Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 03:33:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2023/7m05_23609_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2023/7m05_23609.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2023/7m05_23609_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2023/7m05_23609_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2023/7m05_23609_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2023/7m05_23609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2023/7m05_23609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2023/7m05_23609_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2023/7m05_23609_trim_updated.pdb" } resolution = 2.39 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 148 5.16 5 Cl 4 4.86 5 C 18452 2.51 5 N 4960 2.21 5 O 5400 1.98 5 H 28188 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A ASP 165": "OD1" <-> "OD2" Residue "A ARG 193": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A ARG 368": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ARG 421": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A ASP 459": "OD1" <-> "OD2" Residue "A TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 505": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 527": "OD1" <-> "OD2" Residue "A PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "A ARG 631": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ARG 29": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C ASP 165": "OD1" <-> "OD2" Residue "C ARG 193": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "C ARG 368": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C ARG 421": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C ASP 459": "OD1" <-> "OD2" Residue "C TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 505": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 527": "OD1" <-> "OD2" Residue "C PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 594": "OE1" <-> "OE2" Residue "C PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 614": "OE1" <-> "OE2" Residue "C ARG 631": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D ARG 29": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D ASP 109": "OD1" <-> "OD2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 146": "OD1" <-> "OD2" Residue "D ASP 153": "OD1" <-> "OD2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 161": "OE1" <-> "OE2" Residue "E ASP 165": "OD1" <-> "OD2" Residue "E ARG 193": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "E ARG 368": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 402": "OE1" <-> "OE2" Residue "E ARG 421": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 442": "OD1" <-> "OD2" Residue "E ASP 459": "OD1" <-> "OD2" Residue "E TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 505": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 527": "OD1" <-> "OD2" Residue "E PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 594": "OE1" <-> "OE2" Residue "E PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 614": "OE1" <-> "OE2" Residue "E ARG 631": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F ARG 29": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F ASP 109": "OD1" <-> "OD2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 146": "OD1" <-> "OD2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 104": "OE1" <-> "OE2" Residue "G ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G ASP 165": "OD1" <-> "OD2" Residue "G ARG 193": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 224": "OE1" <-> "OE2" Residue "G PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 325": "OE1" <-> "OE2" Residue "G ARG 368": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 402": "OE1" <-> "OE2" Residue "G ARG 421": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 442": "OD1" <-> "OD2" Residue "G ASP 459": "OD1" <-> "OD2" Residue "G TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 505": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 527": "OD1" <-> "OD2" Residue "G PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 594": "OE1" <-> "OE2" Residue "G PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 614": "OE1" <-> "OE2" Residue "G ARG 631": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 28": "OE1" <-> "OE2" Residue "H ARG 29": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H ASP 109": "OD1" <-> "OD2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 146": "OD1" <-> "OD2" Residue "H ASP 153": "OD1" <-> "OD2" Residue "H PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 57152 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 9868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 9868 Classifications: {'peptide': 615} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 39, 'TRANS': 570} Chain breaks: 2 Chain: "B" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4389 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Chain: "C" Number of atoms: 9868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 9868 Classifications: {'peptide': 615} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 39, 'TRANS': 570} Chain breaks: 2 Chain: "D" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4389 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Chain: "E" Number of atoms: 9868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 9868 Classifications: {'peptide': 615} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 39, 'TRANS': 570} Chain breaks: 2 Chain: "F" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4389 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Chain: "G" Number of atoms: 9868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 9868 Classifications: {'peptide': 615} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 39, 'TRANS': 570} Chain breaks: 2 Chain: "H" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4389 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'YJG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'YJG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'YJG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'YJG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.95, per 1000 atoms: 0.31 Number of scatterers: 57152 At special positions: 0 Unit cell: (126.36, 143.64, 137.16, 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) Cl 4 17.00 S 148 16.00 O 5400 8.00 N 4960 7.00 C 18452 6.00 H 28188 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 33.82 Conformation dependent library (CDL) restraints added in 3.7 seconds 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 52 sheets defined 20.4% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 75 through 81 Processing helix chain 'A' and resid 97 through 117 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.571A pdb=" N TRP A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.678A pdb=" N LYS A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 321 through 329 removed outlier: 3.674A pdb=" N LYS A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 348 Processing helix chain 'A' and resid 370 through 382 Processing helix chain 'A' and resid 395 through 407 removed outlier: 3.749A pdb=" N THR A 400 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 478 through 487 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 75 through 81 Processing helix chain 'C' and resid 97 through 117 Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 184 through 196 removed outlier: 3.571A pdb=" N TRP C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 248 through 260 removed outlier: 3.679A pdb=" N LYS C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 289 Processing helix chain 'C' and resid 296 through 300 Processing helix chain 'C' and resid 321 through 329 removed outlier: 3.674A pdb=" N LYS C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 348 Processing helix chain 'C' and resid 370 through 382 Processing helix chain 'C' and resid 395 through 407 removed outlier: 3.749A pdb=" N THR C 400 " --> pdb=" O ASN C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 451 Processing helix chain 'C' and resid 478 through 487 Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 628 through 630 No H-bonds generated for 'chain 'C' and resid 628 through 630' Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 75 through 81 Processing helix chain 'E' and resid 97 through 117 Processing helix chain 'E' and resid 132 through 142 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 184 through 196 removed outlier: 3.571A pdb=" N TRP E 189 " --> pdb=" O THR E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 220 Processing helix chain 'E' and resid 233 through 235 No H-bonds generated for 'chain 'E' and resid 233 through 235' Processing helix chain 'E' and resid 248 through 260 removed outlier: 3.678A pdb=" N LYS E 259 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 289 Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 321 through 329 removed outlier: 3.674A pdb=" N LYS E 329 " --> pdb=" O GLU E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 348 Processing helix chain 'E' and resid 370 through 382 Processing helix chain 'E' and resid 395 through 407 removed outlier: 3.748A pdb=" N THR E 400 " --> pdb=" O ASN E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 451 Processing helix chain 'E' and resid 478 through 487 Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'E' and resid 628 through 630 No H-bonds generated for 'chain 'E' and resid 628 through 630' Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 75 through 81 Processing helix chain 'G' and resid 97 through 117 Processing helix chain 'G' and resid 132 through 142 Processing helix chain 'G' and resid 161 through 163 No H-bonds generated for 'chain 'G' and resid 161 through 163' Processing helix chain 'G' and resid 184 through 196 removed outlier: 3.571A pdb=" N TRP G 189 " --> pdb=" O THR G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 220 Processing helix chain 'G' and resid 233 through 235 No H-bonds generated for 'chain 'G' and resid 233 through 235' Processing helix chain 'G' and resid 248 through 260 removed outlier: 3.679A pdb=" N LYS G 259 " --> pdb=" O PHE G 255 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 289 Processing helix chain 'G' and resid 296 through 300 Processing helix chain 'G' and resid 321 through 329 removed outlier: 3.674A pdb=" N LYS G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 348 Processing helix chain 'G' and resid 370 through 382 Processing helix chain 'G' and resid 395 through 407 removed outlier: 3.749A pdb=" N THR G 400 " --> pdb=" O ASN G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 451 Processing helix chain 'G' and resid 478 through 487 Processing helix chain 'G' and resid 496 through 498 No H-bonds generated for 'chain 'G' and resid 496 through 498' Processing helix chain 'G' and resid 628 through 630 No H-bonds generated for 'chain 'G' and resid 628 through 630' Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing sheet with id= A, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.600A pdb=" N PHE A 40 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE A 264 " --> pdb=" O GLY A 17 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP A 19 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 266 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LYS A 227 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL A 204 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA A 229 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU A 231 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE A 151 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA A 205 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET A 153 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU A 207 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A 155 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 462 through 464 Processing sheet with id= C, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.554A pdb=" N GLU A 467 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 550 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 582 " --> pdb=" O GLY A 553 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 534 through 541 Processing sheet with id= E, first strand: chain 'A' and resid 546 through 548 Processing sheet with id= F, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.890A pdb=" N ILE A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 75 through 79 removed outlier: 3.735A pdb=" N GLY B 56 " --> pdb=" O THR B 79 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 33 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER B 47 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU B 31 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.600A pdb=" N ALA B 97 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU B 86 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 95 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TRP B 88 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY B 93 " --> pdb=" O TRP B 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 98 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU B 107 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER B 117 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 128 through 133 removed outlier: 6.990A pdb=" N GLY B 143 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL B 131 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 141 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL B 133 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLN B 139 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 161 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP B 153 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL B 159 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 203 through 205 removed outlier: 3.673A pdb=" N PHE B 183 " --> pdb=" O TRP B 195 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS B 172 " --> pdb=" O CYS B 186 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 249 through 252 removed outlier: 4.430A pdb=" N THR B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 217 " --> pdb=" O GLY B 231 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 258 through 263 removed outlier: 6.930A pdb=" N LEU B 274 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU B 261 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 272 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 291 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 323 through 326 removed outlier: 3.988A pdb=" N ASP B 302 " --> pdb=" O VAL B 316 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 40 through 42 removed outlier: 3.600A pdb=" N PHE C 40 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE C 264 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ASP C 19 " --> pdb=" O PHE C 264 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 266 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LYS C 227 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL C 204 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA C 229 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU C 206 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU C 231 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE C 151 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA C 205 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET C 153 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU C 207 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 155 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 462 through 464 Processing sheet with id= P, first strand: chain 'C' and resid 520 through 522 removed outlier: 3.554A pdb=" N GLU C 467 " --> pdb=" O VAL C 558 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 550 " --> pdb=" O ILE C 475 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 582 " --> pdb=" O GLY C 553 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 534 through 541 Processing sheet with id= R, first strand: chain 'C' and resid 546 through 548 Processing sheet with id= S, first strand: chain 'C' and resid 556 through 560 removed outlier: 6.890A pdb=" N ILE C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 75 through 79 removed outlier: 3.736A pdb=" N GLY D 56 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 33 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER D 47 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU D 31 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.600A pdb=" N ALA D 97 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D 86 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU D 95 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TRP D 88 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY D 93 " --> pdb=" O TRP D 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 98 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA D 102 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU D 107 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER D 117 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 128 through 133 removed outlier: 6.991A pdb=" N GLY D 143 " --> pdb=" O SER D 129 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL D 131 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL D 141 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL D 133 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLN D 139 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 161 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP D 153 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL D 159 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 203 through 205 removed outlier: 3.673A pdb=" N PHE D 183 " --> pdb=" O TRP D 195 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS D 172 " --> pdb=" O CYS D 186 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 249 through 252 removed outlier: 4.430A pdb=" N THR D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER D 217 " --> pdb=" O GLY D 231 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 258 through 263 removed outlier: 6.929A pdb=" N LEU D 274 " --> pdb=" O THR D 259 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU D 261 " --> pdb=" O ALA D 272 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA D 272 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D 291 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 323 through 326 removed outlier: 3.987A pdb=" N ASP D 302 " --> pdb=" O VAL D 316 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 82 through 85 removed outlier: 6.562A pdb=" N LEU E 41 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LYS E 85 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N MET E 43 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE E 40 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE E 264 " --> pdb=" O GLY E 17 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP E 19 " --> pdb=" O PHE E 264 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE E 266 " --> pdb=" O ASP E 19 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LYS E 227 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL E 204 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA E 229 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU E 206 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU E 231 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE E 151 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA E 205 " --> pdb=" O PHE E 151 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET E 153 " --> pdb=" O ALA E 205 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU E 207 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E 155 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 462 through 464 Processing sheet with id= AC, first strand: chain 'E' and resid 520 through 522 removed outlier: 3.555A pdb=" N GLU E 467 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY E 550 " --> pdb=" O ILE E 475 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE E 582 " --> pdb=" O GLY E 553 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 534 through 541 Processing sheet with id= AE, first strand: chain 'E' and resid 546 through 548 Processing sheet with id= AF, first strand: chain 'E' and resid 556 through 560 removed outlier: 6.890A pdb=" N ILE E 563 " --> pdb=" O LEU E 559 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 75 through 79 removed outlier: 3.735A pdb=" N GLY F 56 " --> pdb=" O THR F 79 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA F 33 " --> pdb=" O GLY F 45 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER F 47 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU F 31 " --> pdb=" O SER F 47 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 83 through 89 removed outlier: 6.599A pdb=" N ALA F 97 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU F 86 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU F 95 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TRP F 88 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY F 93 " --> pdb=" O TRP F 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER F 98 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA F 102 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU F 107 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER F 117 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 128 through 133 removed outlier: 6.990A pdb=" N GLY F 143 " --> pdb=" O SER F 129 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL F 131 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL F 141 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL F 133 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLN F 139 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER F 161 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP F 153 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL F 159 " --> pdb=" O ASP F 153 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 203 through 205 removed outlier: 3.673A pdb=" N PHE F 183 " --> pdb=" O TRP F 195 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS F 172 " --> pdb=" O CYS F 186 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 249 through 252 removed outlier: 4.430A pdb=" N THR F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER F 217 " --> pdb=" O GLY F 231 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 258 through 263 removed outlier: 6.929A pdb=" N LEU F 274 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU F 261 " --> pdb=" O ALA F 272 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA F 272 " --> pdb=" O LEU F 261 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE F 291 " --> pdb=" O VAL F 282 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'F' and resid 323 through 326 removed outlier: 3.988A pdb=" N ASP F 302 " --> pdb=" O VAL F 316 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 40 through 42 removed outlier: 3.600A pdb=" N PHE G 40 " --> pdb=" O SER G 16 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE G 264 " --> pdb=" O GLY G 17 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP G 19 " --> pdb=" O PHE G 264 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE G 266 " --> pdb=" O ASP G 19 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LYS G 227 " --> pdb=" O ILE G 202 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL G 204 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA G 229 " --> pdb=" O VAL G 204 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU G 206 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU G 231 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE G 151 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA G 205 " --> pdb=" O PHE G 151 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET G 153 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU G 207 " --> pdb=" O MET G 153 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL G 155 " --> pdb=" O GLU G 207 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 462 through 464 Processing sheet with id= AP, first strand: chain 'G' and resid 520 through 522 removed outlier: 3.554A pdb=" N GLU G 467 " --> pdb=" O VAL G 558 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY G 550 " --> pdb=" O ILE G 475 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE G 582 " --> pdb=" O GLY G 553 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 534 through 541 Processing sheet with id= AR, first strand: chain 'G' and resid 546 through 548 Processing sheet with id= AS, first strand: chain 'G' and resid 556 through 560 removed outlier: 6.890A pdb=" N ILE G 563 " --> pdb=" O LEU G 559 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'H' and resid 75 through 79 removed outlier: 3.736A pdb=" N GLY H 56 " --> pdb=" O THR H 79 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA H 33 " --> pdb=" O GLY H 45 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER H 47 " --> pdb=" O LEU H 31 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU H 31 " --> pdb=" O SER H 47 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'H' and resid 83 through 89 removed outlier: 6.600A pdb=" N ALA H 97 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU H 86 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU H 95 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TRP H 88 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY H 93 " --> pdb=" O TRP H 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER H 98 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA H 102 " --> pdb=" O SER H 98 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU H 107 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER H 117 " --> pdb=" O GLU H 107 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 128 through 133 removed outlier: 6.991A pdb=" N GLY H 143 " --> pdb=" O SER H 129 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL H 131 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL H 141 " --> pdb=" O VAL H 131 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL H 133 " --> pdb=" O GLN H 139 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLN H 139 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER H 161 " --> pdb=" O VAL H 151 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP H 153 " --> pdb=" O VAL H 159 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL H 159 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 203 through 205 removed outlier: 3.672A pdb=" N PHE H 183 " --> pdb=" O TRP H 195 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS H 172 " --> pdb=" O CYS H 186 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'H' and resid 249 through 252 removed outlier: 4.430A pdb=" N THR H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER H 217 " --> pdb=" O GLY H 231 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'H' and resid 258 through 263 removed outlier: 6.930A pdb=" N LEU H 274 " --> pdb=" O THR H 259 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU H 261 " --> pdb=" O ALA H 272 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA H 272 " --> pdb=" O LEU H 261 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE H 291 " --> pdb=" O VAL H 282 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'H' and resid 323 through 326 removed outlier: 3.988A pdb=" N ASP H 302 " --> pdb=" O VAL H 316 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2604 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: 19.16 Time building geometry restraints manager: 35.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 28100 1.02 - 1.22: 88 1.22 - 1.42: 12700 1.42 - 1.62: 16816 1.62 - 1.82: 208 Bond restraints: 57912 Sorted by residual: bond pdb=" C12 YJG A 701 " pdb=" N11 YJG A 701 " ideal model delta sigma weight residual 1.478 1.285 0.193 2.00e-02 2.50e+03 9.33e+01 bond pdb=" C12 YJG E 701 " pdb=" N11 YJG E 701 " ideal model delta sigma weight residual 1.478 1.285 0.193 2.00e-02 2.50e+03 9.30e+01 bond pdb=" C12 YJG C 701 " pdb=" N11 YJG C 701 " ideal model delta sigma weight residual 1.478 1.286 0.192 2.00e-02 2.50e+03 9.25e+01 bond pdb=" C12 YJG G 701 " pdb=" N11 YJG G 701 " ideal model delta sigma weight residual 1.478 1.286 0.192 2.00e-02 2.50e+03 9.25e+01 bond pdb=" C13 YJG A 701 " pdb=" C14 YJG A 701 " ideal model delta sigma weight residual 1.467 1.329 0.138 2.00e-02 2.50e+03 4.75e+01 ... (remaining 57907 not shown) Histogram of bond angle deviations from ideal: 70.85 - 84.95: 5 84.95 - 99.06: 26 99.06 - 113.17: 68180 113.17 - 127.27: 35860 127.27 - 141.38: 473 Bond angle restraints: 104544 Sorted by residual: angle pdb=" CG2 THR E 238 " pdb=" CB THR E 238 " pdb=" HB THR E 238 " ideal model delta sigma weight residual 108.00 70.85 37.15 3.00e+00 1.11e-01 1.53e+02 angle pdb=" CA THR E 238 " pdb=" CB THR E 238 " pdb=" HB THR E 238 " ideal model delta sigma weight residual 109.00 73.66 35.34 3.00e+00 1.11e-01 1.39e+02 angle pdb=" OG1 THR E 238 " pdb=" CB THR E 238 " pdb=" HB THR E 238 " ideal model delta sigma weight residual 109.00 73.81 35.19 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CG GLU E 182 " pdb=" CB GLU E 182 " pdb=" HB3 GLU E 182 " ideal model delta sigma weight residual 108.00 73.03 34.97 3.00e+00 1.11e-01 1.36e+02 angle pdb=" CG GLU E 182 " pdb=" CB GLU E 182 " pdb=" HB2 GLU E 182 " ideal model delta sigma weight residual 108.00 74.01 33.99 3.00e+00 1.11e-01 1.28e+02 ... (remaining 104539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 20904 17.83 - 35.66: 1967 35.66 - 53.49: 423 53.49 - 71.31: 106 71.31 - 89.14: 36 Dihedral angle restraints: 23436 sinusoidal: 10728 harmonic: 12708 Sorted by residual: dihedral pdb=" CA SER C 606 " pdb=" C SER C 606 " pdb=" N ASN C 607 " pdb=" CA ASN C 607 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA SER G 606 " pdb=" C SER G 606 " pdb=" N ASN G 607 " pdb=" CA ASN G 607 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA SER A 606 " pdb=" C SER A 606 " pdb=" N ASN A 607 " pdb=" CA ASN A 607 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 23433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2413 0.043 - 0.086: 1369 0.086 - 0.129: 591 0.129 - 0.172: 71 0.172 - 0.215: 4 Chirality restraints: 4448 Sorted by residual: chirality pdb=" CB THR C 238 " pdb=" CA THR C 238 " pdb=" OG1 THR C 238 " pdb=" CG2 THR C 238 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB THR G 238 " pdb=" CA THR G 238 " pdb=" OG1 THR G 238 " pdb=" CG2 THR G 238 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB THR A 238 " pdb=" CA THR A 238 " pdb=" OG1 THR A 238 " pdb=" CG2 THR A 238 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 4445 not shown) Planarity restraints: 8620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 21 " -0.021 2.00e-02 2.50e+03 2.36e-02 8.39e+00 pdb=" CG ASN A 21 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN A 21 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 21 " -0.010 2.00e-02 2.50e+03 pdb="HD21 ASN A 21 " 0.039 2.00e-02 2.50e+03 pdb="HD22 ASN A 21 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 21 " -0.021 2.00e-02 2.50e+03 2.36e-02 8.39e+00 pdb=" CG ASN G 21 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN G 21 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN G 21 " -0.010 2.00e-02 2.50e+03 pdb="HD21 ASN G 21 " 0.039 2.00e-02 2.50e+03 pdb="HD22 ASN G 21 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 21 " 0.021 2.00e-02 2.50e+03 2.36e-02 8.39e+00 pdb=" CG ASN C 21 " 0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN C 21 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN C 21 " 0.011 2.00e-02 2.50e+03 pdb="HD21 ASN C 21 " -0.039 2.00e-02 2.50e+03 pdb="HD22 ASN C 21 " 0.029 2.00e-02 2.50e+03 ... (remaining 8617 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.12: 1777 2.12 - 2.74: 102459 2.74 - 3.36: 150205 3.36 - 3.98: 209831 3.98 - 4.60: 327095 Nonbonded interactions: 791367 Sorted by model distance: nonbonded pdb=" HB THR E 238 " pdb=" HG1 THR E 238 " model vdw 1.506 1.816 nonbonded pdb=" O ALA A 135 " pdb=" HG1 THR A 139 " model vdw 1.515 1.850 nonbonded pdb=" O ALA C 135 " pdb=" HG1 THR C 139 " model vdw 1.515 1.850 nonbonded pdb=" O ALA G 135 " pdb=" HG1 THR G 139 " model vdw 1.515 1.850 nonbonded pdb=" O ALA E 135 " pdb=" HG1 THR E 139 " model vdw 1.522 1.850 ... (remaining 791362 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.630 Extract box with map and model: 11.040 Check model and map are aligned: 0.640 Set scattering table: 0.420 Process input model: 131.190 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 0.193 29724 Z= 0.884 Angle : 0.886 18.790 40476 Z= 0.461 Chirality : 0.058 0.215 4448 Planarity : 0.007 0.060 5232 Dihedral : 14.642 89.142 10824 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.91 % Favored : 92.31 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -3.01 (0.12), residues: 3588 helix: -1.82 (0.15), residues: 808 sheet: -1.17 (0.14), residues: 1124 loop : -2.66 (0.13), residues: 1656 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 591 time to evaluate : 3.643 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 outliers start: 16 outliers final: 7 residues processed: 603 average time/residue: 3.3332 time to fit residues: 2272.8834 Evaluate side-chains 298 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 291 time to evaluate : 3.651 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 4.5043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 3.9990 chunk 272 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 184 optimal weight: 0.4980 chunk 145 optimal weight: 0.7980 chunk 282 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 326 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 290 ASN B 221 HIS ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN C 290 ASN D 178 HIS D 221 HIS ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN E 140 ASN F 178 HIS F 221 HIS G 36 GLN G 290 ASN H 178 HIS H 221 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 29724 Z= 0.162 Angle : 0.560 10.761 40476 Z= 0.293 Chirality : 0.048 1.258 4448 Planarity : 0.004 0.041 5232 Dihedral : 6.516 79.560 3972 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 3588 helix: 0.29 (0.18), residues: 808 sheet: -0.64 (0.14), residues: 1144 loop : -1.91 (0.14), residues: 1636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 327 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 9 residues processed: 351 average time/residue: 2.5052 time to fit residues: 1035.3793 Evaluate side-chains 276 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 267 time to evaluate : 3.606 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 2 average time/residue: 0.6000 time to fit residues: 6.5366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 4.9990 chunk 101 optimal weight: 0.0070 chunk 272 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 327 optimal weight: 3.9990 chunk 353 optimal weight: 2.9990 chunk 291 optimal weight: 0.6980 chunk 324 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 overall best weight: 1.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 61 ASN G 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 29724 Z= 0.221 Angle : 0.562 11.319 40476 Z= 0.294 Chirality : 0.049 1.375 4448 Planarity : 0.004 0.039 5232 Dihedral : 6.344 82.723 3972 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.96 % Favored : 95.93 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.79 (0.14), residues: 3588 helix: 1.14 (0.19), residues: 812 sheet: -0.44 (0.14), residues: 1160 loop : -1.43 (0.14), residues: 1616 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 294 time to evaluate : 3.632 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 15 residues processed: 320 average time/residue: 2.5912 time to fit residues: 977.1370 Evaluate side-chains 289 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 274 time to evaluate : 3.615 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.7740 time to fit residues: 11.8186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 328 optimal weight: 3.9990 chunk 347 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 311 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 29724 Z= 0.258 Angle : 0.591 11.497 40476 Z= 0.311 Chirality : 0.050 1.431 4448 Planarity : 0.005 0.054 5232 Dihedral : 6.474 86.074 3972 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.40 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.48 (0.14), residues: 3588 helix: 1.31 (0.19), residues: 816 sheet: -0.23 (0.15), residues: 1092 loop : -1.18 (0.15), residues: 1680 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 275 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 26 residues processed: 320 average time/residue: 2.5078 time to fit residues: 944.7691 Evaluate side-chains 288 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 262 time to evaluate : 3.567 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 6 average time/residue: 1.8597 time to fit residues: 18.1835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 259 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 312 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 29724 Z= 0.292 Angle : 0.603 11.544 40476 Z= 0.319 Chirality : 0.050 1.433 4448 Planarity : 0.005 0.066 5232 Dihedral : 6.585 87.488 3972 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.79 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.39 (0.14), residues: 3588 helix: 1.36 (0.18), residues: 816 sheet: -0.26 (0.14), residues: 1132 loop : -1.04 (0.15), residues: 1640 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 274 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 33 residues processed: 311 average time/residue: 2.5051 time to fit residues: 924.4193 Evaluate side-chains 277 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 244 time to evaluate : 3.607 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 30 residues processed: 3 average time/residue: 1.7167 time to fit residues: 10.9774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.8980 chunk 313 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 348 optimal weight: 0.4980 chunk 289 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 29724 Z= 0.166 Angle : 0.533 11.431 40476 Z= 0.277 Chirality : 0.049 1.426 4448 Planarity : 0.004 0.037 5232 Dihedral : 6.249 87.156 3972 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.79 % Favored : 97.10 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.06 (0.14), residues: 3588 helix: 2.04 (0.19), residues: 788 sheet: -0.08 (0.15), residues: 1092 loop : -0.81 (0.15), residues: 1708 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 265 time to evaluate : 3.895 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 32 residues processed: 308 average time/residue: 2.4153 time to fit residues: 891.9566 Evaluate side-chains 275 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 243 time to evaluate : 3.683 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 1 average time/residue: 2.1172 time to fit residues: 7.2490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 0.0060 chunk 39 optimal weight: 0.1980 chunk 198 optimal weight: 0.9990 chunk 254 optimal weight: 0.0870 chunk 197 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 346 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 29724 Z= 0.131 Angle : 0.494 11.385 40476 Z= 0.253 Chirality : 0.048 1.424 4448 Planarity : 0.003 0.031 5232 Dihedral : 5.876 85.596 3972 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.15 % Favored : 97.74 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.35 (0.14), residues: 3588 helix: 2.33 (0.19), residues: 788 sheet: -0.09 (0.15), residues: 1172 loop : -0.51 (0.16), residues: 1628 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 270 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 33 residues processed: 310 average time/residue: 2.3587 time to fit residues: 871.8172 Evaluate side-chains 281 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 248 time to evaluate : 3.575 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 31 residues processed: 2 average time/residue: 2.0931 time to fit residues: 9.5049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 29724 Z= 0.257 Angle : 0.572 11.543 40476 Z= 0.300 Chirality : 0.050 1.432 4448 Planarity : 0.004 0.049 5232 Dihedral : 6.200 86.049 3972 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.04 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.08 (0.14), residues: 3588 helix: 1.85 (0.19), residues: 796 sheet: -0.12 (0.15), residues: 1152 loop : -0.66 (0.15), residues: 1640 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 251 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 35 residues processed: 291 average time/residue: 2.3441 time to fit residues: 824.2581 Evaluate side-chains 273 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 238 time to evaluate : 3.623 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 32 residues processed: 3 average time/residue: 1.6965 time to fit residues: 11.0140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 0.8980 chunk 332 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 323 optimal weight: 0.9980 chunk 194 optimal weight: 0.0060 chunk 140 optimal weight: 0.7980 chunk 253 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 chunk 322 optimal weight: 0.7980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 29724 Z= 0.137 Angle : 0.507 11.403 40476 Z= 0.260 Chirality : 0.048 1.425 4448 Planarity : 0.003 0.030 5232 Dihedral : 5.860 85.279 3972 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.03 % Favored : 97.85 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.46 (0.14), residues: 3588 helix: 2.43 (0.19), residues: 772 sheet: 0.03 (0.15), residues: 1148 loop : -0.45 (0.16), residues: 1668 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 263 time to evaluate : 3.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 29 residues processed: 293 average time/residue: 2.3731 time to fit residues: 843.3884 Evaluate side-chains 271 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 242 time to evaluate : 3.601 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 0 time to fit residues: 4.4995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 4.9990 chunk 341 optimal weight: 4.9990 chunk 208 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 358 optimal weight: 1.9990 chunk 330 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 220 optimal weight: 0.0370 chunk 175 optimal weight: 4.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 29724 Z= 0.175 Angle : 0.523 11.490 40476 Z= 0.270 Chirality : 0.049 1.427 4448 Planarity : 0.003 0.030 5232 Dihedral : 5.899 85.107 3972 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.93 % Favored : 96.96 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.42 (0.14), residues: 3588 helix: 2.38 (0.19), residues: 772 sheet: -0.07 (0.15), residues: 1180 loop : -0.41 (0.16), residues: 1636 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 245 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 29 residues processed: 279 average time/residue: 2.3649 time to fit residues: 788.6020 Evaluate side-chains 272 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 243 time to evaluate : 3.593 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 0 time to fit residues: 4.4904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 3.9990 chunk 304 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 293 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.149245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.128772 restraints weight = 112491.269| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.73 r_work: 0.3740 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 29724 Z= 0.253 Angle : 0.578 11.558 40476 Z= 0.303 Chirality : 0.050 1.439 4448 Planarity : 0.004 0.054 5232 Dihedral : 6.202 86.059 3972 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.57 % Favored : 96.32 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.16 (0.14), residues: 3588 helix: 1.91 (0.19), residues: 792 sheet: -0.04 (0.15), residues: 1136 loop : -0.62 (0.15), residues: 1660 =============================================================================== Job complete usr+sys time: 16028.47 seconds wall clock time: 275 minutes 54.81 seconds (16554.81 seconds total)