Starting phenix.real_space_refine on Sat Aug 10 06:05:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xrp_38609/08_2024/8xrp_38609.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xrp_38609/08_2024/8xrp_38609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xrp_38609/08_2024/8xrp_38609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xrp_38609/08_2024/8xrp_38609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xrp_38609/08_2024/8xrp_38609.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xrp_38609/08_2024/8xrp_38609.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 18120 2.51 5 N 4868 2.21 5 O 5556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A ASP 148": "OD1" <-> "OD2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "B TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 74": "OD1" <-> "OD2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ASP 109": "OD1" <-> "OD2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 182": "OD1" <-> "OD2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 310": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D ASP 40": "OD1" <-> "OD2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "E TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E ASP 148": "OD1" <-> "OD2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 210": "OD1" <-> "OD2" Residue "F TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F ASP 84": "OD1" <-> "OD2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "F ASP 115": "OD1" <-> "OD2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F ARG 130": "NH1" <-> "NH2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 164": "OD1" <-> "OD2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F ASP 196": "OD1" <-> "OD2" Residue "F GLU 221": "OE1" <-> "OE2" Residue "F TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 301": "NH1" <-> "NH2" Residue "F ASP 312": "OD1" <-> "OD2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "G ARG 65": "NH1" <-> "NH2" Residue "G TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 74": "OD1" <-> "OD2" Residue "G ARG 75": "NH1" <-> "NH2" Residue "G ASP 109": "OD1" <-> "OD2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G ARG 147": "NH1" <-> "NH2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 182": "OD1" <-> "OD2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "G TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 260": "NH1" <-> "NH2" Residue "G GLU 289": "OE1" <-> "OE2" Residue "G TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 310": "OE1" <-> "OE2" Residue "H GLU 28": "OE1" <-> "OE2" Residue "H ASP 38": "OD1" <-> "OD2" Residue "H ASP 40": "OD1" <-> "OD2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 78": "NH1" <-> "NH2" Residue "H PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 120": "NH1" <-> "NH2" Residue "H GLU 128": "OE1" <-> "OE2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 83": "OE1" <-> "OE2" Residue "I ARG 100": "NH1" <-> "NH2" Residue "I ARG 114": "NH1" <-> "NH2" Residue "I GLU 129": "OE1" <-> "OE2" Residue "I ASP 148": "OD1" <-> "OD2" Residue "I PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 185": "OE1" <-> "OE2" Residue "I TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 210": "OD1" <-> "OD2" Residue "J TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J ASP 84": "OD1" <-> "OD2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "J GLU 108": "OE1" <-> "OE2" Residue "J ASP 115": "OD1" <-> "OD2" Residue "J GLU 122": "OE1" <-> "OE2" Residue "J ARG 130": "NH1" <-> "NH2" Residue "J GLU 132": "OE1" <-> "OE2" Residue "J TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 164": "OD1" <-> "OD2" Residue "J GLU 188": "OE1" <-> "OE2" Residue "J ASP 196": "OD1" <-> "OD2" Residue "J GLU 221": "OE1" <-> "OE2" Residue "J TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 301": "NH1" <-> "NH2" Residue "J ASP 312": "OD1" <-> "OD2" Residue "J ARG 313": "NH1" <-> "NH2" Residue "K ARG 65": "NH1" <-> "NH2" Residue "K TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 74": "OD1" <-> "OD2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K ASP 109": "OD1" <-> "OD2" Residue "K GLU 117": "OE1" <-> "OE2" Residue "K ARG 147": "NH1" <-> "NH2" Residue "K TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 182": "OD1" <-> "OD2" Residue "K GLU 190": "OE1" <-> "OE2" Residue "K ARG 223": "NH1" <-> "NH2" Residue "K TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 260": "NH1" <-> "NH2" Residue "K GLU 289": "OE1" <-> "OE2" Residue "K TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 310": "OE1" <-> "OE2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L ASP 38": "OD1" <-> "OD2" Residue "L ASP 40": "OD1" <-> "OD2" Residue "L ARG 51": "NH1" <-> "NH2" Residue "L TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 120": "NH1" <-> "NH2" Residue "L GLU 128": "OE1" <-> "OE2" Residue "M TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 83": "OE1" <-> "OE2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M GLU 129": "OE1" <-> "OE2" Residue "M ASP 148": "OD1" <-> "OD2" Residue "M PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 165": "OE1" <-> "OE2" Residue "M PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 185": "OE1" <-> "OE2" Residue "M TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 210": "OD1" <-> "OD2" Residue "N TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 56": "OD1" <-> "OD2" Residue "N ASP 84": "OD1" <-> "OD2" Residue "N GLU 95": "OE1" <-> "OE2" Residue "N GLU 108": "OE1" <-> "OE2" Residue "N ASP 115": "OD1" <-> "OD2" Residue "N GLU 122": "OE1" <-> "OE2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "N GLU 132": "OE1" <-> "OE2" Residue "N TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 164": "OD1" <-> "OD2" Residue "N GLU 188": "OE1" <-> "OE2" Residue "N ASP 196": "OD1" <-> "OD2" Residue "N GLU 221": "OE1" <-> "OE2" Residue "N TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 301": "NH1" <-> "NH2" Residue "N ASP 312": "OD1" <-> "OD2" Residue "N ARG 313": "NH1" <-> "NH2" Residue "O ARG 65": "NH1" <-> "NH2" Residue "O TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 74": "OD1" <-> "OD2" Residue "O ARG 75": "NH1" <-> "NH2" Residue "O ASP 109": "OD1" <-> "OD2" Residue "O GLU 117": "OE1" <-> "OE2" Residue "O ARG 147": "NH1" <-> "NH2" Residue "O TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 182": "OD1" <-> "OD2" Residue "O GLU 190": "OE1" <-> "OE2" Residue "O ARG 223": "NH1" <-> "NH2" Residue "O TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 260": "NH1" <-> "NH2" Residue "O GLU 289": "OE1" <-> "OE2" Residue "O TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 310": "OE1" <-> "OE2" Residue "P GLU 28": "OE1" <-> "OE2" Residue "P ASP 38": "OD1" <-> "OD2" Residue "P ASP 40": "OD1" <-> "OD2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 78": "NH1" <-> "NH2" Residue "P PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 120": "NH1" <-> "NH2" Residue "P GLU 128": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 28740 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1485 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "B" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2413 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Chain: "C" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2335 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 276} Chain: "D" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "E" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1485 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "F" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2413 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Chain: "G" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2335 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 276} Chain: "H" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "I" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1485 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "J" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2413 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Chain: "K" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2335 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 276} Chain: "L" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "M" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1485 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "N" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2413 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Chain: "O" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2335 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 276} Chain: "P" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 17.44, per 1000 atoms: 0.61 Number of scatterers: 28740 At special positions: 0 Unit cell: (225.252, 121.758, 167.852, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 5556 8.00 N 4868 7.00 C 18120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=64, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 110 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS B 199 " distance=2.25 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 327 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 114 " distance=2.02 Simple disulfide: pdb=" SG CYS C 51 " - pdb=" SG CYS C 101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 105 " distance=2.04 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 173 " - pdb=" SG CYS C 178 " distance=2.02 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 86 " distance=2.05 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS E 110 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 85 " - pdb=" SG CYS E 123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 96 " - pdb=" SG CYS F 199 " distance=2.25 Simple disulfide: pdb=" SG CYS F 50 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 142 " distance=2.04 Simple disulfide: pdb=" SG CYS F 170 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS F 300 " - pdb=" SG CYS F 327 " distance=2.03 Simple disulfide: pdb=" SG CYS G 28 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 51 " - pdb=" SG CYS G 101 " distance=2.03 Simple disulfide: pdb=" SG CYS G 59 " - pdb=" SG CYS G 105 " distance=2.04 Simple disulfide: pdb=" SG CYS G 132 " - pdb=" SG CYS G 143 " distance=2.03 Simple disulfide: pdb=" SG CYS G 173 " - pdb=" SG CYS G 178 " distance=2.02 Simple disulfide: pdb=" SG CYS H 29 " - pdb=" SG CYS H 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 62 " distance=2.03 Simple disulfide: pdb=" SG CYS H 80 " - pdb=" SG CYS H 86 " distance=2.05 Simple disulfide: pdb=" SG CYS I 37 " - pdb=" SG CYS I 110 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 85 " - pdb=" SG CYS I 123 " distance=2.03 Simple disulfide: pdb=" SG CYS I 96 " - pdb=" SG CYS J 199 " distance=2.25 Simple disulfide: pdb=" SG CYS J 50 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 142 " distance=2.04 Simple disulfide: pdb=" SG CYS J 170 " - pdb=" SG CYS J 193 " distance=2.03 Simple disulfide: pdb=" SG CYS J 300 " - pdb=" SG CYS J 327 " distance=2.03 Simple disulfide: pdb=" SG CYS K 28 " - pdb=" SG CYS K 114 " distance=2.04 Simple disulfide: pdb=" SG CYS K 51 " - pdb=" SG CYS K 101 " distance=2.03 Simple disulfide: pdb=" SG CYS K 59 " - pdb=" SG CYS K 105 " distance=2.04 Simple disulfide: pdb=" SG CYS K 132 " - pdb=" SG CYS K 143 " distance=2.03 Simple disulfide: pdb=" SG CYS K 173 " - pdb=" SG CYS K 178 " distance=2.02 Simple disulfide: pdb=" SG CYS L 29 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 52 " - pdb=" SG CYS L 62 " distance=2.03 Simple disulfide: pdb=" SG CYS L 80 " - pdb=" SG CYS L 86 " distance=2.05 Simple disulfide: pdb=" SG CYS M 37 " - pdb=" SG CYS M 110 " distance=2.03 Simple disulfide: pdb=" SG CYS M 64 " - pdb=" SG CYS M 196 " distance=2.03 Simple disulfide: pdb=" SG CYS M 85 " - pdb=" SG CYS M 123 " distance=2.03 Simple disulfide: pdb=" SG CYS M 96 " - pdb=" SG CYS N 199 " distance=2.25 Simple disulfide: pdb=" SG CYS N 50 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 142 " distance=2.04 Simple disulfide: pdb=" SG CYS N 170 " - pdb=" SG CYS N 193 " distance=2.03 Simple disulfide: pdb=" SG CYS N 300 " - pdb=" SG CYS N 327 " distance=2.03 Simple disulfide: pdb=" SG CYS O 28 " - pdb=" SG CYS O 114 " distance=2.04 Simple disulfide: pdb=" SG CYS O 51 " - pdb=" SG CYS O 101 " distance=2.03 Simple disulfide: pdb=" SG CYS O 59 " - pdb=" SG CYS O 105 " distance=2.04 Simple disulfide: pdb=" SG CYS O 132 " - pdb=" SG CYS O 143 " distance=2.03 Simple disulfide: pdb=" SG CYS O 173 " - pdb=" SG CYS O 178 " distance=2.02 Simple disulfide: pdb=" SG CYS P 29 " - pdb=" SG CYS P 87 " distance=2.03 Simple disulfide: pdb=" SG CYS P 52 " - pdb=" SG CYS P 62 " distance=2.03 Simple disulfide: pdb=" SG CYS P 80 " - pdb=" SG CYS P 86 " distance=2.05 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 Links applied BETA1-4 " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " NAG-ASN " NAG C 401 " - " ASN C 48 " " NAG C 402 " - " ASN C 166 " " NAG C 403 " - " ASN C 195 " " NAG G 401 " - " ASN G 48 " " NAG G 402 " - " ASN G 166 " " NAG G 403 " - " ASN G 195 " " NAG K 401 " - " ASN K 48 " " NAG K 402 " - " ASN K 166 " " NAG K 403 " - " ASN K 195 " " NAG O 401 " - " ASN O 48 " " NAG O 402 " - " ASN O 166 " " NAG O 403 " - " ASN O 195 " " NAG Q 1 " - " ASN B 222 " " NAG R 1 " - " ASN F 222 " " NAG S 1 " - " ASN J 222 " " NAG T 1 " - " ASN N 222 " Time building additional restraints: 10.97 Conformation dependent library (CDL) restraints added in 5.1 seconds 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6800 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 75 sheets defined 14.6% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'A' and resid 35 through 59 Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 117 through 147 removed outlier: 4.010A pdb=" N MET A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.937A pdb=" N THR A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'E' and resid 35 through 59 Processing helix chain 'E' and resid 80 through 85 Processing helix chain 'E' and resid 117 through 147 removed outlier: 4.009A pdb=" N MET E 147 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 171 Processing helix chain 'E' and resid 187 through 218 removed outlier: 3.937A pdb=" N THR E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'F' and resid 228 through 233 Processing helix chain 'G' and resid 217 through 221 Processing helix chain 'H' and resid 100 through 104 Processing helix chain 'I' and resid 35 through 59 Processing helix chain 'I' and resid 80 through 85 Processing helix chain 'I' and resid 117 through 147 removed outlier: 4.010A pdb=" N MET I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 171 Processing helix chain 'I' and resid 187 through 218 removed outlier: 3.938A pdb=" N THR I 191 " --> pdb=" O ASP I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 85 Processing helix chain 'J' and resid 228 through 233 Processing helix chain 'K' and resid 217 through 221 Processing helix chain 'L' and resid 100 through 104 Processing helix chain 'M' and resid 35 through 59 Processing helix chain 'M' and resid 80 through 85 Processing helix chain 'M' and resid 117 through 147 removed outlier: 4.010A pdb=" N MET M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 171 Processing helix chain 'M' and resid 187 through 218 removed outlier: 3.938A pdb=" N THR M 191 " --> pdb=" O ASP M 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 Processing helix chain 'N' and resid 228 through 233 Processing helix chain 'O' and resid 217 through 221 Processing helix chain 'P' and resid 100 through 104 Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 181 removed outlier: 3.676A pdb=" N VAL G 141 " --> pdb=" O PHE G 183 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N THR G 140 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS G 135 " --> pdb=" O THR G 140 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ARG G 223 " --> pdb=" O CYS G 132 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN G 134 " --> pdb=" O ARG G 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE B 23 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU B 25 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 32 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 27 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B 31 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS B 105 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 33 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS B 107 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 35 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS B 92 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS B 91 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY B 70 " --> pdb=" O TRP B 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE B 23 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU B 25 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 32 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 27 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B 31 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS B 105 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 33 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS B 107 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 35 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AA5, first strand: chain 'B' and resid 130 through 133 removed outlier: 6.526A pdb=" N GLU B 188 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'B' and resid 156 through 160 Processing sheet with id=AA8, first strand: chain 'B' and resid 239 through 245 removed outlier: 5.333A pdb=" N ASN B 240 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 257 " --> pdb=" O ASN B 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 289 through 291 removed outlier: 4.261A pdb=" N ALA B 304 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS B 327 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 31 through 34 Processing sheet with id=AB2, first strand: chain 'C' and resid 40 through 42 removed outlier: 5.754A pdb=" N ILE C 41 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN C 112 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU C 103 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS C 114 " --> pdb=" O CYS C 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 95 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU C 68 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHE C 79 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU C 70 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 182 removed outlier: 7.658A pdb=" N ARG C 223 " --> pdb=" O CYS C 132 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN C 134 " --> pdb=" O ARG C 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 168 through 173 removed outlier: 3.505A pdb=" N LEU C 161 " --> pdb=" O TRP C 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 168 through 173 removed outlier: 3.505A pdb=" N LEU C 161 " --> pdb=" O TRP C 169 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 186 through 187 removed outlier: 5.362A pdb=" N ASN C 186 " --> pdb=" O SER E 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 232 through 233 Processing sheet with id=AB8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'D' and resid 47 through 56 removed outlier: 4.035A pdb=" N LEU D 50 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER D 63 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS D 52 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU D 61 " --> pdb=" O CYS D 52 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ARG D 54 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG D 59 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AC2, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.765A pdb=" N VAL D 111 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 23 through 27 removed outlier: 6.269A pdb=" N ILE F 23 " --> pdb=" O GLU F 34 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU F 34 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU F 25 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL F 32 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS F 27 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR F 31 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS F 105 " --> pdb=" O TYR F 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL F 33 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS F 107 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU F 35 " --> pdb=" O LYS F 107 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL F 96 " --> pdb=" O LYS F 92 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS F 92 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS F 91 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY F 70 " --> pdb=" O TRP F 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 23 through 27 removed outlier: 6.269A pdb=" N ILE F 23 " --> pdb=" O GLU F 34 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU F 34 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU F 25 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL F 32 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS F 27 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR F 31 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS F 105 " --> pdb=" O TYR F 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL F 33 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS F 107 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU F 35 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 47 through 49 Processing sheet with id=AC6, first strand: chain 'F' and resid 130 through 133 removed outlier: 6.525A pdb=" N GLU F 188 " --> pdb=" O SER F 176 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AC8, first strand: chain 'F' and resid 156 through 160 Processing sheet with id=AC9, first strand: chain 'F' and resid 239 through 245 removed outlier: 5.332A pdb=" N ASN F 240 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU F 257 " --> pdb=" O ASN F 240 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 289 through 291 removed outlier: 4.261A pdb=" N ALA F 304 " --> pdb=" O CYS F 327 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS F 327 " --> pdb=" O ALA F 304 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 31 through 34 Processing sheet with id=AD3, first strand: chain 'G' and resid 40 through 42 removed outlier: 5.755A pdb=" N ILE G 41 " --> pdb=" O GLY G 121 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN G 112 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU G 103 " --> pdb=" O GLN G 112 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS G 114 " --> pdb=" O CYS G 101 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY G 95 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU G 68 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE G 79 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU G 70 " --> pdb=" O ILE G 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 168 through 173 Processing sheet with id=AD5, first strand: chain 'G' and resid 168 through 173 Processing sheet with id=AD6, first strand: chain 'G' and resid 232 through 233 Processing sheet with id=AD7, first strand: chain 'G' and resid 256 through 257 Processing sheet with id=AD8, first strand: chain 'H' and resid 47 through 56 removed outlier: 4.034A pdb=" N LEU H 50 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER H 63 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS H 52 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU H 61 " --> pdb=" O CYS H 52 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG H 54 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG H 59 " --> pdb=" O ARG H 54 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 87 through 88 Processing sheet with id=AE1, first strand: chain 'H' and resid 87 through 88 removed outlier: 3.764A pdb=" N VAL H 111 " --> pdb=" O LEU H 131 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 180 through 181 Processing sheet with id=AE3, first strand: chain 'J' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE J 23 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLU J 34 " --> pdb=" O ILE J 23 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU J 25 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL J 32 " --> pdb=" O GLU J 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS J 27 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL J 96 " --> pdb=" O LYS J 92 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS J 92 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS J 91 " --> pdb=" O THR J 59 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY J 70 " --> pdb=" O TRP J 60 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE J 23 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLU J 34 " --> pdb=" O ILE J 23 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU J 25 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL J 32 " --> pdb=" O GLU J 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS J 27 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 47 through 49 Processing sheet with id=AE6, first strand: chain 'J' and resid 130 through 133 removed outlier: 6.525A pdb=" N GLU J 188 " --> pdb=" O SER J 176 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 152 through 153 Processing sheet with id=AE8, first strand: chain 'J' and resid 156 through 160 Processing sheet with id=AE9, first strand: chain 'J' and resid 239 through 245 removed outlier: 5.332A pdb=" N ASN J 240 " --> pdb=" O GLU J 257 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU J 257 " --> pdb=" O ASN J 240 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 289 through 291 removed outlier: 4.263A pdb=" N ALA J 304 " --> pdb=" O CYS J 327 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS J 327 " --> pdb=" O ALA J 304 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE J 306 " --> pdb=" O VAL J 325 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 31 through 34 Processing sheet with id=AF3, first strand: chain 'K' and resid 40 through 42 removed outlier: 5.755A pdb=" N ILE K 41 " --> pdb=" O GLY K 121 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN K 112 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU K 103 " --> pdb=" O GLN K 112 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS K 114 " --> pdb=" O CYS K 101 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY K 95 " --> pdb=" O VAL K 120 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU K 68 " --> pdb=" O PHE K 79 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE K 79 " --> pdb=" O LEU K 68 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU K 70 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 181 through 182 removed outlier: 7.658A pdb=" N ARG K 223 " --> pdb=" O CYS K 132 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN K 134 " --> pdb=" O ARG K 223 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 168 through 173 removed outlier: 3.505A pdb=" N LEU K 161 " --> pdb=" O TRP K 169 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 168 through 173 removed outlier: 3.505A pdb=" N LEU K 161 " --> pdb=" O TRP K 169 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 186 through 187 removed outlier: 5.373A pdb=" N ASN K 186 " --> pdb=" O SER M 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'K' and resid 232 through 233 Processing sheet with id=AF9, first strand: chain 'K' and resid 256 through 257 Processing sheet with id=AG1, first strand: chain 'L' and resid 47 through 56 removed outlier: 4.036A pdb=" N LEU L 50 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER L 63 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS L 52 " --> pdb=" O GLU L 61 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU L 61 " --> pdb=" O CYS L 52 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG L 54 " --> pdb=" O ARG L 59 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG L 59 " --> pdb=" O ARG L 54 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 87 through 88 Processing sheet with id=AG3, first strand: chain 'L' and resid 87 through 88 removed outlier: 3.764A pdb=" N VAL L 111 " --> pdb=" O LEU L 131 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE N 23 " --> pdb=" O GLU N 34 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLU N 34 " --> pdb=" O ILE N 23 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU N 25 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL N 32 " --> pdb=" O GLU N 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS N 27 " --> pdb=" O VAL N 30 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR N 31 " --> pdb=" O LEU N 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS N 105 " --> pdb=" O TYR N 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL N 33 " --> pdb=" O HIS N 105 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS N 107 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU N 35 " --> pdb=" O LYS N 107 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL N 96 " --> pdb=" O LYS N 92 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS N 92 " --> pdb=" O VAL N 96 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS N 91 " --> pdb=" O THR N 59 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY N 70 " --> pdb=" O TRP N 60 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE N 23 " --> pdb=" O GLU N 34 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLU N 34 " --> pdb=" O ILE N 23 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU N 25 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL N 32 " --> pdb=" O GLU N 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS N 27 " --> pdb=" O VAL N 30 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR N 31 " --> pdb=" O LEU N 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS N 105 " --> pdb=" O TYR N 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL N 33 " --> pdb=" O HIS N 105 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS N 107 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU N 35 " --> pdb=" O LYS N 107 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 47 through 49 Processing sheet with id=AG7, first strand: chain 'N' and resid 130 through 133 removed outlier: 6.525A pdb=" N GLU N 188 " --> pdb=" O SER N 176 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 152 through 153 Processing sheet with id=AG9, first strand: chain 'N' and resid 156 through 160 Processing sheet with id=AH1, first strand: chain 'N' and resid 239 through 245 removed outlier: 5.332A pdb=" N ASN N 240 " --> pdb=" O GLU N 257 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU N 257 " --> pdb=" O ASN N 240 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 289 through 291 removed outlier: 4.263A pdb=" N ALA N 304 " --> pdb=" O CYS N 327 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS N 327 " --> pdb=" O ALA N 304 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE N 306 " --> pdb=" O VAL N 325 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 31 through 34 Processing sheet with id=AH4, first strand: chain 'O' and resid 40 through 42 removed outlier: 5.757A pdb=" N ILE O 41 " --> pdb=" O GLY O 121 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN O 112 " --> pdb=" O LEU O 103 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU O 103 " --> pdb=" O GLN O 112 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS O 114 " --> pdb=" O CYS O 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY O 95 " --> pdb=" O VAL O 120 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU O 68 " --> pdb=" O PHE O 79 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE O 79 " --> pdb=" O LEU O 68 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU O 70 " --> pdb=" O ILE O 77 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 181 through 182 removed outlier: 7.658A pdb=" N ARG O 223 " --> pdb=" O CYS O 132 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN O 134 " --> pdb=" O ARG O 223 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 168 through 173 removed outlier: 3.505A pdb=" N LEU O 161 " --> pdb=" O TRP O 169 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 168 through 173 removed outlier: 3.505A pdb=" N LEU O 161 " --> pdb=" O TRP O 169 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 232 through 233 Processing sheet with id=AH9, first strand: chain 'O' and resid 256 through 257 Processing sheet with id=AI1, first strand: chain 'P' and resid 47 through 56 removed outlier: 4.035A pdb=" N LEU P 50 " --> pdb=" O SER P 63 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER P 63 " --> pdb=" O LEU P 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS P 52 " --> pdb=" O GLU P 61 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU P 61 " --> pdb=" O CYS P 52 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ARG P 54 " --> pdb=" O ARG P 59 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG P 59 " --> pdb=" O ARG P 54 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'P' and resid 87 through 88 Processing sheet with id=AI3, first strand: chain 'P' and resid 87 through 88 removed outlier: 3.764A pdb=" N VAL P 111 " --> pdb=" O LEU P 131 " (cutoff:3.500A) 1013 hydrogen bonds defined for protein. 2652 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: 12.26 Time building geometry restraints manager: 11.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5466 1.32 - 1.45: 7313 1.45 - 1.57: 16357 1.57 - 1.69: 0 1.69 - 1.82: 248 Bond restraints: 29384 Sorted by residual: bond pdb=" CA VAL D 107 " pdb=" CB VAL D 107 " ideal model delta sigma weight residual 1.537 1.479 0.058 1.24e-02 6.50e+03 2.22e+01 bond pdb=" CA PRO J 237 " pdb=" C PRO J 237 " ideal model delta sigma weight residual 1.514 1.538 -0.024 5.50e-03 3.31e+04 1.90e+01 bond pdb=" CA LYS C 165 " pdb=" C LYS C 165 " ideal model delta sigma weight residual 1.528 1.476 0.053 1.28e-02 6.10e+03 1.71e+01 bond pdb=" CA PRO F 237 " pdb=" C PRO F 237 " ideal model delta sigma weight residual 1.514 1.537 -0.023 5.50e-03 3.31e+04 1.69e+01 bond pdb=" CA PRO N 237 " pdb=" C PRO N 237 " ideal model delta sigma weight residual 1.514 1.537 -0.023 5.50e-03 3.31e+04 1.68e+01 ... (remaining 29379 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.98: 776 105.98 - 113.11: 15311 113.11 - 120.24: 13864 120.24 - 127.37: 9604 127.37 - 134.50: 261 Bond angle restraints: 39816 Sorted by residual: angle pdb=" N LYS G 165 " pdb=" CA LYS G 165 " pdb=" C LYS G 165 " ideal model delta sigma weight residual 110.35 98.85 11.50 1.38e+00 5.25e-01 6.94e+01 angle pdb=" N ARG G 65 " pdb=" CA ARG G 65 " pdb=" C ARG G 65 " ideal model delta sigma weight residual 114.62 106.79 7.83 1.14e+00 7.69e-01 4.72e+01 angle pdb=" N ARG O 65 " pdb=" CA ARG O 65 " pdb=" C ARG O 65 " ideal model delta sigma weight residual 114.62 106.82 7.80 1.14e+00 7.69e-01 4.68e+01 angle pdb=" N ARG K 65 " pdb=" CA ARG K 65 " pdb=" C ARG K 65 " ideal model delta sigma weight residual 114.62 106.82 7.80 1.14e+00 7.69e-01 4.68e+01 angle pdb=" N ARG C 65 " pdb=" CA ARG C 65 " pdb=" C ARG C 65 " ideal model delta sigma weight residual 114.62 106.86 7.76 1.14e+00 7.69e-01 4.63e+01 ... (remaining 39811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.21: 16980 20.21 - 40.41: 1029 40.41 - 60.62: 186 60.62 - 80.83: 32 80.83 - 101.03: 21 Dihedral angle restraints: 18248 sinusoidal: 7772 harmonic: 10476 Sorted by residual: dihedral pdb=" CB CYS K 59 " pdb=" SG CYS K 59 " pdb=" SG CYS K 105 " pdb=" CB CYS K 105 " ideal model delta sinusoidal sigma weight residual 93.00 166.33 -73.33 1 1.00e+01 1.00e-02 6.85e+01 dihedral pdb=" CB CYS G 59 " pdb=" SG CYS G 59 " pdb=" SG CYS G 105 " pdb=" CB CYS G 105 " ideal model delta sinusoidal sigma weight residual 93.00 166.26 -73.26 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS C 59 " pdb=" SG CYS C 59 " pdb=" SG CYS C 105 " pdb=" CB CYS C 105 " ideal model delta sinusoidal sigma weight residual 93.00 166.23 -73.23 1 1.00e+01 1.00e-02 6.83e+01 ... (remaining 18245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2035 0.076 - 0.151: 1624 0.151 - 0.227: 619 0.227 - 0.302: 184 0.302 - 0.377: 22 Chirality restraints: 4484 Sorted by residual: chirality pdb=" CA THR P 123 " pdb=" N THR P 123 " pdb=" C THR P 123 " pdb=" CB THR P 123 " both_signs ideal model delta sigma weight residual False 2.53 2.90 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA THR D 123 " pdb=" N THR D 123 " pdb=" C THR D 123 " pdb=" CB THR D 123 " both_signs ideal model delta sigma weight residual False 2.53 2.90 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA THR H 123 " pdb=" N THR H 123 " pdb=" C THR H 123 " pdb=" CB THR H 123 " both_signs ideal model delta sigma weight residual False 2.53 2.90 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 4481 not shown) Planarity restraints: 5048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 100 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.16e+00 pdb=" C SER D 100 " 0.052 2.00e-02 2.50e+03 pdb=" O SER D 100 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP D 101 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 196 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C ASP F 196 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP F 196 " 0.019 2.00e-02 2.50e+03 pdb=" N SER F 197 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP N 196 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C ASP N 196 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP N 196 " -0.019 2.00e-02 2.50e+03 pdb=" N SER N 197 " -0.018 2.00e-02 2.50e+03 ... (remaining 5045 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 659 2.68 - 3.23: 25146 3.23 - 3.79: 41409 3.79 - 4.34: 59167 4.34 - 4.90: 93834 Nonbonded interactions: 220215 Sorted by model distance: nonbonded pdb=" CD2 LEU J 117 " pdb=" CG2 THR J 146 " model vdw 2.120 3.880 nonbonded pdb=" CD2 LEU B 117 " pdb=" CG2 THR B 146 " model vdw 2.121 3.880 nonbonded pdb=" CD2 LEU F 117 " pdb=" CG2 THR F 146 " model vdw 2.122 3.880 nonbonded pdb=" CD2 LEU N 117 " pdb=" CG2 THR N 146 " model vdw 2.122 3.880 nonbonded pdb=" N LYS G 165 " pdb=" O LYS G 165 " model vdw 2.333 2.496 ... (remaining 220210 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.210 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 82.430 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.300 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: 0.020 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 0.058 29384 Z= 0.848 Angle : 1.591 11.496 39816 Z= 1.202 Chirality : 0.114 0.377 4484 Planarity : 0.004 0.030 5032 Dihedral : 13.235 101.032 11256 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.92 % Allowed : 9.89 % Favored : 88.18 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 5.00 % 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: 0.65 (0.14), residues: 3520 helix: 2.86 (0.24), residues: 500 sheet: 0.92 (0.16), residues: 1164 loop : -0.58 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 60 HIS 0.004 0.001 HIS N 266 PHE 0.027 0.002 PHE P 99 TYR 0.025 0.002 TYR J 268 ARG 0.005 0.001 ARG O 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 626 time to evaluate : 3.616 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: A 210 ASP cc_start: 0.7950 (t0) cc_final: 0.7445 (t0) REVERT: B 240 ASN cc_start: 0.7430 (t0) cc_final: 0.7222 (t0) REVERT: C 251 LEU cc_start: 0.8606 (mt) cc_final: 0.8037 (tt) REVERT: D 58 ASP cc_start: 0.7685 (p0) cc_final: 0.7420 (p0) REVERT: D 64 TRP cc_start: 0.5470 (p90) cc_final: 0.3437 (p90) REVERT: D 123 THR cc_start: 0.6044 (m) cc_final: 0.5762 (p) REVERT: F 82 PHE cc_start: 0.3553 (m-80) cc_final: 0.3347 (m-80) REVERT: G 41 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8320 (pt) REVERT: G 251 LEU cc_start: 0.8511 (mt) cc_final: 0.8258 (tt) REVERT: G 253 LEU cc_start: 0.8037 (mt) cc_final: 0.7788 (mm) REVERT: J 191 VAL cc_start: 0.7769 (p) cc_final: 0.7460 (p) REVERT: K 228 TRP cc_start: 0.6244 (p-90) cc_final: 0.5782 (p90) REVERT: K 249 GLU cc_start: 0.7040 (mm-30) cc_final: 0.5783 (mm-30) REVERT: N 32 VAL cc_start: 0.6789 (t) cc_final: 0.5735 (t) outliers start: 62 outliers final: 11 residues processed: 676 average time/residue: 0.4322 time to fit residues: 451.4342 Evaluate side-chains 302 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 290 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 276 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 7.9990 chunk 266 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 205 optimal weight: 0.3980 chunk 319 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN B 91 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN C 268 ASN D 102 GLN E 50 ASN F 87 GLN F 120 GLN G 134 GLN G 255 ASN G 268 ASN H 102 GLN I 42 GLN I 57 GLN I 152 GLN J 87 GLN J 248 ASN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN K 255 ASN K 268 ASN L 102 GLN M 168 GLN N 87 GLN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 255 ASN O 268 ASN P 102 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29384 Z= 0.228 Angle : 0.622 10.160 39816 Z= 0.331 Chirality : 0.043 0.263 4484 Planarity : 0.004 0.059 5032 Dihedral : 7.623 63.117 4382 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.26 % Allowed : 15.26 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.73 (0.14), residues: 3520 helix: 3.20 (0.22), residues: 472 sheet: 1.01 (0.15), residues: 1224 loop : -0.65 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 228 HIS 0.013 0.001 HIS B 91 PHE 0.021 0.002 PHE O 60 TYR 0.024 0.002 TYR J 314 ARG 0.007 0.001 ARG E 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 322 time to evaluate : 3.243 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: A 34 MET cc_start: 0.7354 (tmm) cc_final: 0.6806 (tpp) REVERT: A 88 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7945 (mm) REVERT: A 157 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6706 (mp10) REVERT: A 210 ASP cc_start: 0.8400 (t0) cc_final: 0.7920 (t0) REVERT: B 240 ASN cc_start: 0.7615 (t0) cc_final: 0.7353 (t0) REVERT: C 251 LEU cc_start: 0.8376 (mt) cc_final: 0.7979 (tt) REVERT: D 64 TRP cc_start: 0.4976 (p90) cc_final: 0.3968 (p90) REVERT: D 98 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7730 (mm-40) REVERT: D 99 PHE cc_start: 0.8240 (p90) cc_final: 0.8032 (p90) REVERT: F 194 GLN cc_start: 0.7072 (tm-30) cc_final: 0.6856 (tm-30) REVERT: G 251 LEU cc_start: 0.8360 (mt) cc_final: 0.7988 (tt) REVERT: G 253 LEU cc_start: 0.8175 (mt) cc_final: 0.7865 (mm) REVERT: G 259 TYR cc_start: 0.6741 (p90) cc_final: 0.5840 (p90) REVERT: G 302 LYS cc_start: 0.7276 (mtpp) cc_final: 0.6931 (ttpp) REVERT: I 73 ASP cc_start: 0.7710 (t70) cc_final: 0.7339 (t0) REVERT: J 87 GLN cc_start: 0.2332 (OUTLIER) cc_final: 0.1940 (mt0) REVERT: M 88 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7028 (mm) REVERT: M 164 ASP cc_start: 0.8233 (t0) cc_final: 0.7999 (t0) REVERT: M 175 GLU cc_start: 0.7040 (tp30) cc_final: 0.6805 (tp30) outliers start: 73 outliers final: 37 residues processed: 381 average time/residue: 0.4165 time to fit residues: 252.4750 Evaluate side-chains 306 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 264 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain I residue 119 MET Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain N residue 31 TYR Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 250 ARG Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 266 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 320 optimal weight: 0.9990 chunk 345 optimal weight: 0.3980 chunk 285 optimal weight: 3.9990 chunk 317 optimal weight: 0.9990 chunk 109 optimal weight: 20.0000 chunk 256 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN I 57 GLN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN K 299 HIS M 53 GLN M 57 GLN M 168 GLN ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN N 166 GLN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29384 Z= 0.185 Angle : 0.549 11.313 39816 Z= 0.289 Chirality : 0.040 0.249 4484 Planarity : 0.004 0.038 5032 Dihedral : 5.712 53.543 4372 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.70 % Allowed : 15.38 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.66 (0.14), residues: 3520 helix: 3.08 (0.22), residues: 472 sheet: 0.98 (0.15), residues: 1224 loop : -0.68 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP J 24 HIS 0.006 0.001 HIS F 105 PHE 0.020 0.001 PHE E 118 TYR 0.018 0.001 TYR J 220 ARG 0.005 0.000 ARG F 179 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 299 time to evaluate : 3.528 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: A 34 MET cc_start: 0.7466 (tmm) cc_final: 0.6956 (tpp) REVERT: A 88 LEU cc_start: 0.8236 (pt) cc_final: 0.7848 (mm) REVERT: A 157 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6779 (mp10) REVERT: A 210 ASP cc_start: 0.8449 (t0) cc_final: 0.8055 (t0) REVERT: B 240 ASN cc_start: 0.7781 (t0) cc_final: 0.7560 (t0) REVERT: C 137 GLU cc_start: 0.6619 (pt0) cc_final: 0.5445 (pt0) REVERT: C 251 LEU cc_start: 0.8342 (mt) cc_final: 0.7985 (tp) REVERT: C 259 TYR cc_start: 0.6944 (p90) cc_final: 0.6644 (p90) REVERT: D 99 PHE cc_start: 0.8276 (p90) cc_final: 0.7936 (p90) REVERT: D 124 GLU cc_start: 0.5587 (mp0) cc_final: 0.5005 (mp0) REVERT: E 51 MET cc_start: 0.8375 (tpp) cc_final: 0.8059 (tpp) REVERT: F 194 GLN cc_start: 0.7108 (tm-30) cc_final: 0.6596 (tm-30) REVERT: G 253 LEU cc_start: 0.8291 (mt) cc_final: 0.7948 (mm) REVERT: I 73 ASP cc_start: 0.7688 (t70) cc_final: 0.7330 (t0) REVERT: L 79 CYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6746 (p) REVERT: M 88 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6840 (mm) REVERT: O 299 HIS cc_start: 0.7882 (t70) cc_final: 0.7560 (t70) outliers start: 87 outliers final: 45 residues processed: 364 average time/residue: 0.4164 time to fit residues: 239.7815 Evaluate side-chains 304 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 256 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 119 MET Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain L residue 79 CYS Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 270 SER Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain O residue 60 PHE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 4.9990 chunk 240 optimal weight: 0.3980 chunk 166 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 321 optimal weight: 2.9990 chunk 340 optimal weight: 0.6980 chunk 167 optimal weight: 9.9990 chunk 304 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN K 61 HIS K 138 GLN M 168 GLN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 29384 Z= 0.226 Angle : 0.550 8.324 39816 Z= 0.290 Chirality : 0.040 0.291 4484 Planarity : 0.004 0.038 5032 Dihedral : 4.930 47.566 4372 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 2.92 % Allowed : 15.48 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.56 (0.14), residues: 3520 helix: 2.94 (0.23), residues: 472 sheet: 0.91 (0.15), residues: 1248 loop : -0.75 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 60 HIS 0.007 0.001 HIS F 105 PHE 0.024 0.002 PHE J 128 TYR 0.018 0.001 TYR J 220 ARG 0.007 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 286 time to evaluate : 3.503 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: A 34 MET cc_start: 0.7496 (tmm) cc_final: 0.7014 (tpp) REVERT: A 88 LEU cc_start: 0.8318 (pt) cc_final: 0.7884 (mm) REVERT: A 157 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6973 (mp10) REVERT: A 164 ASP cc_start: 0.8072 (t0) cc_final: 0.7862 (m-30) REVERT: A 210 ASP cc_start: 0.8431 (t0) cc_final: 0.8128 (t0) REVERT: E 51 MET cc_start: 0.8444 (tpp) cc_final: 0.8201 (tpp) REVERT: E 210 ASP cc_start: 0.7782 (t0) cc_final: 0.6870 (t0) REVERT: F 314 TYR cc_start: 0.8640 (m-10) cc_final: 0.8251 (m-10) REVERT: I 73 ASP cc_start: 0.7756 (t70) cc_final: 0.7392 (t0) REVERT: L 79 CYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6806 (p) REVERT: M 88 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6899 (mm) REVERT: M 120 MET cc_start: 0.7189 (mmp) cc_final: 0.6741 (mmp) REVERT: M 175 GLU cc_start: 0.7183 (tp30) cc_final: 0.6818 (tp30) REVERT: N 166 GLN cc_start: 0.5367 (tp-100) cc_final: 0.5159 (tp40) outliers start: 94 outliers final: 58 residues processed: 362 average time/residue: 0.4102 time to fit residues: 235.0856 Evaluate side-chains 309 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 248 time to evaluate : 3.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 170 CYS Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 249 GLU Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain L residue 79 CYS Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 270 SER Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 0.2980 chunk 193 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 253 optimal weight: 30.0000 chunk 140 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 305 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN M 168 GLN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 GLN ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 29384 Z= 0.245 Angle : 0.544 11.800 39816 Z= 0.287 Chirality : 0.040 0.274 4484 Planarity : 0.004 0.037 5032 Dihedral : 4.804 38.024 4372 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.07 % Allowed : 15.88 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.51 (0.14), residues: 3520 helix: 2.83 (0.23), residues: 472 sheet: 0.93 (0.15), residues: 1232 loop : -0.78 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 60 HIS 0.007 0.001 HIS F 105 PHE 0.019 0.002 PHE M 154 TYR 0.021 0.002 TYR J 220 ARG 0.006 0.000 ARG F 179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 266 time to evaluate : 3.257 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: A 34 MET cc_start: 0.7520 (tmm) cc_final: 0.7040 (tpp) REVERT: A 88 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7905 (mm) REVERT: A 157 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: A 210 ASP cc_start: 0.8369 (t0) cc_final: 0.8099 (t0) REVERT: D 58 ASP cc_start: 0.8186 (t0) cc_final: 0.7949 (t0) REVERT: E 51 MET cc_start: 0.8451 (tpp) cc_final: 0.8227 (tpp) REVERT: F 117 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5693 (mt) REVERT: G 190 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6885 (tp30) REVERT: G 253 LEU cc_start: 0.8326 (mp) cc_final: 0.8035 (mm) REVERT: I 73 ASP cc_start: 0.7866 (t70) cc_final: 0.7460 (t0) REVERT: M 120 MET cc_start: 0.7273 (mmp) cc_final: 0.6871 (mmp) REVERT: O 299 HIS cc_start: 0.7389 (t70) cc_final: 0.7135 (t-90) outliers start: 99 outliers final: 65 residues processed: 347 average time/residue: 0.4062 time to fit residues: 223.4237 Evaluate side-chains 313 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 244 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 190 GLU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 170 CYS Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 270 SER Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 6.9990 chunk 306 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 199 optimal weight: 0.0370 chunk 83 optimal weight: 0.5980 chunk 340 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 chunk 157 optimal weight: 0.4980 chunk 28 optimal weight: 0.4980 chunk 112 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN N 105 HIS ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 29384 Z= 0.149 Angle : 0.504 14.061 39816 Z= 0.265 Chirality : 0.039 0.273 4484 Planarity : 0.003 0.043 5032 Dihedral : 4.536 37.339 4372 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.33 % Allowed : 16.56 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.58 (0.14), residues: 3520 helix: 3.01 (0.23), residues: 472 sheet: 0.99 (0.15), residues: 1220 loop : -0.79 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP K 228 HIS 0.007 0.001 HIS F 105 PHE 0.025 0.001 PHE J 128 TYR 0.020 0.001 TYR G 71 ARG 0.015 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 255 time to evaluate : 3.969 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: A 34 MET cc_start: 0.7421 (tmm) cc_final: 0.7077 (tpp) REVERT: A 88 LEU cc_start: 0.8295 (pt) cc_final: 0.7914 (mm) REVERT: A 120 MET cc_start: 0.8465 (mmp) cc_final: 0.8152 (mmp) REVERT: A 157 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7058 (mp10) REVERT: D 58 ASP cc_start: 0.8112 (t0) cc_final: 0.7717 (t0) REVERT: D 99 PHE cc_start: 0.8442 (p90) cc_final: 0.8184 (p90) REVERT: E 51 MET cc_start: 0.8429 (tpp) cc_final: 0.8170 (tpp) REVERT: E 120 MET cc_start: 0.7227 (mmp) cc_final: 0.6731 (mmp) REVERT: F 117 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5620 (mt) REVERT: G 253 LEU cc_start: 0.8298 (mp) cc_final: 0.7997 (mm) REVERT: I 73 ASP cc_start: 0.7841 (t70) cc_final: 0.7431 (t0) REVERT: M 120 MET cc_start: 0.7151 (mmp) cc_final: 0.6778 (mmp) REVERT: M 175 GLU cc_start: 0.7141 (tp30) cc_final: 0.6808 (tp30) outliers start: 75 outliers final: 51 residues processed: 312 average time/residue: 0.4468 time to fit residues: 221.0772 Evaluate side-chains 287 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 234 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 71 TYR Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 270 SER Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 0.0370 chunk 38 optimal weight: 0.6980 chunk 194 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 286 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 339 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN K 81 HIS ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 29384 Z= 0.232 Angle : 0.534 12.350 39816 Z= 0.282 Chirality : 0.039 0.253 4484 Planarity : 0.004 0.041 5032 Dihedral : 4.602 36.621 4372 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.39 % Allowed : 16.84 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.45 (0.14), residues: 3520 helix: 2.88 (0.24), residues: 460 sheet: 0.88 (0.15), residues: 1224 loop : -0.81 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP F 24 HIS 0.006 0.001 HIS F 105 PHE 0.018 0.002 PHE B 228 TYR 0.022 0.001 TYR J 220 ARG 0.007 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 241 time to evaluate : 3.485 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: A 34 MET cc_start: 0.7438 (tmm) cc_final: 0.7048 (tpp) REVERT: A 88 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7945 (mm) REVERT: A 157 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: D 58 ASP cc_start: 0.8132 (t0) cc_final: 0.7819 (t0) REVERT: D 99 PHE cc_start: 0.8505 (p90) cc_final: 0.8285 (p90) REVERT: E 51 MET cc_start: 0.8441 (tpp) cc_final: 0.8223 (tpp) REVERT: F 117 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5621 (mt) REVERT: F 325 VAL cc_start: 0.8061 (OUTLIER) cc_final: 0.7825 (m) REVERT: G 253 LEU cc_start: 0.8317 (mp) cc_final: 0.8034 (mm) REVERT: J 82 PHE cc_start: 0.5790 (OUTLIER) cc_final: 0.4447 (m-80) REVERT: M 120 MET cc_start: 0.7270 (mmp) cc_final: 0.6879 (mmp) outliers start: 77 outliers final: 57 residues processed: 301 average time/residue: 0.4314 time to fit residues: 205.1982 Evaluate side-chains 290 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 228 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 82 PHE Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain O residue 66 ASN Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 215 optimal weight: 0.2980 chunk 231 optimal weight: 0.7980 chunk 167 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 266 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29384 Z= 0.170 Angle : 0.505 14.891 39816 Z= 0.266 Chirality : 0.038 0.258 4484 Planarity : 0.003 0.042 5032 Dihedral : 4.472 37.301 4372 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.05 % Allowed : 17.31 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.50 (0.14), residues: 3520 helix: 3.02 (0.23), residues: 472 sheet: 0.90 (0.15), residues: 1216 loop : -0.83 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP F 24 HIS 0.008 0.001 HIS F 105 PHE 0.014 0.001 PHE M 154 TYR 0.021 0.001 TYR J 220 ARG 0.017 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 233 time to evaluate : 3.255 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: A 34 MET cc_start: 0.7480 (tmm) cc_final: 0.7178 (tpp) REVERT: A 88 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7960 (mm) REVERT: A 157 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: B 31 TYR cc_start: 0.7216 (m-80) cc_final: 0.6937 (m-80) REVERT: B 45 MET cc_start: 0.6221 (mmm) cc_final: 0.5987 (mmm) REVERT: B 221 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6532 (mm-30) REVERT: D 58 ASP cc_start: 0.8093 (t0) cc_final: 0.7410 (t0) REVERT: F 117 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5579 (mt) REVERT: F 325 VAL cc_start: 0.8056 (OUTLIER) cc_final: 0.7833 (m) REVERT: G 253 LEU cc_start: 0.8306 (mp) cc_final: 0.8014 (mm) REVERT: M 120 MET cc_start: 0.7289 (mmp) cc_final: 0.6893 (mmp) REVERT: M 175 GLU cc_start: 0.7160 (tp30) cc_final: 0.6910 (tp30) outliers start: 66 outliers final: 49 residues processed: 282 average time/residue: 0.4385 time to fit residues: 196.5394 Evaluate side-chains 280 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 226 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 6.9990 chunk 325 optimal weight: 0.9990 chunk 296 optimal weight: 0.0030 chunk 316 optimal weight: 4.9990 chunk 324 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 137 optimal weight: 0.0040 chunk 248 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 285 optimal weight: 7.9990 chunk 299 optimal weight: 3.9990 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN I 152 GLN I 179 GLN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 29384 Z= 0.148 Angle : 0.497 14.561 39816 Z= 0.260 Chirality : 0.038 0.240 4484 Planarity : 0.003 0.037 5032 Dihedral : 4.196 37.829 4364 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.83 % Allowed : 17.46 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.59 (0.14), residues: 3520 helix: 3.13 (0.23), residues: 472 sheet: 0.94 (0.15), residues: 1232 loop : -0.78 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP F 24 HIS 0.006 0.001 HIS F 105 PHE 0.014 0.001 PHE M 154 TYR 0.021 0.001 TYR J 220 ARG 0.008 0.000 ARG F 179 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 241 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7440 (tmm) cc_final: 0.7236 (tpp) REVERT: A 88 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7930 (mm) REVERT: A 157 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7227 (mp10) REVERT: B 31 TYR cc_start: 0.7149 (m-80) cc_final: 0.6903 (m-80) REVERT: B 45 MET cc_start: 0.6336 (mmm) cc_final: 0.6092 (mmm) REVERT: B 221 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6453 (mm-30) REVERT: D 58 ASP cc_start: 0.8069 (t0) cc_final: 0.7390 (t0) REVERT: E 38 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7505 (tp) REVERT: E 120 MET cc_start: 0.7375 (mmp) cc_final: 0.6883 (mmp) REVERT: F 117 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5417 (mt) REVERT: F 325 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7795 (m) REVERT: G 253 LEU cc_start: 0.8276 (mp) cc_final: 0.7997 (mm) REVERT: M 120 MET cc_start: 0.7231 (mmp) cc_final: 0.6890 (mmp) REVERT: M 175 GLU cc_start: 0.7217 (tp30) cc_final: 0.6909 (tp30) outliers start: 59 outliers final: 48 residues processed: 289 average time/residue: 0.3923 time to fit residues: 182.7757 Evaluate side-chains 279 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 225 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 334 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 232 optimal weight: 0.9990 chunk 350 optimal weight: 20.0000 chunk 322 optimal weight: 1.9990 chunk 279 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 215 optimal weight: 0.0770 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 29384 Z= 0.158 Angle : 0.501 14.426 39816 Z= 0.261 Chirality : 0.038 0.253 4484 Planarity : 0.003 0.040 5032 Dihedral : 4.162 37.742 4364 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.86 % Allowed : 17.52 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.60 (0.14), residues: 3520 helix: 3.16 (0.23), residues: 472 sheet: 0.96 (0.15), residues: 1224 loop : -0.77 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F 24 HIS 0.008 0.001 HIS F 105 PHE 0.014 0.001 PHE J 128 TYR 0.020 0.001 TYR I 215 ARG 0.008 0.000 ARG E 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 234 time to evaluate : 3.298 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: A 88 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7935 (mm) REVERT: A 157 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: B 31 TYR cc_start: 0.7119 (m-80) cc_final: 0.6851 (m-80) REVERT: B 45 MET cc_start: 0.6384 (mmm) cc_final: 0.6143 (mmm) REVERT: B 221 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6489 (mm-30) REVERT: D 58 ASP cc_start: 0.8056 (t0) cc_final: 0.7424 (t0) REVERT: E 120 MET cc_start: 0.7407 (mmp) cc_final: 0.6920 (mmp) REVERT: F 117 LEU cc_start: 0.5751 (OUTLIER) cc_final: 0.5399 (mt) REVERT: F 325 VAL cc_start: 0.8029 (OUTLIER) cc_final: 0.7783 (m) REVERT: G 253 LEU cc_start: 0.8275 (mp) cc_final: 0.7997 (mm) REVERT: G 259 TYR cc_start: 0.7012 (p90) cc_final: 0.6755 (p90) REVERT: M 120 MET cc_start: 0.7290 (mmp) cc_final: 0.6890 (mmp) REVERT: M 133 MET cc_start: 0.7313 (mtp) cc_final: 0.7097 (mtm) REVERT: M 175 GLU cc_start: 0.7219 (tp30) cc_final: 0.6952 (tp30) outliers start: 60 outliers final: 50 residues processed: 283 average time/residue: 0.4054 time to fit residues: 185.4149 Evaluate side-chains 282 residues out of total 3224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 227 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 0.0970 chunk 221 optimal weight: 0.1980 chunk 297 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 257 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 279 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 287 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.162992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.115223 restraints weight = 55061.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111869 restraints weight = 46260.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112691 restraints weight = 44071.079| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29384 Z= 0.190 Angle : 0.509 14.282 39816 Z= 0.266 Chirality : 0.039 0.237 4484 Planarity : 0.003 0.042 5032 Dihedral : 4.209 37.670 4364 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.89 % Allowed : 17.62 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.58 (0.14), residues: 3520 helix: 3.09 (0.23), residues: 472 sheet: 0.93 (0.15), residues: 1232 loop : -0.77 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP F 24 HIS 0.008 0.001 HIS F 105 PHE 0.016 0.001 PHE M 154 TYR 0.020 0.001 TYR J 220 ARG 0.010 0.000 ARG E 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6155.01 seconds wall clock time: 113 minutes 1.49 seconds (6781.49 seconds total)