Starting phenix.real_space_refine (version: dev) on Wed Feb 22 07:39:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/02_2023/7rfh_24442_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/02_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_24442/02_2023/7rfh_24442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/02_2023/7rfh_24442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/02_2023/7rfh_24442_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/02_2023/7rfh_24442_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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-dev-4877/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: 18.29, per 1000 atoms: 0.33 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: 33.75 Conformation dependent library (CDL) restraints added in 3.4 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: 2.44 Creating SS restraints... Processing helix chain 'A' and resid -17 through -6 Processing helix chain 'A' and resid 4 through 7 No H-bonds generated for 'chain 'A' and resid 4 through 7' Processing helix chain 'A' and resid 20 through 26 removed outlier: 3.789A pdb=" N ALA A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.661A pdb=" N LEU A 131 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 136 No H-bonds generated for 'chain 'A' and resid 133 through 136' Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 224 through 227 No H-bonds generated for 'chain 'A' and resid 224 through 227' Processing helix chain 'A' and resid 254 through 265 removed outlier: 3.986A pdb=" N LYS A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR A 258 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 263 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 343 through 356 removed outlier: 4.291A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 453 through 470 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'B' and resid -17 through -6 Processing helix chain 'B' and resid 4 through 7 No H-bonds generated for 'chain 'B' and resid 4 through 7' Processing helix chain 'B' and resid 20 through 26 removed outlier: 3.658A pdb=" N ALA B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 127 through 129 No H-bonds generated for 'chain 'B' and resid 127 through 129' Processing helix chain 'B' and resid 133 through 136 No H-bonds generated for 'chain 'B' and resid 133 through 136' Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 224 through 227 No H-bonds generated for 'chain 'B' and resid 224 through 227' Processing helix chain 'B' and resid 254 through 265 removed outlier: 3.928A pdb=" N LYS B 257 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR B 258 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 343 through 356 removed outlier: 4.112A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 453 through 470 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 495 through 499 Processing helix chain 'C' and resid -17 through -6 removed outlier: 3.801A pdb=" N ALA C -6 " --> pdb=" O ARG C -10 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 7 No H-bonds generated for 'chain 'C' and resid 4 through 7' Processing helix chain 'C' and resid 20 through 26 removed outlier: 3.689A pdb=" N ALA C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 133 through 136 No H-bonds generated for 'chain 'C' and resid 133 through 136' Processing helix chain 'C' and resid 160 through 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 224 through 227 No H-bonds generated for 'chain 'C' and resid 224 through 227' Processing helix chain 'C' and resid 254 through 265 removed outlier: 3.974A pdb=" N LYS C 257 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR C 258 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 263 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 343 through 356 removed outlier: 4.294A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 453 through 470 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 484 Processing helix chain 'C' and resid 495 through 499 Processing helix chain 'D' and resid -17 through -6 Processing helix chain 'D' and resid 4 through 7 No H-bonds generated for 'chain 'D' and resid 4 through 7' Processing helix chain 'D' and resid 20 through 25 removed outlier: 3.596A pdb=" N ALA D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.649A pdb=" N LEU D 131 " --> pdb=" O GLY D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 136 No H-bonds generated for 'chain 'D' and resid 133 through 136' Processing helix chain 'D' and resid 160 through 163 No H-bonds generated for 'chain 'D' and resid 160 through 163' Processing helix chain 'D' and resid 194 through 204 removed outlier: 3.672A pdb=" N GLN D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 227 No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 254 through 265 removed outlier: 3.955A pdb=" N LYS D 257 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR D 258 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 263 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 343 through 356 removed outlier: 4.306A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 379 Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 453 through 470 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 476 through 484 Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'E' and resid -17 through -6 removed outlier: 3.549A pdb=" N GLN E -7 " --> pdb=" O ALA E -11 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA E -6 " --> pdb=" O ARG E -10 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 20 through 25 removed outlier: 3.709A pdb=" N ALA E 25 " --> pdb=" O GLN E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 127 through 131 removed outlier: 3.607A pdb=" N LEU E 131 " --> pdb=" O GLY E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 136 No H-bonds generated for 'chain 'E' and resid 133 through 136' Processing helix chain 'E' and resid 160 through 163 No H-bonds generated for 'chain 'E' and resid 160 through 163' Processing helix chain 'E' and resid 194 through 204 removed outlier: 3.582A pdb=" N GLU E 199 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 227 No H-bonds generated for 'chain 'E' and resid 224 through 227' Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.953A pdb=" N LYS E 257 " --> pdb=" O GLU E 254 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR E 258 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 Processing helix chain 'E' and resid 343 through 356 removed outlier: 4.287A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 453 through 470 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 484 Processing helix chain 'F' and resid -17 through -6 removed outlier: 3.885A pdb=" N ALA F -6 " --> pdb=" O ARG F -10 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 7 No H-bonds generated for 'chain 'F' and resid 4 through 7' Processing helix chain 'F' and resid 20 through 23 No H-bonds generated for 'chain 'F' and resid 20 through 23' Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 97 through 108 Processing helix chain 'F' and resid 133 through 136 No H-bonds generated for 'chain 'F' and resid 133 through 136' Processing helix chain 'F' and resid 160 through 163 No H-bonds generated for 'chain 'F' and resid 160 through 163' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 224 through 227 No H-bonds generated for 'chain 'F' and resid 224 through 227' Processing helix chain 'F' and resid 254 through 265 removed outlier: 3.973A pdb=" N LYS F 257 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR F 258 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 263 " --> pdb=" O LEU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 Processing helix chain 'F' and resid 343 through 356 removed outlier: 4.140A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 379 Processing helix chain 'F' and resid 388 through 390 No H-bonds generated for 'chain 'F' and resid 388 through 390' Processing helix chain 'F' and resid 453 through 470 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 476 through 484 Processing helix chain 'F' and resid 495 through 497 No H-bonds generated for 'chain 'F' and resid 495 through 497' Processing helix chain 'G' and resid -17 through -6 removed outlier: 3.979A pdb=" N ALA G -6 " --> pdb=" O ARG G -10 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 25 removed outlier: 3.780A pdb=" N ALA G 25 " --> pdb=" O GLN G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 84 Processing helix chain 'G' and resid 97 through 108 Processing helix chain 'G' and resid 127 through 131 removed outlier: 3.613A pdb=" N LEU G 131 " --> pdb=" O GLY G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 136 No H-bonds generated for 'chain 'G' and resid 133 through 136' Processing helix chain 'G' and resid 160 through 163 No H-bonds generated for 'chain 'G' and resid 160 through 163' Processing helix chain 'G' and resid 194 through 204 removed outlier: 3.990A pdb=" N GLU G 199 " --> pdb=" O LYS G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 227 No H-bonds generated for 'chain 'G' and resid 224 through 227' Processing helix chain 'G' and resid 254 through 266 removed outlier: 4.000A pdb=" N LYS G 257 " --> pdb=" O GLU G 254 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR G 258 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU G 263 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 Processing helix chain 'G' and resid 343 through 356 removed outlier: 4.310A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 388 through 390 No H-bonds generated for 'chain 'G' and resid 388 through 390' Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 476 through 484 Processing helix chain 'H' and resid -17 through -6 removed outlier: 3.502A pdb=" N GLN H -7 " --> pdb=" O ALA H -11 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA H -6 " --> pdb=" O ARG H -10 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 7 No H-bonds generated for 'chain 'H' and resid 4 through 7' Processing helix chain 'H' and resid 20 through 26 removed outlier: 3.722A pdb=" N ALA H 25 " --> pdb=" O GLN H 21 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER H 26 " --> pdb=" O GLN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 84 Processing helix chain 'H' and resid 97 through 109 Processing helix chain 'H' and resid 128 through 131 No H-bonds generated for 'chain 'H' and resid 128 through 131' Processing helix chain 'H' and resid 133 through 136 No H-bonds generated for 'chain 'H' and resid 133 through 136' Processing helix chain 'H' and resid 160 through 163 No H-bonds generated for 'chain 'H' and resid 160 through 163' Processing helix chain 'H' and resid 194 through 204 removed outlier: 3.520A pdb=" N GLN H 202 " --> pdb=" O ASN H 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 227 No H-bonds generated for 'chain 'H' and resid 224 through 227' Processing helix chain 'H' and resid 254 through 265 removed outlier: 3.910A pdb=" N LYS H 257 " --> pdb=" O GLU H 254 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR H 258 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 Processing helix chain 'H' and resid 343 through 356 removed outlier: 4.250A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 388 through 390 No H-bonds generated for 'chain 'H' and resid 388 through 390' Processing helix chain 'H' and resid 453 through 470 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 484 Processing helix chain 'H' and resid 495 through 499 removed outlier: 3.744A pdb=" N ILE H 499 " --> pdb=" O SER H 496 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.533A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.609A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 208 through 212 Processing sheet with id= E, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= F, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.574A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.698A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 208 through 212 Processing sheet with id= I, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= J, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.539A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.647A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 208 through 213 removed outlier: 5.542A pdb=" N ASN C 213 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU C 218 " --> pdb=" O ASN C 213 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.561A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 142 through 144 removed outlier: 3.664A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.626A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 208 through 212 Processing sheet with id= R, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= S, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.534A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.645A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 142 through 144 removed outlier: 4.501A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 208 through 212 Processing sheet with id= W, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= X, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.500A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.682A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 321 through 323 Processing sheet with id= AA, first strand: chain 'F' and resid 208 through 213 removed outlier: 5.386A pdb=" N ASN F 213 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU F 218 " --> pdb=" O ASN F 213 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AC, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.497A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET G 385 " --> pdb=" O ALA G 363 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 208 through 210 Processing sheet with id= AE, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.582A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AG, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.534A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.684A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'H' and resid 321 through 323 Processing sheet with id= AJ, first strand: chain 'H' and resid 208 through 212 removed outlier: 3.605A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 1929 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.78 Time building geometry restraints manager: 35.60 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: 19407 17.83 - 35.66: 1476 35.66 - 53.49: 408 53.49 - 71.31: 327 71.31 - 89.14: 69 Dihedral angle restraints: 21687 sinusoidal: 10318 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 21684 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 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. 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: 1.190 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: 0.620 Extract box with map and model: 9.680 Check model and map are aligned: 0.590 Process input model: 125.960 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Set scattering table: 0.390 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 14.463 89.142 10126 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 % 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 *********************** 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 : 3.155 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: 0.7765 time to fit residues: 1019.6226 Evaluate side-chains 743 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 715 time to evaluate : 3.134 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 28 outliers final: 1 residues processed: 28 average time/residue: 0.5405 time to fit residues: 31.3335 ------------------------------------------------------------------------------- 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: 0.8980 chunk 268 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 206 optimal weight: 0.8980 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 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 H 230 ASN H 466 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 27954 Z= 0.247 Angle : 0.678 7.066 37896 Z= 0.359 Chirality : 0.043 0.184 4459 Planarity : 0.005 0.068 4763 Dihedral : 7.561 89.014 3859 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.43 % Favored : 93.17 % Rotamer Outliers : 1.52 % 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: -2.34 (0.13), residues: 3499 helix: -1.25 (0.12), residues: 1342 sheet: -1.10 (0.25), residues: 331 loop : -1.86 (0.15), residues: 1826 *********************** 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 797 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 753 time to evaluate : 3.165 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: 44 outliers final: 26 residues processed: 780 average time/residue: 0.7397 time to fit residues: 911.2379 Evaluate side-chains 740 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 714 time to evaluate : 3.103 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.5428 time to fit residues: 30.0425 ------------------------------------------------------------------------------- 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: 0.5980 chunk 99 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 322 optimal weight: 5.9990 chunk 347 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 230 ASN H 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 27954 Z= 0.295 Angle : 0.612 7.597 37896 Z= 0.319 Chirality : 0.043 0.161 4459 Planarity : 0.004 0.045 4763 Dihedral : 6.726 89.185 3859 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.32 % Favored : 92.28 % Rotamer Outliers : 1.41 % 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: -2.13 (0.14), residues: 3499 helix: -0.79 (0.13), residues: 1344 sheet: -1.24 (0.24), residues: 361 loop : -1.95 (0.15), residues: 1794 *********************** 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 759 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 718 time to evaluate : 3.144 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 outliers start: 41 outliers final: 26 residues processed: 738 average time/residue: 0.7858 time to fit residues: 916.7280 Evaluate side-chains 719 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 693 time to evaluate : 3.121 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.5872 time to fit residues: 31.0685 ------------------------------------------------------------------------------- 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: 4.9990 chunk 242 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 323 optimal weight: 10.0000 chunk 342 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 306 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN B 283 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 27954 Z= 0.181 Angle : 0.541 5.036 37896 Z= 0.282 Chirality : 0.042 0.156 4459 Planarity : 0.004 0.044 4763 Dihedral : 6.263 89.139 3859 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.66 % Favored : 93.97 % Rotamer Outliers : 0.69 % 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: -1.80 (0.14), residues: 3499 helix: -0.44 (0.14), residues: 1371 sheet: -1.10 (0.25), residues: 351 loop : -1.83 (0.15), residues: 1777 *********************** 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 726 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 706 time to evaluate : 3.115 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 outliers start: 20 outliers final: 8 residues processed: 714 average time/residue: 0.8027 time to fit residues: 904.3609 Evaluate side-chains 692 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 684 time to evaluate : 3.142 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.5054 time to fit residues: 12.0752 ------------------------------------------------------------------------------- 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: 2.9990 chunk 194 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 307 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** A 283 GLN A 454 GLN B 94 ASN C 94 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN F 454 GLN H 94 ASN H 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3605 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= 0.288 Angle : 0.554 5.273 37896 Z= 0.290 Chirality : 0.042 0.152 4459 Planarity : 0.004 0.042 4763 Dihedral : 6.043 87.325 3859 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.29 % Favored : 92.31 % Rotamer Outliers : 1.21 % 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: -1.76 (0.14), residues: 3499 helix: -0.29 (0.14), residues: 1371 sheet: -1.18 (0.26), residues: 343 loop : -1.89 (0.15), residues: 1785 *********************** 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 716 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 681 time to evaluate : 3.124 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 outliers start: 35 outliers final: 22 residues processed: 692 average time/residue: 0.8015 time to fit residues: 875.6345 Evaluate side-chains 691 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 669 time to evaluate : 3.120 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.5266 time to fit residues: 25.4640 ------------------------------------------------------------------------------- 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: 0.2980 chunk 67 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 342 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 179 optimal weight: 0.1980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN E 213 ASN F 230 ASN H 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 27954 Z= 0.229 Angle : 0.534 4.889 37896 Z= 0.279 Chirality : 0.042 0.151 4459 Planarity : 0.003 0.045 4763 Dihedral : 5.800 84.163 3859 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.40 % Favored : 93.17 % Rotamer Outliers : 0.69 % 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: -1.61 (0.14), residues: 3499 helix: -0.11 (0.14), residues: 1377 sheet: -1.09 (0.27), residues: 343 loop : -1.87 (0.15), residues: 1779 *********************** 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 713 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 693 time to evaluate : 3.168 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: 20 outliers final: 10 residues processed: 705 average time/residue: 0.7555 time to fit residues: 836.4091 Evaluate side-chains 687 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 677 time to evaluate : 3.167 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4910 time to fit residues: 13.3985 ------------------------------------------------------------------------------- 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: 2.9990 chunk 38 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 C 283 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN F 454 GLN H 94 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 27954 Z= 0.305 Angle : 0.557 6.524 37896 Z= 0.291 Chirality : 0.042 0.151 4459 Planarity : 0.003 0.043 4763 Dihedral : 5.714 79.176 3859 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.77 % Favored : 91.80 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3499 helix: 0.00 (0.14), residues: 1335 sheet: -1.14 (0.27), residues: 353 loop : -1.82 (0.15), residues: 1811 *********************** 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 729 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 689 time to evaluate : 3.553 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: 40 outliers final: 24 residues processed: 708 average time/residue: 0.7779 time to fit residues: 869.2235 Evaluate side-chains 701 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 677 time to evaluate : 3.119 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.5089 time to fit residues: 26.7003 ------------------------------------------------------------------------------- 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: 0.8980 chunk 136 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 268 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN F 94 ASN F 230 ASN H 94 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 27954 Z= 0.215 Angle : 0.534 9.395 37896 Z= 0.276 Chirality : 0.042 0.159 4459 Planarity : 0.004 0.043 4763 Dihedral : 5.568 76.134 3859 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.37 % Favored : 93.20 % Rotamer Outliers : 0.59 % 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: -1.36 (0.14), residues: 3499 helix: 0.16 (0.14), residues: 1329 sheet: -0.99 (0.28), residues: 333 loop : -1.72 (0.15), residues: 1837 *********************** 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 728 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 711 time to evaluate : 3.162 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: 17 outliers final: 5 residues processed: 718 average time/residue: 0.7587 time to fit residues: 848.8183 Evaluate side-chains 688 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 683 time to evaluate : 3.101 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4665 time to fit residues: 8.4564 ------------------------------------------------------------------------------- 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: 1.9990 chunk 298 optimal weight: 0.8980 chunk 317 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 138 optimal weight: 0.0170 chunk 249 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 287 optimal weight: 1.9990 chunk 300 optimal weight: 0.7980 chunk 316 optimal weight: 0.6980 overall best weight: 0.8820 ------------------------------------------------------------------------------- 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 ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN E 213 ASN F 94 ASN F 454 GLN G 94 ASN H 94 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4182 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= 0.189 Angle : 0.525 6.233 37896 Z= 0.271 Chirality : 0.041 0.151 4459 Planarity : 0.003 0.043 4763 Dihedral : 5.448 84.404 3859 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.43 % Favored : 93.14 % Rotamer Outliers : 0.52 % 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: 0.35 (0.15), residues: 1322 sheet: -0.97 (0.28), residues: 343 loop : -1.62 (0.15), residues: 1834 *********************** 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 702 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 687 time to evaluate : 3.184 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 outliers start: 15 outliers final: 7 residues processed: 689 average time/residue: 0.7608 time to fit residues: 815.0937 Evaluate side-chains 681 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 674 time to evaluate : 3.138 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6392 time to fit residues: 11.3725 ------------------------------------------------------------------------------- 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: 0.6980 chunk 159 optimal weight: 0.6980 chunk 233 optimal weight: 0.0470 chunk 352 optimal weight: 1.9990 chunk 324 optimal weight: 4.9990 chunk 280 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 216 optimal weight: 0.2980 chunk 172 optimal weight: 0.8980 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7795 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 27954 Z= 0.148 Angle : 0.511 6.647 37896 Z= 0.262 Chirality : 0.041 0.151 4459 Planarity : 0.003 0.043 4763 Dihedral : 5.216 85.000 3859 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.12 % Favored : 94.46 % Rotamer Outliers : 0.31 % 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: -0.88 (0.15), residues: 3499 helix: 0.61 (0.15), residues: 1317 sheet: -1.13 (0.24), residues: 419 loop : -1.37 (0.15), residues: 1763 ********************** 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 698 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 689 time to evaluate : 3.179 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: 9 outliers final: 3 residues processed: 690 average time/residue: 0.7570 time to fit residues: 813.3032 Evaluate side-chains 675 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 672 time to evaluate : 3.075 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4604 time to fit residues: 6.6315 ------------------------------------------------------------------------------- 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: 0.4980 chunk 299 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 258 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 281 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 213 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN F 94 ASN F 454 GLN G 94 ASN H 94 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.156304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.109498 restraints weight = 99446.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.114640 restraints weight = 53537.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.117961 restraints weight = 37118.115| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 27954 Z= 0.174 Angle : 0.518 6.807 37896 Z= 0.266 Chirality : 0.041 0.150 4459 Planarity : 0.003 0.058 4763 Dihedral : 5.118 85.597 3859 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.54 % Favored : 94.03 % Rotamer Outliers : 0.55 % 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: -0.85 (0.15), residues: 3499 helix: 0.61 (0.15), residues: 1351 sheet: -1.07 (0.25), residues: 419 loop : -1.38 (0.16), residues: 1729 =============================================================================== Job complete usr+sys time: 12881.94 seconds wall clock time: 222 minutes 51.82 seconds (13371.82 seconds total)