: -1.07 (0.25), residues: 331 loop : -1.90 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 125 PHE 0.015 0.002 PHE G 456 TYR 0.038 0.002 TYR F 282 ARG 0.003 0.000 ARG G 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 795 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 750 time to evaluate : 3.112 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 outliers start: 45 outliers final: 29 residues processed: 780 average time/residue: 0.7330 time to fit residues: 901.5525 Evaluate side-chains 732 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 703 time to evaluate : 3.567 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.5346 time to fit residues: 33.3424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 267 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 322 optimal weight: 5.9990 chunk 347 optimal weight: 3.9990 chunk 286 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 258 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN H 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27954 Z= 0.347 Angle : 0.634 7.551 37896 Z= 0.334 Chirality : 0.044 0.161 4459 Planarity : 0.004 0.047 4763 Dihedral : 14.465 89.965 4355 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.35 % Favored : 91.28 % Rotamer: Outliers : 1.45 % Allowed : 14.11 % Favored : 84.44 % 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: -2.28 (0.14), residues: 3499 helix: -0.94 (0.13), residues: 1338 sheet: -1.28 (0.24), residues: 361 loop : -2.01 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 125 PHE 0.012 0.002 PHE B 456 TYR 0.030 0.002 TYR G 282 ARG 0.004 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 761 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 719 time to evaluate : 3.070 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 outliers start: 42 outliers final: 24 residues processed: 741 average time/residue: 0.7922 time to fit residues: 934.1137 Evaluate side-chains 711 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 687 time to evaluate : 3.134 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.5795 time to fit residues: 28.7469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 3.9990 chunk 242 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 153 optimal weight: 0.8980 chunk 216 optimal weight: 0.8980 chunk 323 optimal weight: 10.0000 chunk 342 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 306 optimal weight: 0.0980 chunk 92 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN E 213 ASN F 454 GLN H 94 ASN H 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27954 Z= 0.162 Angle : 0.549 5.126 37896 Z= 0.289 Chirality : 0.042 0.161 4459 Planarity : 0.004 0.047 4763 Dihedral : 13.532 88.085 4355 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.14 % Favored : 93.48 % Rotamer: Outliers : 0.72 % Allowed : 15.45 % Favored : 83.82 % 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: -1.93 (0.14), residues: 3499 helix: -0.60 (0.14), residues: 1370 sheet: -1.13 (0.25), residues: 351 loop : -1.86 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS C 125 PHE 0.010 0.001 PHE G 456 TYR 0.021 0.001 TYR G 282 ARG 0.002 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 723 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 702 time to evaluate : 3.060 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 outliers start: 21 outliers final: 8 residues processed: 711 average time/residue: 0.8043 time to fit residues: 902.5812 Evaluate side-chains 695 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 687 time to evaluate : 3.102 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5381 time to fit residues: 11.7661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 94 ASN B 454 GLN C 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN H 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 27954 Z= 0.247 Angle : 0.549 5.163 37896 Z= 0.289 Chirality : 0.042 0.152 4459 Planarity : 0.004 0.047 4763 Dihedral : 13.176 86.162 4355 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.34 % Favored : 92.25 % Rotamer: Outliers : 0.90 % Allowed : 15.49 % Favored : 83.62 % 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: -1.73 (0.14), residues: 3499 helix: -0.31 (0.14), residues: 1359 sheet: -0.97 (0.26), residues: 311 loop : -1.86 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 125 PHE 0.012 0.001 PHE B 456 TYR 0.021 0.002 TYR G 282 ARG 0.003 0.000 ARG F 341 *********************** 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 719 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 693 time to evaluate : 3.130 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 outliers start: 26 outliers final: 14 residues processed: 703 average time/residue: 0.7788 time to fit residues: 862.9536 Evaluate side-chains 689 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 675 time to evaluate : 3.061 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5100 time to fit residues: 17.3015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 342 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN F 454 GLN H 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 27954 Z= 0.264 Angle : 0.552 5.109 37896 Z= 0.290 Chirality : 0.042 0.151 4459 Planarity : 0.004 0.047 4763 Dihedral : 12.927 86.613 4355 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.17 % Favored : 92.40 % Rotamer: Outliers : 0.79 % Allowed : 15.66 % Favored : 83.55 % 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: -1.69 (0.14), residues: 3499 helix: -0.20 (0.14), residues: 1371 sheet: -1.14 (0.26), residues: 347 loop : -1.87 (0.15), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS C 125 PHE 0.035 0.001 PHE B 456 TYR 0.023 0.002 TYR C 289 ARG 0.003 0.000 ARG A 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 724 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 701 time to evaluate : 3.262 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 outliers start: 23 outliers final: 10 residues processed: 709 average time/residue: 0.7684 time to fit residues: 851.0287 Evaluate side-chains 691 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 681 time to evaluate : 3.078 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4877 time to fit residues: 12.9549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 195 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 341 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN C 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN D 241 GLN E 94 ASN F 94 ASN F 230 ASN H 94 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27954 Z= 0.214 Angle : 0.533 6.275 37896 Z= 0.279 Chirality : 0.042 0.151 4459 Planarity : 0.004 0.048 4763 Dihedral : 12.575 88.633 4355 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.80 % Favored : 92.77 % Rotamer: Outliers : 0.72 % Allowed : 15.83 % Favored : 83.44 % 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: -1.51 (0.14), residues: 3499 helix: 0.01 (0.14), residues: 1358 sheet: -1.07 (0.27), residues: 343 loop : -1.81 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS C 125 PHE 0.009 0.001 PHE G 110 TYR 0.026 0.001 TYR C 294 ARG 0.003 0.000 ARG E 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 715 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 694 time to evaluate : 3.066 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 outliers start: 21 outliers final: 9 residues processed: 702 average time/residue: 0.8029 time to fit residues: 887.0478 Evaluate side-chains 693 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 684 time to evaluate : 3.055 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4802 time to fit residues: 12.1432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 203 optimal weight: 0.5980 chunk 102 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 232 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN C 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN E 94 ASN E 213 ASN F 94 ASN F 454 GLN H 94 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4044 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= 0.173 Angle : 0.518 5.667 37896 Z= 0.271 Chirality : 0.041 0.152 4459 Planarity : 0.004 0.047 4763 Dihedral : 12.028 87.701 4355 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.03 % Favored : 93.54 % Rotamer: Outliers : 0.72 % Allowed : 16.35 % Favored : 82.93 % 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: -1.18 (0.14), residues: 3499 helix: 0.31 (0.15), residues: 1328 sheet: -0.98 (0.27), residues: 343 loop : -1.60 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 125 PHE 0.032 0.001 PHE G 456 TYR 0.017 0.001 TYR C 294 ARG 0.003 0.000 ARG E 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 714 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 693 time to evaluate : 3.174 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 outliers start: 21 outliers final: 10 residues processed: 702 average time/residue: 0.7765 time to fit residues: 854.7128 Evaluate side-chains 691 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 681 time to evaluate : 3.903 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5003 time to fit residues: 13.4279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 298 optimal weight: 0.8980 chunk 317 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 138 optimal weight: 0.0770 chunk 249 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 287 optimal weight: 4.9990 chunk 300 optimal weight: 0.7980 chunk 316 optimal weight: 0.9980 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN C 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN D 94 ASN E 94 ASN F 94 ASN F 454 GLN G 94 ASN H 94 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27954 Z= 0.220 Angle : 0.529 6.158 37896 Z= 0.277 Chirality : 0.042 0.150 4459 Planarity : 0.004 0.047 4763 Dihedral : 11.934 85.541 4355 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.66 % Favored : 92.91 % Rotamer: Outliers : 0.62 % Allowed : 16.45 % Favored : 82.93 % 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: -1.13 (0.14), residues: 3499 helix: 0.37 (0.15), residues: 1328 sheet: -0.94 (0.28), residues: 343 loop : -1.58 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 125 PHE 0.020 0.001 PHE F 456 TYR 0.021 0.001 TYR G 289 ARG 0.003 0.000 ARG G 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 715 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 697 time to evaluate : 3.102 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 outliers start: 18 outliers final: 9 residues processed: 704 average time/residue: 0.7643 time to fit residues: 843.2042 Evaluate side-chains 689 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 680 time to evaluate : 3.065 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4891 time to fit residues: 12.2863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 159 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 352 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN C 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN D 94 ASN E 94 ASN F 94 ASN G 94 ASN H 94 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27954 Z= 0.270 Angle : 0.546 6.510 37896 Z= 0.287 Chirality : 0.042 0.149 4459 Planarity : 0.004 0.047 4763 Dihedral : 12.078 83.784 4355 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.03 % Favored : 92.54 % Rotamer: Outliers : 0.38 % Allowed : 16.80 % Favored : 82.82 % 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: -1.16 (0.15), residues: 3499 helix: 0.33 (0.15), residues: 1328 sheet: -1.00 (0.27), residues: 353 loop : -1.58 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 125 PHE 0.016 0.001 PHE G 456 TYR 0.025 0.002 TYR E 289 ARG 0.003 0.000 ARG B 224 ********************** 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 690 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 679 time to evaluate : 3.084 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 outliers start: 11 outliers final: 7 residues processed: 680 average time/residue: 0.7772 time to fit residues: 832.1463 Evaluate side-chains 683 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 676 time to evaluate : 3.079 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4969 time to fit residues: 10.4540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 86 optimal weight: 0.0770 chunk 258 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 281 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 288 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 0.0570 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN C 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN D 94 ASN E 94 ASN F 94 ASN G 94 ASN H 94 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.156437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.111014 restraints weight = 99488.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.116149 restraints weight = 52414.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.119117 restraints weight = 35227.280| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27954 Z= 0.154 Angle : 0.516 6.849 37896 Z= 0.269 Chirality : 0.041 0.151 4459 Planarity : 0.004 0.046 4763 Dihedral : 11.413 78.442 4355 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.32 % Favored : 94.28 % Rotamer: Outliers : 0.31 % Allowed : 17.01 % Favored : 82.68 % 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: -0.95 (0.15), residues: 3499 helix: 0.52 (0.15), residues: 1327 sheet: -1.11 (0.25), residues: 419 loop : -1.40 (0.16), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 125 PHE 0.035 0.001 PHE A 456 TYR 0.018 0.001 TYR G 289 ARG 0.002 0.000 ARG B 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13263.82 seconds wall clock time: 229 minutes 20.88 seconds (13760.88 seconds total)