Starting phenix.real_space_refine on Sun Feb 25 07:20:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1f_11028/02_2024/6z1f_11028_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1f_11028/02_2024/6z1f_11028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1f_11028/02_2024/6z1f_11028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1f_11028/02_2024/6z1f_11028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1f_11028/02_2024/6z1f_11028_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1f_11028/02_2024/6z1f_11028_updated.pdb" } resolution = 2.86 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 12 5.21 5 S 182 5.16 5 C 31680 2.51 5 N 8613 2.21 5 O 9297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 8": "NH1" <-> "NH2" Residue "1 PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 38": "NH1" <-> "NH2" Residue "1 GLU 52": "OE1" <-> "OE2" Residue "1 GLU 57": "OE1" <-> "OE2" Residue "1 ARG 76": "NH1" <-> "NH2" Residue "1 ARG 83": "NH1" <-> "NH2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 ARG 231": "NH1" <-> "NH2" Residue "2 ARG 8": "NH1" <-> "NH2" Residue "2 ARG 38": "NH1" <-> "NH2" Residue "2 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 67": "OE1" <-> "OE2" Residue "2 ARG 76": "NH1" <-> "NH2" Residue "2 ARG 83": "NH1" <-> "NH2" Residue "2 ARG 109": "NH1" <-> "NH2" Residue "2 TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 150": "NH1" <-> "NH2" Residue "2 ARG 169": "NH1" <-> "NH2" Residue "2 GLU 174": "OE1" <-> "OE2" Residue "2 GLU 179": "OE1" <-> "OE2" Residue "2 GLU 204": "OE1" <-> "OE2" Residue "2 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 231": "NH1" <-> "NH2" Residue "2 PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 8": "NH1" <-> "NH2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 GLU 67": "OE1" <-> "OE2" Residue "3 ARG 76": "NH1" <-> "NH2" Residue "3 ARG 83": "NH1" <-> "NH2" Residue "3 ARG 109": "NH1" <-> "NH2" Residue "3 ARG 150": "NH1" <-> "NH2" Residue "3 ARG 169": "NH1" <-> "NH2" Residue "3 GLU 174": "OE1" <-> "OE2" Residue "3 GLU 179": "OE1" <-> "OE2" Residue "3 GLU 204": "OE1" <-> "OE2" Residue "3 ARG 231": "NH1" <-> "NH2" Residue "4 TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 8": "NH1" <-> "NH2" Residue "4 ARG 38": "NH1" <-> "NH2" Residue "4 GLU 67": "OE1" <-> "OE2" Residue "4 ARG 76": "NH1" <-> "NH2" Residue "4 ARG 83": "NH1" <-> "NH2" Residue "4 ARG 109": "NH1" <-> "NH2" Residue "4 ARG 150": "NH1" <-> "NH2" Residue "4 ARG 169": "NH1" <-> "NH2" Residue "4 GLU 174": "OE1" <-> "OE2" Residue "4 GLU 179": "OE1" <-> "OE2" Residue "4 GLU 204": "OE1" <-> "OE2" Residue "4 ARG 231": "NH1" <-> "NH2" Residue "4 ARG 241": "NH1" <-> "NH2" Residue "5 ARG 8": "NH1" <-> "NH2" Residue "5 ARG 38": "NH1" <-> "NH2" Residue "5 GLU 67": "OE1" <-> "OE2" Residue "5 ARG 76": "NH1" <-> "NH2" Residue "5 ARG 83": "NH1" <-> "NH2" Residue "5 ARG 109": "NH1" <-> "NH2" Residue "5 TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 150": "NH1" <-> "NH2" Residue "5 ARG 169": "NH1" <-> "NH2" Residue "5 GLU 174": "OE1" <-> "OE2" Residue "5 GLU 179": "OE1" <-> "OE2" Residue "5 GLU 204": "OE1" <-> "OE2" Residue "5 ARG 231": "NH1" <-> "NH2" Residue "6 ARG 8": "NH1" <-> "NH2" Residue "6 ARG 38": "NH1" <-> "NH2" Residue "6 GLU 67": "OE1" <-> "OE2" Residue "6 ARG 76": "NH1" <-> "NH2" Residue "6 ARG 83": "NH1" <-> "NH2" Residue "6 ARG 109": "NH1" <-> "NH2" Residue "6 ARG 150": "NH1" <-> "NH2" Residue "6 ARG 169": "NH1" <-> "NH2" Residue "6 GLU 174": "OE1" <-> "OE2" Residue "6 GLU 179": "OE1" <-> "OE2" Residue "6 GLU 204": "OE1" <-> "OE2" Residue "6 ARG 231": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 87": "OD1" <-> "OD2" Residue "D PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 87": "OD1" <-> "OD2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E ARG 340": "NH1" <-> "NH2" Residue "E TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 22": "NH1" <-> "NH2" Residue "F TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 87": "OD1" <-> "OD2" Residue "F TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 283": "NH1" <-> "NH2" Residue "F ARG 340": "NH1" <-> "NH2" Residue "F TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 22": "NH1" <-> "NH2" Residue "G TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G ARG 340": "NH1" <-> "NH2" Residue "G TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 22": "NH1" <-> "NH2" Residue "H TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 87": "OD1" <-> "OD2" Residue "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 132": "NH1" <-> "NH2" Residue "H TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 283": "NH1" <-> "NH2" Residue "H ARG 340": "NH1" <-> "NH2" Residue "H TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "I ARG 77": "NH1" <-> "NH2" Residue "I TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 8": "NH1" <-> "NH2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 77": "NH1" <-> "NH2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 8": "NH1" <-> "NH2" Residue "K ARG 67": "NH1" <-> "NH2" Residue "K ARG 77": "NH1" <-> "NH2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L ARG 67": "NH1" <-> "NH2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "M ARG 8": "NH1" <-> "NH2" Residue "M ARG 67": "NH1" <-> "NH2" Residue "M ARG 77": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 67": "NH1" <-> "NH2" Residue "O ARG 77": "NH1" <-> "NH2" Residue "P ARG 8": "NH1" <-> "NH2" Residue "P ARG 67": "NH1" <-> "NH2" Residue "P ARG 77": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 49815 Number of models: 1 Model: "" Number of chains: 36 Chain: "1" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2184 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 264} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "2" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2215 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 265} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "3" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2241 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 268} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "4" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2222 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 265} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "5" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2206 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 264} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "6" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2174 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3665 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 444} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3601 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 437} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'KCX:plan-1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3649 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'KCX:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3649 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'KCX:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3649 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'KCX:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3649 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'KCX:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3649 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'KCX:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3649 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'KCX:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "1" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.21, per 1000 atoms: 0.51 Number of scatterers: 49815 At special positions: 0 Unit cell: (145.555, 199.181, 163.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 182 16.00 P 31 15.00 Mg 12 11.99 O 9297 8.00 N 8613 7.00 C 31680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS B 248 " distance=2.05 Simple disulfide: pdb=" SG CYS C 248 " - pdb=" SG CYS D 248 " distance=2.04 Simple disulfide: pdb=" SG CYS E 248 " - pdb=" SG CYS F 248 " distance=2.04 Simple disulfide: pdb=" SG CYS G 248 " - pdb=" SG CYS H 248 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.90 Conformation dependent library (CDL) restraints added in 9.6 seconds 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11500 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 245 helices and 38 sheets defined 40.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.51 Creating SS restraints... Processing helix chain '1' and resid 7 through 21 Processing helix chain '1' and resid 43 through 54 Processing helix chain '1' and resid 63 through 65 No H-bonds generated for 'chain '1' and resid 63 through 65' Processing helix chain '1' and resid 74 through 92 removed outlier: 3.849A pdb=" N ARG 1 79 " --> pdb=" O ALA 1 75 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE 1 89 " --> pdb=" O THR 1 85 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS 1 90 " --> pdb=" O ALA 1 86 " (cutoff:3.500A) Processing helix chain '1' and resid 118 through 132 Processing helix chain '1' and resid 162 through 170 Proline residue: 1 166 - end of helix Processing helix chain '1' and resid 182 through 192 Processing helix chain '1' and resid 200 through 209 Processing helix chain '1' and resid 215 through 223 removed outlier: 3.758A pdb=" N SER 1 219 " --> pdb=" O ILE 1 215 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG 1 222 " --> pdb=" O PHE 1 218 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER 1 223 " --> pdb=" O SER 1 219 " (cutoff:3.500A) Processing helix chain '1' and resid 227 through 237 removed outlier: 3.649A pdb=" N HIS 1 235 " --> pdb=" O ARG 1 231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS 1 236 " --> pdb=" O ASP 1 232 " (cutoff:3.500A) Processing helix chain '1' and resid 239 through 241 No H-bonds generated for 'chain '1' and resid 239 through 241' Processing helix chain '1' and resid 243 through 247 Processing helix chain '1' and resid 263 through 280 Processing helix chain '2' and resid 7 through 21 removed outlier: 3.646A pdb=" N HIS 2 16 " --> pdb=" O LYS 2 12 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE 2 21 " --> pdb=" O ILE 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 53 Processing helix chain '2' and resid 73 through 92 removed outlier: 3.551A pdb=" N ILE 2 78 " --> pdb=" O PRO 2 74 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG 2 79 " --> pdb=" O ALA 2 75 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE 2 89 " --> pdb=" O THR 2 85 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS 2 90 " --> pdb=" O ALA 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 119 through 130 removed outlier: 3.614A pdb=" N ASN 2 124 " --> pdb=" O THR 2 120 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN 2 129 " --> pdb=" O ALA 2 125 " (cutoff:3.500A) Processing helix chain '2' and resid 165 through 167 No H-bonds generated for 'chain '2' and resid 165 through 167' Processing helix chain '2' and resid 182 through 192 Processing helix chain '2' and resid 200 through 209 Processing helix chain '2' and resid 215 through 224 removed outlier: 3.510A pdb=" N LEU 2 221 " --> pdb=" O PHE 2 218 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER 2 223 " --> pdb=" O ALA 2 220 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 237 Processing helix chain '2' and resid 239 through 241 No H-bonds generated for 'chain '2' and resid 239 through 241' Processing helix chain '2' and resid 263 through 281 Processing helix chain '3' and resid 7 through 21 removed outlier: 3.537A pdb=" N ASN 3 20 " --> pdb=" O HIS 3 16 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE 3 21 " --> pdb=" O ILE 3 17 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 54 removed outlier: 3.641A pdb=" N CYS 3 47 " --> pdb=" O LYS 3 43 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU 3 52 " --> pdb=" O GLU 3 48 " (cutoff:3.500A) Processing helix chain '3' and resid 63 through 65 No H-bonds generated for 'chain '3' and resid 63 through 65' Processing helix chain '3' and resid 74 through 92 removed outlier: 3.659A pdb=" N ILE 3 78 " --> pdb=" O PRO 3 74 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG 3 79 " --> pdb=" O ALA 3 75 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU 3 88 " --> pdb=" O GLU 3 84 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE 3 89 " --> pdb=" O THR 3 85 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS 3 90 " --> pdb=" O ALA 3 86 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 132 removed outlier: 3.519A pdb=" N MET 3 128 " --> pdb=" O ASN 3 124 " (cutoff:3.500A) Processing helix chain '3' and resid 165 through 167 No H-bonds generated for 'chain '3' and resid 165 through 167' Processing helix chain '3' and resid 182 through 192 Processing helix chain '3' and resid 200 through 209 removed outlier: 3.541A pdb=" N VAL 3 207 " --> pdb=" O ILE 3 203 " (cutoff:3.500A) Processing helix chain '3' and resid 215 through 219 Processing helix chain '3' and resid 227 through 237 Processing helix chain '3' and resid 239 through 241 No H-bonds generated for 'chain '3' and resid 239 through 241' Processing helix chain '3' and resid 243 through 245 No H-bonds generated for 'chain '3' and resid 243 through 245' Processing helix chain '3' and resid 263 through 281 removed outlier: 3.835A pdb=" N VAL 3 280 " --> pdb=" O GLU 3 276 " (cutoff:3.500A) Processing helix chain '4' and resid 7 through 21 removed outlier: 3.636A pdb=" N HIS 4 16 " --> pdb=" O LYS 4 12 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN 4 20 " --> pdb=" O HIS 4 16 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE 4 21 " --> pdb=" O ILE 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 43 through 54 removed outlier: 3.592A pdb=" N CYS 4 47 " --> pdb=" O LYS 4 43 " (cutoff:3.500A) Processing helix chain '4' and resid 63 through 65 No H-bonds generated for 'chain '4' and resid 63 through 65' Processing helix chain '4' and resid 73 through 92 removed outlier: 3.527A pdb=" N ARG 4 79 " --> pdb=" O ALA 4 75 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE 4 89 " --> pdb=" O THR 4 85 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS 4 90 " --> pdb=" O ALA 4 86 " (cutoff:3.500A) Processing helix chain '4' and resid 104 through 107 No H-bonds generated for 'chain '4' and resid 104 through 107' Processing helix chain '4' and resid 118 through 130 removed outlier: 3.758A pdb=" N ASN 4 124 " --> pdb=" O THR 4 120 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET 4 128 " --> pdb=" O ASN 4 124 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 167 No H-bonds generated for 'chain '4' and resid 165 through 167' Processing helix chain '4' and resid 182 through 192 Processing helix chain '4' and resid 200 through 209 Processing helix chain '4' and resid 215 through 237 removed outlier: 3.526A pdb=" N LEU 4 221 " --> pdb=" O PHE 4 217 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG 4 222 " --> pdb=" O PHE 4 218 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER 4 223 " --> pdb=" O SER 4 219 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG 4 224 " --> pdb=" O ALA 4 220 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR 4 226 " --> pdb=" O ARG 4 222 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP 4 227 " --> pdb=" O SER 4 223 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE 4 228 " --> pdb=" O ARG 4 224 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLN 4 229 " --> pdb=" O ILE 4 225 " (cutoff:3.500A) Processing helix chain '4' and resid 239 through 241 No H-bonds generated for 'chain '4' and resid 239 through 241' Processing helix chain '4' and resid 263 through 281 removed outlier: 3.741A pdb=" N VAL 4 280 " --> pdb=" O GLU 4 276 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 21 removed outlier: 3.675A pdb=" N ASN 5 20 " --> pdb=" O HIS 5 16 " (cutoff:3.500A) Processing helix chain '5' and resid 43 through 54 Processing helix chain '5' and resid 63 through 65 No H-bonds generated for 'chain '5' and resid 63 through 65' Processing helix chain '5' and resid 73 through 92 removed outlier: 3.513A pdb=" N ILE 5 78 " --> pdb=" O PRO 5 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG 5 79 " --> pdb=" O ALA 5 75 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG 5 83 " --> pdb=" O ARG 5 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU 5 88 " --> pdb=" O GLU 5 84 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE 5 89 " --> pdb=" O THR 5 85 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS 5 90 " --> pdb=" O ALA 5 86 " (cutoff:3.500A) Processing helix chain '5' and resid 119 through 132 removed outlier: 3.555A pdb=" N ALA 5 125 " --> pdb=" O GLN 5 121 " (cutoff:3.500A) Processing helix chain '5' and resid 165 through 167 No H-bonds generated for 'chain '5' and resid 165 through 167' Processing helix chain '5' and resid 182 through 192 Processing helix chain '5' and resid 200 through 209 Processing helix chain '5' and resid 215 through 237 removed outlier: 3.556A pdb=" N SER 5 219 " --> pdb=" O ILE 5 215 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG 5 222 " --> pdb=" O PHE 5 218 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER 5 223 " --> pdb=" O SER 5 219 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG 5 224 " --> pdb=" O ALA 5 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE 5 225 " --> pdb=" O LEU 5 221 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR 5 226 " --> pdb=" O ARG 5 222 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP 5 227 " --> pdb=" O SER 5 223 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ILE 5 228 " --> pdb=" O ARG 5 224 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLN 5 229 " --> pdb=" O ILE 5 225 " (cutoff:3.500A) Processing helix chain '5' and resid 239 through 247 removed outlier: 4.044A pdb=" N ILE 5 242 " --> pdb=" O PHE 5 239 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER 5 243 " --> pdb=" O GLU 5 240 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU 5 244 " --> pdb=" O ARG 5 241 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL 5 247 " --> pdb=" O LEU 5 244 " (cutoff:3.500A) Processing helix chain '5' and resid 263 through 280 removed outlier: 3.784A pdb=" N VAL 5 280 " --> pdb=" O GLU 5 276 " (cutoff:3.500A) Processing helix chain '6' and resid 7 through 21 Processing helix chain '6' and resid 43 through 54 removed outlier: 3.775A pdb=" N CYS 6 47 " --> pdb=" O LYS 6 43 " (cutoff:3.500A) Processing helix chain '6' and resid 63 through 65 No H-bonds generated for 'chain '6' and resid 63 through 65' Processing helix chain '6' and resid 73 through 91 removed outlier: 3.642A pdb=" N ILE 6 78 " --> pdb=" O PRO 6 74 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG 6 79 " --> pdb=" O ALA 6 75 " (cutoff:3.500A) Processing helix chain '6' and resid 103 through 105 No H-bonds generated for 'chain '6' and resid 103 through 105' Processing helix chain '6' and resid 118 through 132 removed outlier: 3.544A pdb=" N ASN 6 124 " --> pdb=" O THR 6 120 " (cutoff:3.500A) Processing helix chain '6' and resid 165 through 167 No H-bonds generated for 'chain '6' and resid 165 through 167' Processing helix chain '6' and resid 182 through 192 Processing helix chain '6' and resid 200 through 209 Processing helix chain '6' and resid 215 through 237 removed outlier: 3.531A pdb=" N SER 6 219 " --> pdb=" O ILE 6 215 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER 6 223 " --> pdb=" O SER 6 219 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE 6 228 " --> pdb=" O ARG 6 224 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN 6 229 " --> pdb=" O ILE 6 225 " (cutoff:3.500A) Processing helix chain '6' and resid 244 through 247 No H-bonds generated for 'chain '6' and resid 244 through 247' Processing helix chain '6' and resid 263 through 280 removed outlier: 3.573A pdb=" N GLU 6 268 " --> pdb=" O ALA 6 264 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY 6 270 " --> pdb=" O LEU 6 266 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL 6 280 " --> pdb=" O GLU 6 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 143 through 148 removed outlier: 4.615A pdb=" N THR A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 215 through 233 Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 270 through 273 No H-bonds generated for 'chain 'A' and resid 270 through 273' Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.589A pdb=" N GLY A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 395 removed outlier: 3.581A pdb=" N GLU A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 414 through 434 Processing helix chain 'A' and resid 442 through 452 removed outlier: 3.563A pdb=" N ILE A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TRP A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 462 removed outlier: 3.633A pdb=" N ALA A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 81 No H-bonds generated for 'chain 'B' and resid 78 through 81' Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 143 through 148 removed outlier: 4.356A pdb=" N THR B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 163 removed outlier: 3.538A pdb=" N ASP B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.636A pdb=" N GLY B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 233 removed outlier: 3.521A pdb=" N ALA B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.505A pdb=" N TYR B 257 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 273 No H-bonds generated for 'chain 'B' and resid 270 through 273' Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 300 through 303 No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 312 through 322 Processing helix chain 'B' and resid 338 through 351 removed outlier: 3.716A pdb=" N ILE B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 removed outlier: 3.640A pdb=" N MET B 388 " --> pdb=" O VAL B 385 " (cutoff:3.500A) Proline residue: B 389 - end of helix removed outlier: 4.035A pdb=" N VAL B 392 " --> pdb=" O PRO B 389 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 394 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE B 395 " --> pdb=" O VAL B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 414 through 434 removed outlier: 3.582A pdb=" N ASN B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.578A pdb=" N ILE B 446 " --> pdb=" O GLY B 442 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 462 Processing helix chain 'C' and resid 51 through 62 Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 81 No H-bonds generated for 'chain 'C' and resid 78 through 81' Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 143 through 148 removed outlier: 4.201A pdb=" N THR C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 215 through 233 Processing helix chain 'C' and resid 248 through 260 Processing helix chain 'C' and resid 270 through 273 No H-bonds generated for 'chain 'C' and resid 270 through 273' Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 299 through 303 Processing helix chain 'C' and resid 312 through 322 Processing helix chain 'C' and resid 340 through 351 removed outlier: 3.613A pdb=" N LEU C 349 " --> pdb=" O GLY C 345 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 395 removed outlier: 3.502A pdb=" N MET C 388 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Proline residue: C 389 - end of helix removed outlier: 3.622A pdb=" N VAL C 392 " --> pdb=" O PRO C 389 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU C 393 " --> pdb=" O ALA C 390 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 394 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE C 395 " --> pdb=" O VAL C 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 395' Processing helix chain 'C' and resid 405 through 408 No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 414 through 434 Processing helix chain 'C' and resid 438 through 449 removed outlier: 5.983A pdb=" N ASN C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASP C 444 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 462 Processing helix chain 'D' and resid 51 through 62 Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 78 through 81 No H-bonds generated for 'chain 'D' and resid 78 through 81' Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 143 through 148 removed outlier: 4.205A pdb=" N THR D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 163 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 215 through 233 Processing helix chain 'D' and resid 248 through 260 Processing helix chain 'D' and resid 270 through 273 No H-bonds generated for 'chain 'D' and resid 270 through 273' Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 312 through 322 Processing helix chain 'D' and resid 340 through 351 removed outlier: 3.614A pdb=" N LEU D 349 " --> pdb=" O GLY D 345 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 395 removed outlier: 3.548A pdb=" N ILE D 394 " --> pdb=" O ALA D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 408 No H-bonds generated for 'chain 'D' and resid 405 through 408' Processing helix chain 'D' and resid 414 through 434 Processing helix chain 'D' and resid 438 through 449 removed outlier: 5.980A pdb=" N ASN D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASP D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 462 Processing helix chain 'E' and resid 51 through 62 Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 78 through 81 No H-bonds generated for 'chain 'E' and resid 78 through 81' Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 114 through 121 Processing helix chain 'E' and resid 143 through 148 removed outlier: 4.524A pdb=" N THR E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 163 removed outlier: 3.592A pdb=" N ASP E 161 " --> pdb=" O GLN E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.566A pdb=" N GLY E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 233 Processing helix chain 'E' and resid 248 through 260 removed outlier: 3.524A pdb=" N TYR E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 273 No H-bonds generated for 'chain 'E' and resid 270 through 273' Processing helix chain 'E' and resid 275 through 288 Processing helix chain 'E' and resid 300 through 303 No H-bonds generated for 'chain 'E' and resid 300 through 303' Processing helix chain 'E' and resid 312 through 322 removed outlier: 3.505A pdb=" N LEU E 321 " --> pdb=" O LYS E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 351 removed outlier: 3.519A pdb=" N GLY E 345 " --> pdb=" O GLY E 341 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP E 348 " --> pdb=" O MET E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 395 removed outlier: 3.578A pdb=" N MET E 388 " --> pdb=" O VAL E 385 " (cutoff:3.500A) Proline residue: E 389 - end of helix removed outlier: 3.738A pdb=" N VAL E 392 " --> pdb=" O PRO E 389 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU E 393 " --> pdb=" O ALA E 390 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE E 394 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE E 395 " --> pdb=" O VAL E 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 385 through 395' Processing helix chain 'E' and resid 405 through 408 No H-bonds generated for 'chain 'E' and resid 405 through 408' Processing helix chain 'E' and resid 414 through 434 Processing helix chain 'E' and resid 442 through 449 removed outlier: 3.690A pdb=" N ILE E 446 " --> pdb=" O GLY E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 462 removed outlier: 3.538A pdb=" N GLU E 461 " --> pdb=" O ALA E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 62 Processing helix chain 'F' and resid 71 through 73 No H-bonds generated for 'chain 'F' and resid 71 through 73' Processing helix chain 'F' and resid 78 through 81 No H-bonds generated for 'chain 'F' and resid 78 through 81' Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 114 through 121 removed outlier: 3.553A pdb=" N ILE F 121 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 148 removed outlier: 4.453A pdb=" N THR F 148 " --> pdb=" O ALA F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 163 Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.519A pdb=" N GLY F 187 " --> pdb=" O ALA F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 233 Processing helix chain 'F' and resid 248 through 260 removed outlier: 3.565A pdb=" N TYR F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 273 No H-bonds generated for 'chain 'F' and resid 270 through 273' Processing helix chain 'F' and resid 275 through 288 Processing helix chain 'F' and resid 300 through 303 No H-bonds generated for 'chain 'F' and resid 300 through 303' Processing helix chain 'F' and resid 312 through 322 Processing helix chain 'F' and resid 340 through 351 removed outlier: 3.537A pdb=" N GLY F 345 " --> pdb=" O GLY F 341 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP F 348 " --> pdb=" O MET F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 395 removed outlier: 3.593A pdb=" N MET F 388 " --> pdb=" O VAL F 385 " (cutoff:3.500A) Proline residue: F 389 - end of helix removed outlier: 3.795A pdb=" N VAL F 392 " --> pdb=" O PRO F 389 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU F 393 " --> pdb=" O ALA F 390 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE F 394 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE F 395 " --> pdb=" O VAL F 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 385 through 395' Processing helix chain 'F' and resid 405 through 408 No H-bonds generated for 'chain 'F' and resid 405 through 408' Processing helix chain 'F' and resid 414 through 434 removed outlier: 3.541A pdb=" N ASN F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 451 removed outlier: 3.633A pdb=" N ILE F 446 " --> pdb=" O GLY F 442 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS F 451 " --> pdb=" O ARG F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 462 removed outlier: 3.550A pdb=" N ALA F 459 " --> pdb=" O GLU F 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 62 removed outlier: 3.505A pdb=" N VAL G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 74 Processing helix chain 'G' and resid 78 through 81 No H-bonds generated for 'chain 'G' and resid 78 through 81' Processing helix chain 'G' and resid 106 through 108 No H-bonds generated for 'chain 'G' and resid 106 through 108' Processing helix chain 'G' and resid 114 through 121 Processing helix chain 'G' and resid 143 through 148 removed outlier: 4.345A pdb=" N THR G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 163 Processing helix chain 'G' and resid 183 through 196 Processing helix chain 'G' and resid 215 through 233 Processing helix chain 'G' and resid 248 through 260 Processing helix chain 'G' and resid 270 through 273 No H-bonds generated for 'chain 'G' and resid 270 through 273' Processing helix chain 'G' and resid 275 through 288 Processing helix chain 'G' and resid 312 through 322 Processing helix chain 'G' and resid 340 through 351 Processing helix chain 'G' and resid 385 through 395 removed outlier: 3.528A pdb=" N MET G 388 " --> pdb=" O VAL G 385 " (cutoff:3.500A) Proline residue: G 389 - end of helix removed outlier: 3.885A pdb=" N VAL G 392 " --> pdb=" O PRO G 389 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU G 393 " --> pdb=" O ALA G 390 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE G 394 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE G 395 " --> pdb=" O VAL G 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 385 through 395' Processing helix chain 'G' and resid 405 through 408 No H-bonds generated for 'chain 'G' and resid 405 through 408' Processing helix chain 'G' and resid 414 through 434 Processing helix chain 'G' and resid 442 through 449 removed outlier: 3.713A pdb=" N ILE G 446 " --> pdb=" O GLY G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 454 through 462 removed outlier: 3.620A pdb=" N GLU G 461 " --> pdb=" O ALA G 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 62 Processing helix chain 'H' and resid 71 through 73 No H-bonds generated for 'chain 'H' and resid 71 through 73' Processing helix chain 'H' and resid 78 through 81 No H-bonds generated for 'chain 'H' and resid 78 through 81' Processing helix chain 'H' and resid 106 through 108 No H-bonds generated for 'chain 'H' and resid 106 through 108' Processing helix chain 'H' and resid 114 through 121 removed outlier: 3.685A pdb=" N ILE H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 148 removed outlier: 4.427A pdb=" N THR H 148 " --> pdb=" O ALA H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 163 removed outlier: 3.624A pdb=" N ASP H 161 " --> pdb=" O GLN H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 196 removed outlier: 3.660A pdb=" N GLY H 196 " --> pdb=" O GLU H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 233 Processing helix chain 'H' and resid 248 through 260 removed outlier: 3.572A pdb=" N TYR H 257 " --> pdb=" O LYS H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 273 No H-bonds generated for 'chain 'H' and resid 270 through 273' Processing helix chain 'H' and resid 275 through 288 Processing helix chain 'H' and resid 300 through 303 No H-bonds generated for 'chain 'H' and resid 300 through 303' Processing helix chain 'H' and resid 312 through 322 Processing helix chain 'H' and resid 340 through 351 removed outlier: 3.531A pdb=" N GLY H 345 " --> pdb=" O GLY H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 395 removed outlier: 3.596A pdb=" N MET H 388 " --> pdb=" O VAL H 385 " (cutoff:3.500A) Proline residue: H 389 - end of helix removed outlier: 3.772A pdb=" N VAL H 392 " --> pdb=" O PRO H 389 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU H 393 " --> pdb=" O ALA H 390 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE H 395 " --> pdb=" O VAL H 392 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 408 No H-bonds generated for 'chain 'H' and resid 405 through 408' Processing helix chain 'H' and resid 414 through 434 Processing helix chain 'H' and resid 442 through 449 removed outlier: 3.695A pdb=" N ILE H 446 " --> pdb=" O GLY H 442 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 462 removed outlier: 3.611A pdb=" N GLU H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 34 removed outlier: 3.553A pdb=" N ILE I 31 " --> pdb=" O GLN I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 79 Processing helix chain 'J' and resid 21 through 34 removed outlier: 3.514A pdb=" N ILE J 31 " --> pdb=" O GLN J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 79 Processing helix chain 'K' and resid 21 through 34 removed outlier: 3.510A pdb=" N ILE K 31 " --> pdb=" O GLN K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 79 Processing helix chain 'L' and resid 21 through 34 removed outlier: 3.509A pdb=" N ILE L 31 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 79 Processing helix chain 'M' and resid 21 through 34 Processing helix chain 'M' and resid 66 through 79 removed outlier: 3.619A pdb=" N GLU M 72 " --> pdb=" O GLU M 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 34 removed outlier: 3.540A pdb=" N ILE N 31 " --> pdb=" O GLN N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 79 Processing helix chain 'O' and resid 21 through 34 Processing helix chain 'O' and resid 66 through 79 removed outlier: 3.591A pdb=" N GLU O 72 " --> pdb=" O GLU O 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 34 removed outlier: 3.601A pdb=" N ILE P 31 " --> pdb=" O GLN P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 79 Processing sheet with id= A, first strand: chain '1' and resid 173 through 177 removed outlier: 6.783A pdb=" N ILE 1 32 " --> pdb=" O GLU 1 174 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 32 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY 1 34 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE 1 153 " --> pdb=" O LEU 1 33 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE 1 35 " --> pdb=" O ILE 1 153 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL 1 155 " --> pdb=" O ILE 1 35 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ILE 1 154 " --> pdb=" O CYS 1 96 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU 1 98 " --> pdb=" O ILE 1 154 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR 1 156 " --> pdb=" O LEU 1 98 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE 1 100 " --> pdb=" O THR 1 156 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU 1 57 " --> pdb=" O VAL 1 97 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N MET 1 99 " --> pdb=" O GLU 1 57 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR 1 59 " --> pdb=" O MET 1 99 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASN 1 101 " --> pdb=" O THR 1 59 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE 1 61 " --> pdb=" O ASN 1 101 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '2' and resid 173 through 178 removed outlier: 6.586A pdb=" N ILE 2 32 " --> pdb=" O GLU 2 174 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE 2 176 " --> pdb=" O ILE 2 32 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLY 2 34 " --> pdb=" O PHE 2 176 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TRP 2 178 " --> pdb=" O GLY 2 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS 2 36 " --> pdb=" O TRP 2 178 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE 2 153 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE 2 35 " --> pdb=" O ILE 2 153 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL 2 155 " --> pdb=" O ILE 2 35 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N GLY 2 37 " --> pdb=" O VAL 2 155 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N GLY 2 157 " --> pdb=" O GLY 2 37 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE 2 154 " --> pdb=" O CYS 2 96 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU 2 98 " --> pdb=" O ILE 2 154 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR 2 156 " --> pdb=" O LEU 2 98 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE 2 100 " --> pdb=" O THR 2 156 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU 2 57 " --> pdb=" O VAL 2 97 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N MET 2 99 " --> pdb=" O GLU 2 57 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR 2 59 " --> pdb=" O MET 2 99 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN 2 101 " --> pdb=" O THR 2 59 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE 2 61 " --> pdb=" O ASN 2 101 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain '3' and resid 173 through 177 removed outlier: 6.474A pdb=" N ILE 3 32 " --> pdb=" O GLU 3 174 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N PHE 3 176 " --> pdb=" O ILE 3 32 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY 3 34 " --> pdb=" O PHE 3 176 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE 3 153 " --> pdb=" O LEU 3 33 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE 3 35 " --> pdb=" O ILE 3 153 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL 3 155 " --> pdb=" O ILE 3 35 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU 3 57 " --> pdb=" O VAL 3 97 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N MET 3 99 " --> pdb=" O GLU 3 57 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR 3 59 " --> pdb=" O MET 3 99 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '4' and resid 173 through 178 removed outlier: 6.886A pdb=" N ILE 4 32 " --> pdb=" O GLU 4 174 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N PHE 4 176 " --> pdb=" O ILE 4 32 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY 4 34 " --> pdb=" O PHE 4 176 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TRP 4 178 " --> pdb=" O GLY 4 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HIS 4 36 " --> pdb=" O TRP 4 178 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE 4 153 " --> pdb=" O LEU 4 33 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE 4 35 " --> pdb=" O ILE 4 153 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL 4 155 " --> pdb=" O ILE 4 35 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N GLY 4 37 " --> pdb=" O VAL 4 155 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY 4 157 " --> pdb=" O GLY 4 37 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE 4 154 " --> pdb=" O CYS 4 96 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU 4 98 " --> pdb=" O ILE 4 154 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N THR 4 156 " --> pdb=" O LEU 4 98 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE 4 100 " --> pdb=" O THR 4 156 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU 4 57 " --> pdb=" O VAL 4 97 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N MET 4 99 " --> pdb=" O GLU 4 57 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N THR 4 59 " --> pdb=" O MET 4 99 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain '5' and resid 173 through 177 removed outlier: 6.578A pdb=" N ILE 5 32 " --> pdb=" O GLU 5 174 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE 5 176 " --> pdb=" O ILE 5 32 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY 5 34 " --> pdb=" O PHE 5 176 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE 5 153 " --> pdb=" O LEU 5 33 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE 5 35 " --> pdb=" O ILE 5 153 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL 5 155 " --> pdb=" O ILE 5 35 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE 5 154 " --> pdb=" O CYS 5 96 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU 5 98 " --> pdb=" O ILE 5 154 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N THR 5 156 " --> pdb=" O LEU 5 98 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE 5 100 " --> pdb=" O THR 5 156 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU 5 57 " --> pdb=" O VAL 5 97 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N MET 5 99 " --> pdb=" O GLU 5 57 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR 5 59 " --> pdb=" O MET 5 99 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASN 5 101 " --> pdb=" O THR 5 59 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE 5 61 " --> pdb=" O ASN 5 101 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain '6' and resid 173 through 178 removed outlier: 6.777A pdb=" N ILE 6 32 " --> pdb=" O GLU 6 174 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N PHE 6 176 " --> pdb=" O ILE 6 32 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY 6 34 " --> pdb=" O PHE 6 176 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TRP 6 178 " --> pdb=" O GLY 6 34 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N HIS 6 36 " --> pdb=" O TRP 6 178 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE 6 153 " --> pdb=" O LEU 6 33 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE 6 35 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL 6 155 " --> pdb=" O ILE 6 35 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N GLY 6 37 " --> pdb=" O VAL 6 155 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY 6 157 " --> pdb=" O GLY 6 37 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N ILE 6 154 " --> pdb=" O CYS 6 96 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU 6 98 " --> pdb=" O ILE 6 154 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N THR 6 156 " --> pdb=" O LEU 6 98 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE 6 100 " --> pdb=" O THR 6 156 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU 6 57 " --> pdb=" O VAL 6 97 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET 6 99 " --> pdb=" O GLU 6 57 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR 6 59 " --> pdb=" O MET 6 99 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 133 through 140 removed outlier: 6.785A pdb=" N ALA A 40 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A 139 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 38 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 87 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA A 103 " --> pdb=" O CYS A 85 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N CYS A 85 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.375A pdb=" N ALA A 377 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLN A 402 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA A 379 " --> pdb=" O GLN A 402 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 265 through 269 removed outlier: 6.376A pdb=" N LEU A 291 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS A 268 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N HIS A 293 " --> pdb=" O HIS A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 133 through 140 removed outlier: 6.887A pdb=" N ALA B 40 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 139 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 38 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP B 87 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA B 103 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N CYS B 85 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 170 through 173 removed outlier: 6.555A pdb=" N ALA B 377 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLN B 402 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA B 379 " --> pdb=" O GLN B 402 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 265 through 269 removed outlier: 6.222A pdb=" N LEU B 291 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N HIS B 268 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N HIS B 293 " --> pdb=" O HIS B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 133 through 140 removed outlier: 3.754A pdb=" N ALA C 133 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 40 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE C 139 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C 38 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP C 87 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA C 103 " --> pdb=" O CYS C 85 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N CYS C 85 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 170 through 172 removed outlier: 6.572A pdb=" N ALA C 377 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLN C 402 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA C 379 " --> pdb=" O GLN C 402 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 265 through 269 removed outlier: 6.344A pdb=" N LEU C 291 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N HIS C 268 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N HIS C 293 " --> pdb=" O HIS C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 133 through 140 removed outlier: 3.759A pdb=" N ALA D 133 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA D 40 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE D 139 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU D 38 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP D 87 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ALA D 103 " --> pdb=" O CYS D 85 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N CYS D 85 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.572A pdb=" N ALA D 377 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N GLN D 402 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA D 379 " --> pdb=" O GLN D 402 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 265 through 269 removed outlier: 6.336A pdb=" N LEU D 291 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N HIS D 268 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N HIS D 293 " --> pdb=" O HIS D 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 133 through 140 removed outlier: 6.758A pdb=" N ALA E 40 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE E 139 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU E 38 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP E 87 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA E 103 " --> pdb=" O CYS E 85 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N CYS E 85 " --> pdb=" O ALA E 103 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 170 through 172 removed outlier: 6.656A pdb=" N ALA E 377 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLN E 402 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA E 379 " --> pdb=" O GLN E 402 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 265 through 269 removed outlier: 6.267A pdb=" N LEU E 291 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N HIS E 268 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS E 293 " --> pdb=" O HIS E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'F' and resid 133 through 140 removed outlier: 3.594A pdb=" N ALA F 133 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA F 40 " --> pdb=" O GLU F 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE F 139 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU F 38 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP F 87 " --> pdb=" O TYR F 101 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA F 103 " --> pdb=" O CYS F 85 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N CYS F 85 " --> pdb=" O ALA F 103 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 170 through 172 removed outlier: 6.537A pdb=" N ALA F 377 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLN F 402 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA F 379 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 265 through 269 removed outlier: 6.338A pdb=" N LEU F 291 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N HIS F 268 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS F 293 " --> pdb=" O HIS F 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 133 through 140 removed outlier: 3.501A pdb=" N ALA G 133 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA G 40 " --> pdb=" O GLU G 137 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE G 139 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU G 38 " --> pdb=" O ILE G 139 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP G 87 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA G 103 " --> pdb=" O CYS G 85 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N CYS G 85 " --> pdb=" O ALA G 103 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 170 through 172 removed outlier: 6.634A pdb=" N ALA G 377 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLN G 402 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA G 379 " --> pdb=" O GLN G 402 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 265 through 269 removed outlier: 6.242A pdb=" N LEU G 291 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N HIS G 268 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N HIS G 293 " --> pdb=" O HIS G 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'H' and resid 133 through 140 removed outlier: 6.936A pdb=" N ALA H 40 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE H 139 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU H 38 " --> pdb=" O ILE H 139 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP H 87 " --> pdb=" O TYR H 101 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA H 103 " --> pdb=" O CYS H 85 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N CYS H 85 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 170 through 172 removed outlier: 6.533A pdb=" N ALA H 377 " --> pdb=" O VAL H 400 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLN H 402 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA H 379 " --> pdb=" O GLN H 402 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 265 through 269 removed outlier: 6.272A pdb=" N LEU H 291 " --> pdb=" O ILE H 266 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N HIS H 268 " --> pdb=" O LEU H 291 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N HIS H 293 " --> pdb=" O HIS H 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'I' and resid 37 through 43 removed outlier: 6.568A pdb=" N VAL I 87 " --> pdb=" O ILE I 102 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ILE I 102 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLY I 89 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER I 100 " --> pdb=" O GLY I 89 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 37 through 43 removed outlier: 6.444A pdb=" N VAL J 87 " --> pdb=" O ILE J 102 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ILE J 102 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLY J 89 " --> pdb=" O SER J 100 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER J 100 " --> pdb=" O GLY J 89 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 37 through 43 removed outlier: 6.497A pdb=" N VAL K 87 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE K 102 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLY K 89 " --> pdb=" O SER K 100 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER K 100 " --> pdb=" O GLY K 89 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 37 through 43 removed outlier: 6.499A pdb=" N VAL L 87 " --> pdb=" O ILE L 102 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE L 102 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLY L 89 " --> pdb=" O SER L 100 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER L 100 " --> pdb=" O GLY L 89 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'M' and resid 37 through 43 removed outlier: 6.480A pdb=" N VAL M 87 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE M 102 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLY M 89 " --> pdb=" O SER M 100 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER M 100 " --> pdb=" O GLY M 89 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 37 through 43 removed outlier: 6.602A pdb=" N VAL N 87 " --> pdb=" O ILE N 102 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE N 102 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLY N 89 " --> pdb=" O SER N 100 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER N 100 " --> pdb=" O GLY N 89 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'O' and resid 37 through 43 removed outlier: 6.462A pdb=" N VAL O 87 " --> pdb=" O ILE O 102 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ILE O 102 " --> pdb=" O VAL O 87 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLY O 89 " --> pdb=" O SER O 100 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER O 100 " --> pdb=" O GLY O 89 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'P' and resid 37 through 43 removed outlier: 6.575A pdb=" N VAL P 87 " --> pdb=" O ILE P 102 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ILE P 102 " --> pdb=" O VAL P 87 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLY P 89 " --> pdb=" O SER P 100 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER P 100 " --> pdb=" O GLY P 89 " (cutoff:3.500A) 1648 hydrogen bonds defined for protein. 4782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.43 Time building geometry restraints manager: 20.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 20141 1.40 - 1.57: 30497 1.57 - 1.75: 57 1.75 - 1.93: 271 1.93 - 2.10: 2 Bond restraints: 50968 Sorted by residual: bond pdb=" PG AGS 2 301 " pdb=" S1G AGS 2 301 " ideal model delta sigma weight residual 1.949 1.534 0.415 2.00e-02 2.50e+03 4.31e+02 bond pdb=" PG AGS 5 301 " pdb=" S1G AGS 5 301 " ideal model delta sigma weight residual 1.949 1.672 0.277 2.00e-02 2.50e+03 1.91e+02 bond pdb=" C2 AGS 3 301 " pdb=" N3 AGS 3 301 " ideal model delta sigma weight residual 1.335 1.413 -0.078 1.00e-02 1.00e+04 6.12e+01 bond pdb=" PG AGS 6 301 " pdb=" S1G AGS 6 301 " ideal model delta sigma weight residual 1.949 2.103 -0.154 2.00e-02 2.50e+03 5.95e+01 bond pdb=" C2 AGS 2 301 " pdb=" N3 AGS 2 301 " ideal model delta sigma weight residual 1.335 1.410 -0.075 1.00e-02 1.00e+04 5.65e+01 ... (remaining 50963 not shown) Histogram of bond angle deviations from ideal: 100.15 - 107.05: 1736 107.05 - 113.96: 26465 113.96 - 120.86: 23380 120.86 - 127.77: 17248 127.77 - 134.67: 408 Bond angle restraints: 69237 Sorted by residual: angle pdb=" N1 AGS 5 301 " pdb=" C2 AGS 5 301 " pdb=" N3 AGS 5 301 " ideal model delta sigma weight residual 128.80 118.24 10.56 8.41e-01 1.41e+00 1.58e+02 angle pdb=" N1 AGS 4 301 " pdb=" C2 AGS 4 301 " pdb=" N3 AGS 4 301 " ideal model delta sigma weight residual 128.80 118.32 10.48 8.41e-01 1.41e+00 1.55e+02 angle pdb=" N1 AGS 3 301 " pdb=" C2 AGS 3 301 " pdb=" N3 AGS 3 301 " ideal model delta sigma weight residual 128.80 118.56 10.24 8.41e-01 1.41e+00 1.48e+02 angle pdb=" N1 AGS 2 301 " pdb=" C2 AGS 2 301 " pdb=" N3 AGS 2 301 " ideal model delta sigma weight residual 128.80 118.85 9.95 8.41e-01 1.41e+00 1.40e+02 angle pdb=" N1 AGS 6 301 " pdb=" C2 AGS 6 301 " pdb=" N3 AGS 6 301 " ideal model delta sigma weight residual 128.80 119.08 9.72 8.41e-01 1.41e+00 1.33e+02 ... (remaining 69232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 29602 35.94 - 71.88: 674 71.88 - 107.81: 22 107.81 - 143.75: 11 143.75 - 179.69: 8 Dihedral angle restraints: 30317 sinusoidal: 12338 harmonic: 17979 Sorted by residual: dihedral pdb=" C3 CAP A 502 " pdb=" C CAP A 502 " pdb=" C2 CAP A 502 " pdb=" O6 CAP A 502 " ideal model delta sinusoidal sigma weight residual 81.86 -97.83 179.69 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C3 CAP E 502 " pdb=" C CAP E 502 " pdb=" C2 CAP E 502 " pdb=" O6 CAP E 502 " ideal model delta sinusoidal sigma weight residual 81.86 -95.94 177.80 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C3 CAP C 502 " pdb=" C CAP C 502 " pdb=" C2 CAP C 502 " pdb=" O6 CAP C 502 " ideal model delta sinusoidal sigma weight residual 81.86 -101.38 -176.75 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 30314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 5759 0.083 - 0.167: 1538 0.167 - 0.250: 238 0.250 - 0.333: 32 0.333 - 0.417: 7 Chirality restraints: 7574 Sorted by residual: chirality pdb=" PB AGS 6 301 " pdb=" O2B AGS 6 301 " pdb=" O3A AGS 6 301 " pdb=" O3B AGS 6 301 " both_signs ideal model delta sigma weight residual True 3.18 -3.60 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" PA AGS 6 301 " pdb=" O2A AGS 6 301 " pdb=" O3A AGS 6 301 " pdb=" O5' AGS 6 301 " both_signs ideal model delta sigma weight residual True 3.18 3.59 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" PA AGS 2 301 " pdb=" O2A AGS 2 301 " pdb=" O3A AGS 2 301 " pdb=" O5' AGS 2 301 " both_signs ideal model delta sigma weight residual True 3.18 3.56 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 7571 not shown) Planarity restraints: 8972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 210 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO C 211 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 211 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 211 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 210 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO D 211 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 211 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 211 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 210 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.94e+00 pdb=" N PRO H 211 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 211 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 211 " 0.026 5.00e-02 4.00e+02 ... (remaining 8969 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 12 2.19 - 2.86: 14904 2.86 - 3.54: 63511 3.54 - 4.22: 117107 4.22 - 4.90: 203068 Nonbonded interactions: 398602 Sorted by model distance: nonbonded pdb=" NH1 ARG 6 92 " pdb=" OE1 GLU A 52 " model vdw 1.507 2.520 nonbonded pdb=" CD2 TYR 2 143 " pdb=" SD MET P 1 " model vdw 1.675 3.700 nonbonded pdb=" O2G AGS 5 301 " pdb="MG MG 5 302 " model vdw 1.828 2.170 nonbonded pdb=" O2G AGS 2 301 " pdb="MG MG 2 302 " model vdw 1.856 2.170 nonbonded pdb=" O2G AGS 4 301 " pdb="MG MG 4 302 " model vdw 1.916 2.170 ... (remaining 398597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '1' and (resid 2 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 248 or resid 253 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB )) or resid 256 \ through 281)) selection = (chain '2' and (resid 2 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 114 or (resid 115 and (name N or na \ me CA or name C or name O or name CB )) or resid 116 through 200 or (resid 201 a \ nd (name N or name CA or name C or name O or name CB )) or resid 202 through 211 \ or (resid 212 and (name N or name CA or name C or name O or name CB )) or resid \ 213 through 239 or (resid 240 and (name N or name CA or name C or name O or nam \ e CB )) or resid 241 through 248 or resid 253 through 254 or (resid 255 and (nam \ e N or name CA or name C or name O or name CB )) or resid 256 or (resid 257 thro \ ugh 258 and (name N or name CA or name C or name O or name CB )) or resid 259 th \ rough 281)) selection = (chain '3' and (resid 2 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 111 or (resid 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 114 or (resid 115 a \ nd (name N or name CA or name C or name O or name CB )) or resid 116 through 194 \ or (resid 195 and (name N or name CA or name C or name O or name CB )) or resid \ 196 through 200 or (resid 201 and (name N or name CA or name C or name O or nam \ e CB )) or resid 202 through 211 or (resid 212 and (name N or name CA or name C \ or name O or name CB )) or resid 213 through 239 or (resid 240 and (name N or na \ me CA or name C or name O or name CB )) or resid 241 through 248 or resid 253 th \ rough 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) \ or resid 256 or (resid 257 through 258 and (name N or name CA or name C or name \ O or name CB )) or resid 259 through 280 or (resid 281 and (name N or name CA o \ r name C or name O or name CB )))) selection = (chain '4' and (resid 2 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 111 or (resid 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 114 or (resid 115 a \ nd (name N or name CA or name C or name O or name CB )) or resid 116 through 194 \ or (resid 195 and (name N or name CA or name C or name O or name CB )) or resid \ 196 through 200 or (resid 201 and (name N or name CA or name C or name O or nam \ e CB )) or resid 202 through 211 or (resid 212 and (name N or name CA or name C \ or name O or name CB )) or resid 213 through 239 or (resid 240 and (name N or na \ me CA or name C or name O or name CB )) or resid 241 through 248 or resid 253 th \ rough 256 or (resid 257 through 258 and (name N or name CA or name C or name O o \ r name CB )) or resid 259 through 281)) selection = (chain '5' and (resid 2 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 111 or (resid 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 114 or (resid 115 a \ nd (name N or name CA or name C or name O or name CB )) or resid 116 through 200 \ or (resid 201 and (name N or name CA or name C or name O or name CB )) or resid \ 202 through 211 or (resid 212 and (name N or name CA or name C or name O or nam \ e CB )) or resid 213 through 239 or (resid 240 and (name N or name CA or name C \ or name O or name CB )) or resid 241 through 248 or resid 253 through 256 or (re \ sid 257 through 258 and (name N or name CA or name C or name O or name CB )) or \ resid 259 through 281)) selection = (chain '6' and (resid 2 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 111 or (resid 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 114 or (resid 115 a \ nd (name N or name CA or name C or name O or name CB )) or resid 116 through 200 \ or (resid 201 and (name N or name CA or name C or name O or name CB )) or resid \ 202 through 211 or (resid 212 and (name N or name CA or name C or name O or nam \ e CB )) or resid 213 through 239 or (resid 240 and (name N or name CA or name C \ or name O or name CB )) or resid 241 through 281)) } ncs_group { reference = (chain 'A' and (resid 3 or resid 9 or resid 24 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 through 338 or (resi \ d 339 and (name N or name CA or name C or name O or name CB )) or resid 340 thro \ ugh 468 or (resid 469 and (name N or name CA or name C or name O or name CB )) o \ r resid 470 or (resid 471 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'B' and (resid 14 or resid 19 or resid 24 through 471)) selection = (chain 'C' and (resid 14 or resid 19 or resid 24 through 338 or (resid 339 and ( \ name N or name CA or name C or name O or name CB )) or resid 340 through 468 or \ (resid 469 and (name N or name CA or name C or name O or name CB )) or resid 470 \ or (resid 471 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 14 or resid 19 or resid 24 through 338 or (resid 339 and ( \ name N or name CA or name C or name O or name CB )) or resid 340 through 468 or \ (resid 469 and (name N or name CA or name C or name O or name CB )) or resid 470 \ or (resid 471 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 14 or resid 19 or resid 24 through 338 or (resid 339 and ( \ name N or name CA or name C or name O or name CB )) or resid 340 through 468 or \ (resid 469 and (name N or name CA or name C or name O or name CB )) or resid 470 \ or (resid 471 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'F' and (resid 14 or resid 19 or resid 24 through 338 or (resid 339 and ( \ name N or name CA or name C or name O or name CB )) or resid 340 through 468 or \ (resid 469 and (name N or name CA or name C or name O or name CB )) or resid 470 \ or (resid 471 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 14 or resid 19 or resid 24 through 338 or (resid 339 and ( \ name N or name CA or name C or name O or name CB )) or resid 340 through 468 or \ (resid 469 and (name N or name CA or name C or name O or name CB )) or resid 470 \ or (resid 471 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 14 or resid 19 or resid 24 through 338 or (resid 339 and ( \ name N or name CA or name C or name O or name CB )) or resid 340 through 468 or \ (resid 469 and (name N or name CA or name C or name O or name CB )) or resid 470 \ or (resid 471 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 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: 0.040 Extract box with map and model: 12.630 Check model and map are aligned: 0.750 Set scattering table: 0.450 Process input model: 124.080 Find NCS groups from input model: 4.180 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 : 0.008 0.415 50968 Z= 0.552 Angle : 1.333 10.728 69237 Z= 0.897 Chirality : 0.075 0.417 7574 Planarity : 0.004 0.057 8972 Dihedral : 15.600 179.689 18805 Min Nonbonded Distance : 1.507 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 1.00 % Allowed : 5.36 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.09), residues: 6183 helix: -1.42 (0.08), residues: 2506 sheet: 0.20 (0.16), residues: 909 loop : -1.54 (0.10), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 53 HIS 0.007 0.001 HIS 1 265 PHE 0.017 0.002 PHE A 346 TYR 0.015 0.002 TYR H 240 ARG 0.005 0.000 ARG 1 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1408 time to evaluate : 6.442 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: 1 62 SER cc_start: 0.7517 (t) cc_final: 0.7228 (p) REVERT: 1 76 ARG cc_start: 0.8288 (ttt-90) cc_final: 0.7673 (ttt180) REVERT: 1 87 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7440 (mt-10) REVERT: 1 149 ARG cc_start: 0.7838 (mmm-85) cc_final: 0.7527 (tpp80) REVERT: 2 128 MET cc_start: 0.6456 (mtm) cc_final: 0.6186 (mtp) REVERT: 3 257 LYS cc_start: 0.7178 (pttt) cc_final: 0.6175 (tppt) REVERT: 3 282 ASN cc_start: 0.4863 (m-40) cc_final: 0.4268 (p0) REVERT: 4 51 PHE cc_start: 0.4914 (m-10) cc_final: 0.4584 (m-80) REVERT: 4 213 GLN cc_start: 0.3918 (mm-40) cc_final: 0.3639 (mm110) REVERT: 4 258 LYS cc_start: 0.5231 (mmtt) cc_final: 0.4863 (tmmt) REVERT: 6 104 ASP cc_start: 0.6664 (t0) cc_final: 0.6413 (p0) REVERT: 6 164 TYR cc_start: 0.7382 (t80) cc_final: 0.6962 (t80) REVERT: 6 206 LEU cc_start: 0.7079 (tp) cc_final: 0.6753 (tt) REVERT: B 15 LYS cc_start: 0.7877 (tttt) cc_final: 0.7658 (ttpp) REVERT: C 27 THR cc_start: 0.8435 (p) cc_final: 0.8230 (t) REVERT: C 437 ASN cc_start: 0.7462 (t0) cc_final: 0.7114 (t0) REVERT: D 467 LYS cc_start: 0.8447 (tptt) cc_final: 0.8085 (mttp) REVERT: E 89 GLU cc_start: 0.7619 (tt0) cc_final: 0.7213 (tm-30) REVERT: E 437 ASN cc_start: 0.7382 (t0) cc_final: 0.7140 (t0) REVERT: E 447 ARG cc_start: 0.7412 (ttm110) cc_final: 0.7161 (mtm-85) REVERT: E 475 THR cc_start: 0.4942 (OUTLIER) cc_final: 0.4601 (p) REVERT: E 476 VAL cc_start: 0.2392 (OUTLIER) cc_final: 0.2109 (t) REVERT: F 47 PRO cc_start: 0.7604 (Cg_exo) cc_final: 0.7035 (Cg_endo) REVERT: F 73 ASP cc_start: 0.6722 (m-30) cc_final: 0.6470 (p0) REVERT: F 397 ASP cc_start: 0.7500 (m-30) cc_final: 0.7294 (m-30) REVERT: F 464 LYS cc_start: 0.7305 (tptt) cc_final: 0.6485 (ttmt) REVERT: F 466 ILE cc_start: 0.8015 (mm) cc_final: 0.7749 (mp) REVERT: F 475 THR cc_start: 0.5765 (OUTLIER) cc_final: 0.5389 (p) REVERT: F 476 VAL cc_start: 0.4647 (OUTLIER) cc_final: 0.4332 (m) REVERT: G 15 LYS cc_start: 0.8561 (tttt) cc_final: 0.8114 (mtmt) REVERT: G 22 ARG cc_start: 0.7665 (ttp-170) cc_final: 0.7378 (tpt90) REVERT: G 248 CYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6877 (m) REVERT: G 361 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7406 (mtt90) REVERT: G 443 ASN cc_start: 0.8033 (m110) cc_final: 0.7730 (m-40) REVERT: G 469 GLU cc_start: 0.6264 (mt-10) cc_final: 0.6018 (mp0) REVERT: G 475 THR cc_start: 0.6164 (OUTLIER) cc_final: 0.5140 (m) REVERT: H 81 TYR cc_start: 0.8787 (m-80) cc_final: 0.8476 (m-80) REVERT: H 303 ASP cc_start: 0.7740 (p0) cc_final: 0.7465 (t0) REVERT: H 441 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6874 (mp0) REVERT: I 57 LYS cc_start: 0.8252 (mtpp) cc_final: 0.7877 (mtpt) REVERT: I 72 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7838 (mm-30) REVERT: J 6 LYS cc_start: 0.8584 (mttt) cc_final: 0.8269 (mmtp) REVERT: J 93 ILE cc_start: 0.7946 (mt) cc_final: 0.7521 (mt) REVERT: J 94 LYS cc_start: 0.8477 (mmtt) cc_final: 0.8217 (mtmt) REVERT: O 65 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7279 (m) REVERT: P 7 GLU cc_start: 0.6782 (tt0) cc_final: 0.6162 (pm20) REVERT: P 79 GLN cc_start: 0.8552 (tp40) cc_final: 0.8270 (tp40) REVERT: P 93 ILE cc_start: 0.8847 (mt) cc_final: 0.8641 (mm) outliers start: 52 outliers final: 11 residues processed: 1448 average time/residue: 1.7860 time to fit residues: 3169.7961 Evaluate side-chains 627 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 609 time to evaluate : 6.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 271 ASN Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 6 residue 183 ASP Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain G residue 248 CYS Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain O residue 65 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 518 optimal weight: 3.9990 chunk 465 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 313 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 481 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 292 optimal weight: 4.9990 chunk 358 optimal weight: 6.9990 chunk 557 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 158 ASN 1 265 HIS 2 158 ASN 2 271 ASN 3 158 ASN ** 4 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 119 ASN 4 133 ASN 4 158 ASN 4 265 HIS 5 16 HIS 5 46 GLN 5 213 GLN 5 229 GLN 6 20 ASN 6 36 HIS 6 129 ASN 6 146 ASN 6 213 GLN 6 248 ASN A 116 ASN A 154 HIS A 157 GLN B 96 ASN B 154 HIS B 213 GLN B 421 ASN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS C 213 GLN D 46 GLN D 116 ASN D 154 HIS ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN E 154 HIS ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN F 154 HIS F 437 ASN G 97 GLN G 116 ASN G 154 HIS G 185 ASN G 213 GLN H 154 HIS H 213 GLN H 443 ASN I 27 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 GLN M 2 GLN M 97 GLN N 79 GLN O 95 GLN O 97 GLN P 95 GLN P 97 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 50968 Z= 0.326 Angle : 0.658 7.749 69237 Z= 0.345 Chirality : 0.046 0.216 7574 Planarity : 0.005 0.056 8972 Dihedral : 9.671 176.987 7120 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.96 % Allowed : 15.73 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: -0.52 (0.10), residues: 6183 helix: 0.46 (0.09), residues: 2553 sheet: 0.14 (0.17), residues: 874 loop : -1.23 (0.10), residues: 2756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 215 HIS 0.008 0.001 HIS 6 36 PHE 0.036 0.002 PHE A 346 TYR 0.017 0.002 TYR C 270 ARG 0.009 0.001 ARG 4 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 635 time to evaluate : 6.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 62 SER cc_start: 0.7595 (t) cc_final: 0.7321 (p) REVERT: 1 87 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7575 (mt-10) REVERT: 1 149 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7524 (mtt-85) REVERT: 1 205 GLN cc_start: 0.6824 (tp40) cc_final: 0.6584 (tp40) REVERT: 2 258 LYS cc_start: 0.5067 (OUTLIER) cc_final: 0.4787 (tptt) REVERT: 3 240 GLU cc_start: 0.4639 (OUTLIER) cc_final: 0.4294 (pm20) REVERT: 3 241 ARG cc_start: 0.5212 (OUTLIER) cc_final: 0.4204 (mpp80) REVERT: 4 38 ARG cc_start: 0.5113 (OUTLIER) cc_final: 0.4290 (mmp80) REVERT: 4 235 HIS cc_start: 0.6446 (OUTLIER) cc_final: 0.6016 (t70) REVERT: 6 73 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: 6 81 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7490 (mtt-85) REVERT: 6 87 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: 6 104 ASP cc_start: 0.6662 (t0) cc_final: 0.6385 (p0) REVERT: 6 226 TYR cc_start: 0.6545 (OUTLIER) cc_final: 0.6198 (t80) REVERT: 6 233 PHE cc_start: 0.7596 (t80) cc_final: 0.7091 (t80) REVERT: B 15 LYS cc_start: 0.7856 (tttt) cc_final: 0.7623 (ttpp) REVERT: B 303 ASP cc_start: 0.7620 (p0) cc_final: 0.7136 (t0) REVERT: B 466 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8013 (pp) REVERT: C 90 PRO cc_start: 0.7963 (Cg_endo) cc_final: 0.7717 (Cg_exo) REVERT: D 467 LYS cc_start: 0.8385 (tptt) cc_final: 0.8116 (mttp) REVERT: E 89 GLU cc_start: 0.7835 (tt0) cc_final: 0.7292 (tm-30) REVERT: E 118 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8667 (mp) REVERT: E 447 ARG cc_start: 0.7447 (ttm110) cc_final: 0.6960 (mtm-85) REVERT: F 47 PRO cc_start: 0.7672 (Cg_exo) cc_final: 0.7157 (Cg_endo) REVERT: F 73 ASP cc_start: 0.6745 (m-30) cc_final: 0.6459 (p0) REVERT: F 451 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7866 (pttp) REVERT: F 475 THR cc_start: 0.5801 (OUTLIER) cc_final: 0.5446 (p) REVERT: F 476 VAL cc_start: 0.4631 (OUTLIER) cc_final: 0.4185 (t) REVERT: G 15 LYS cc_start: 0.8546 (tttt) cc_final: 0.8055 (mtpt) REVERT: G 22 ARG cc_start: 0.7826 (ttp-170) cc_final: 0.7478 (tpt90) REVERT: G 128 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: G 157 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7499 (mm-40) REVERT: G 249 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: G 303 ASP cc_start: 0.7490 (p0) cc_final: 0.7203 (t0) REVERT: G 467 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6211 (mttp) REVERT: G 469 GLU cc_start: 0.6128 (mt-10) cc_final: 0.5905 (mp0) REVERT: H 157 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7551 (mm-40) REVERT: H 441 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6917 (mp0) REVERT: J 2 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7398 (mt0) REVERT: J 94 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8380 (mtmt) REVERT: L 20 THR cc_start: 0.7577 (OUTLIER) cc_final: 0.7169 (p) REVERT: L 21 ASP cc_start: 0.7821 (m-30) cc_final: 0.7515 (m-30) REVERT: M 79 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: N 51 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8485 (pp) REVERT: O 72 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7351 (tp30) REVERT: P 2 GLN cc_start: 0.6934 (mm-40) cc_final: 0.6686 (mt0) REVERT: P 9 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8392 (mpt90) REVERT: P 79 GLN cc_start: 0.8572 (tp40) cc_final: 0.8317 (tp40) outliers start: 258 outliers final: 93 residues processed: 832 average time/residue: 1.7414 time to fit residues: 1795.3732 Evaluate side-chains 628 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 511 time to evaluate : 6.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 91 VAL Chi-restraints excluded: chain 1 residue 98 LEU Chi-restraints excluded: chain 1 residue 146 ASN Chi-restraints excluded: chain 1 residue 225 ILE Chi-restraints excluded: chain 1 residue 227 ASP Chi-restraints excluded: chain 1 residue 239 PHE Chi-restraints excluded: chain 2 residue 2 SER Chi-restraints excluded: chain 2 residue 24 ILE Chi-restraints excluded: chain 2 residue 258 LYS Chi-restraints excluded: chain 3 residue 48 GLU Chi-restraints excluded: chain 3 residue 62 SER Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 3 residue 97 VAL Chi-restraints excluded: chain 3 residue 115 GLN Chi-restraints excluded: chain 3 residue 118 VAL Chi-restraints excluded: chain 3 residue 129 ASN Chi-restraints excluded: chain 3 residue 155 VAL Chi-restraints excluded: chain 3 residue 240 GLU Chi-restraints excluded: chain 3 residue 241 ARG Chi-restraints excluded: chain 3 residue 265 HIS Chi-restraints excluded: chain 4 residue 2 SER Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 60 LEU Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 4 residue 104 ASP Chi-restraints excluded: chain 4 residue 150 ARG Chi-restraints excluded: chain 4 residue 155 VAL Chi-restraints excluded: chain 4 residue 161 SER Chi-restraints excluded: chain 4 residue 235 HIS Chi-restraints excluded: chain 5 residue 44 THR Chi-restraints excluded: chain 5 residue 54 MET Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 5 residue 267 ILE Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 62 SER Chi-restraints excluded: chain 6 residue 73 ASP Chi-restraints excluded: chain 6 residue 81 ARG Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 226 TYR Chi-restraints excluded: chain 6 residue 231 ARG Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 464 LYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 157 GLN Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 157 GLN Chi-restraints excluded: chain H residue 376 MET Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 2 GLN Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain P residue 9 ARG Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 78 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 309 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 464 optimal weight: 4.9990 chunk 379 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 558 optimal weight: 0.7980 chunk 603 optimal weight: 0.5980 chunk 497 optimal weight: 8.9990 chunk 553 optimal weight: 4.9990 chunk 190 optimal weight: 0.5980 chunk 448 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 16 HIS 1 248 ASN ** 2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 36 HIS ** 3 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 115 GLN 4 133 ASN 4 213 GLN 4 277 GLN 5 46 GLN 5 138 GLN 6 36 HIS ** 6 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN B 307 ASN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN F 414 ASN G 97 GLN G 208 ASN I 27 GLN K 95 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 50968 Z= 0.204 Angle : 0.549 12.517 69237 Z= 0.283 Chirality : 0.042 0.184 7574 Planarity : 0.004 0.059 8972 Dihedral : 8.851 179.186 7103 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.48 % Allowed : 17.61 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 0.04 (0.10), residues: 6183 helix: 1.12 (0.10), residues: 2566 sheet: 0.57 (0.18), residues: 747 loop : -1.14 (0.10), residues: 2870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 215 HIS 0.011 0.001 HIS 6 235 PHE 0.032 0.002 PHE B 346 TYR 0.016 0.001 TYR 6 164 ARG 0.011 0.001 ARG O 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 593 time to evaluate : 5.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 84 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7428 (mm-30) REVERT: 1 87 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7601 (mt-10) REVERT: 1 149 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7385 (mtt-85) REVERT: 1 245 ARG cc_start: 0.4942 (OUTLIER) cc_final: 0.3493 (ptm-80) REVERT: 2 258 LYS cc_start: 0.5176 (OUTLIER) cc_final: 0.4776 (tptm) REVERT: 3 213 GLN cc_start: 0.5409 (mm-40) cc_final: 0.5160 (mm-40) REVERT: 3 236 LYS cc_start: 0.6534 (pptt) cc_final: 0.5967 (mmpt) REVERT: 4 38 ARG cc_start: 0.5199 (OUTLIER) cc_final: 0.4404 (mmp80) REVERT: 4 44 THR cc_start: 0.5117 (OUTLIER) cc_final: 0.3784 (t) REVERT: 4 150 ARG cc_start: 0.5828 (OUTLIER) cc_final: 0.5395 (ttt180) REVERT: 4 235 HIS cc_start: 0.6236 (OUTLIER) cc_final: 0.5865 (t70) REVERT: 5 279 ARG cc_start: 0.6069 (tpp-160) cc_final: 0.5524 (tmm160) REVERT: 6 53 LYS cc_start: 0.8385 (tptm) cc_final: 0.8177 (tttp) REVERT: 6 73 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7269 (m-30) REVERT: 6 81 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7404 (mtt-85) REVERT: 6 104 ASP cc_start: 0.6701 (t0) cc_final: 0.6426 (p0) REVERT: 6 226 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.6202 (t80) REVERT: 6 233 PHE cc_start: 0.7622 (t80) cc_final: 0.7199 (t80) REVERT: A 89 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: B 15 LYS cc_start: 0.7894 (tttt) cc_final: 0.7653 (ttpp) REVERT: B 140 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.6739 (tmm160) REVERT: B 303 ASP cc_start: 0.7638 (p0) cc_final: 0.7283 (t0) REVERT: B 466 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8384 (pp) REVERT: C 90 PRO cc_start: 0.8036 (Cg_endo) cc_final: 0.7813 (Cg_exo) REVERT: C 448 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: D 120 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8465 (m) REVERT: D 352 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8070 (mt-10) REVERT: D 371 SER cc_start: 0.8065 (m) cc_final: 0.7700 (t) REVERT: D 444 ASP cc_start: 0.7703 (t0) cc_final: 0.7467 (t0) REVERT: E 89 GLU cc_start: 0.7916 (tt0) cc_final: 0.7354 (tm-30) REVERT: E 447 ARG cc_start: 0.7383 (ttm110) cc_final: 0.6873 (mtm-85) REVERT: F 19 GLN cc_start: 0.6966 (tt0) cc_final: 0.6605 (tt0) REVERT: F 73 ASP cc_start: 0.6700 (m-30) cc_final: 0.6438 (p0) REVERT: F 451 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7838 (pttp) REVERT: F 475 THR cc_start: 0.5997 (OUTLIER) cc_final: 0.5703 (p) REVERT: G 15 LYS cc_start: 0.8525 (tttt) cc_final: 0.8021 (mtpt) REVERT: G 22 ARG cc_start: 0.7935 (ttp-170) cc_final: 0.7516 (tpt90) REVERT: G 249 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7130 (mt-10) REVERT: G 303 ASP cc_start: 0.7359 (p0) cc_final: 0.7130 (t0) REVERT: G 361 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7383 (mtt180) REVERT: G 467 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6305 (mttp) REVERT: G 469 GLU cc_start: 0.6083 (mt-10) cc_final: 0.5864 (mp0) REVERT: H 441 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6844 (mp0) REVERT: J 2 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: J 25 GLU cc_start: 0.7639 (tp30) cc_final: 0.7066 (tp30) REVERT: J 94 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8398 (mtmt) REVERT: L 49 THR cc_start: 0.8570 (m) cc_final: 0.8336 (p) REVERT: M 79 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: M 92 ASN cc_start: 0.7460 (t0) cc_final: 0.7247 (t0) REVERT: N 51 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8549 (pp) REVERT: O 72 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7316 (tp30) REVERT: P 2 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6777 (mt0) REVERT: P 51 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8422 (pp) REVERT: P 79 GLN cc_start: 0.8460 (tp40) cc_final: 0.8253 (tp40) outliers start: 233 outliers final: 93 residues processed: 762 average time/residue: 1.7604 time to fit residues: 1660.1098 Evaluate side-chains 626 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 511 time to evaluate : 6.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 98 LEU Chi-restraints excluded: chain 1 residue 117 THR Chi-restraints excluded: chain 1 residue 225 ILE Chi-restraints excluded: chain 1 residue 227 ASP Chi-restraints excluded: chain 1 residue 245 ARG Chi-restraints excluded: chain 2 residue 2 SER Chi-restraints excluded: chain 2 residue 39 LYS Chi-restraints excluded: chain 2 residue 234 ILE Chi-restraints excluded: chain 2 residue 258 LYS Chi-restraints excluded: chain 3 residue 62 SER Chi-restraints excluded: chain 3 residue 76 ARG Chi-restraints excluded: chain 3 residue 97 VAL Chi-restraints excluded: chain 3 residue 118 VAL Chi-restraints excluded: chain 3 residue 129 ASN Chi-restraints excluded: chain 3 residue 155 VAL Chi-restraints excluded: chain 3 residue 189 VAL Chi-restraints excluded: chain 3 residue 192 ILE Chi-restraints excluded: chain 3 residue 265 HIS Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 60 LEU Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 4 residue 104 ASP Chi-restraints excluded: chain 4 residue 150 ARG Chi-restraints excluded: chain 4 residue 155 VAL Chi-restraints excluded: chain 4 residue 170 ASP Chi-restraints excluded: chain 4 residue 235 HIS Chi-restraints excluded: chain 5 residue 54 MET Chi-restraints excluded: chain 5 residue 135 THR Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 73 ASP Chi-restraints excluded: chain 6 residue 81 ARG Chi-restraints excluded: chain 6 residue 167 LEU Chi-restraints excluded: chain 6 residue 175 LYS Chi-restraints excluded: chain 6 residue 226 TYR Chi-restraints excluded: chain 6 residue 231 ARG Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain G residue 376 MET Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 337 GLU Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 2 GLN Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 68 GLU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 65 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 551 optimal weight: 5.9990 chunk 419 optimal weight: 0.3980 chunk 289 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 266 optimal weight: 0.0570 chunk 375 optimal weight: 3.9990 chunk 560 optimal weight: 0.9980 chunk 593 optimal weight: 2.9990 chunk 292 optimal weight: 0.0020 chunk 531 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 overall best weight: 0.4306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 200 GLN 1 205 GLN ** 1 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 133 ASN 4 158 ASN 4 213 GLN 4 277 GLN 5 46 GLN 5 138 GLN 6 36 HIS ** 6 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 129 ASN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN F 414 ASN F 421 ASN F 437 ASN ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN H 308 HIS I 27 GLN J 29 GLN K 74 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 50968 Z= 0.132 Angle : 0.499 9.816 69237 Z= 0.253 Chirality : 0.040 0.164 7574 Planarity : 0.004 0.058 8972 Dihedral : 8.453 176.871 7100 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.65 % Allowed : 19.30 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.10), residues: 6183 helix: 1.59 (0.10), residues: 2523 sheet: 0.77 (0.18), residues: 819 loop : -1.01 (0.10), residues: 2841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 215 HIS 0.009 0.001 HIS 5 16 PHE 0.030 0.001 PHE B 346 TYR 0.022 0.001 TYR 6 164 ARG 0.005 0.000 ARG I 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 583 time to evaluate : 7.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 84 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7501 (mm-30) REVERT: 1 87 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7667 (mt-10) REVERT: 1 149 ARG cc_start: 0.7712 (mmm-85) cc_final: 0.7403 (mtt-85) REVERT: 1 205 GLN cc_start: 0.7300 (tp40) cc_final: 0.7072 (tp-100) REVERT: 1 245 ARG cc_start: 0.4901 (OUTLIER) cc_final: 0.3392 (ptm-80) REVERT: 2 241 ARG cc_start: 0.5095 (OUTLIER) cc_final: 0.4287 (ptp90) REVERT: 2 258 LYS cc_start: 0.5267 (OUTLIER) cc_final: 0.4813 (tptm) REVERT: 3 213 GLN cc_start: 0.5578 (mm-40) cc_final: 0.5139 (mm-40) REVERT: 3 236 LYS cc_start: 0.6425 (pptt) cc_final: 0.5926 (mmpt) REVERT: 3 267 ILE cc_start: 0.5205 (mp) cc_final: 0.4919 (tp) REVERT: 4 150 ARG cc_start: 0.5866 (OUTLIER) cc_final: 0.3988 (mtt180) REVERT: 6 44 THR cc_start: 0.8120 (m) cc_final: 0.7793 (p) REVERT: 6 73 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: 6 81 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7378 (mtm-85) REVERT: 6 226 TYR cc_start: 0.6533 (OUTLIER) cc_final: 0.6090 (t80) REVERT: 6 233 PHE cc_start: 0.7691 (t80) cc_final: 0.7251 (t80) REVERT: A 108 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8549 (tt) REVERT: B 15 LYS cc_start: 0.7899 (tttt) cc_final: 0.7646 (ttpp) REVERT: B 140 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.6632 (tmm160) REVERT: B 303 ASP cc_start: 0.7650 (p0) cc_final: 0.7321 (t0) REVERT: C 448 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: D 120 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8585 (m) REVERT: D 352 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8028 (mt-10) REVERT: D 371 SER cc_start: 0.8108 (m) cc_final: 0.7751 (t) REVERT: D 444 ASP cc_start: 0.7652 (t0) cc_final: 0.7280 (t0) REVERT: D 467 LYS cc_start: 0.8319 (tptt) cc_final: 0.7904 (mttp) REVERT: E 89 GLU cc_start: 0.7767 (tt0) cc_final: 0.7287 (tm-30) REVERT: E 447 ARG cc_start: 0.7375 (ttm110) cc_final: 0.6876 (mtm-85) REVERT: F 19 GLN cc_start: 0.6857 (tt0) cc_final: 0.6513 (tt0) REVERT: F 73 ASP cc_start: 0.6685 (m-30) cc_final: 0.6453 (p0) REVERT: F 132 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7605 (ptm160) REVERT: F 437 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7951 (t0) REVERT: G 15 LYS cc_start: 0.8521 (tttt) cc_final: 0.8028 (mtpt) REVERT: G 249 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: G 303 ASP cc_start: 0.7439 (p0) cc_final: 0.7212 (t0) REVERT: G 467 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6339 (mttp) REVERT: G 469 GLU cc_start: 0.6119 (mt-10) cc_final: 0.5894 (mp0) REVERT: H 53 GLU cc_start: 0.7362 (tp30) cc_final: 0.7124 (tm-30) REVERT: H 441 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6852 (mp0) REVERT: J 94 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8362 (mtmt) REVERT: J 99 LEU cc_start: 0.7816 (mm) cc_final: 0.7318 (tp) REVERT: L 20 THR cc_start: 0.7450 (OUTLIER) cc_final: 0.7183 (p) REVERT: L 49 THR cc_start: 0.8605 (m) cc_final: 0.8403 (p) REVERT: N 51 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8547 (pp) REVERT: P 2 GLN cc_start: 0.7019 (mm-40) cc_final: 0.6762 (mt0) REVERT: P 51 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8387 (pp) REVERT: P 79 GLN cc_start: 0.8438 (tp40) cc_final: 0.8212 (tp40) outliers start: 190 outliers final: 83 residues processed: 721 average time/residue: 1.7234 time to fit residues: 1533.8024 Evaluate side-chains 608 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 507 time to evaluate : 5.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 62 SER Chi-restraints excluded: chain 1 residue 98 LEU Chi-restraints excluded: chain 1 residue 117 THR Chi-restraints excluded: chain 1 residue 146 ASN Chi-restraints excluded: chain 1 residue 225 ILE Chi-restraints excluded: chain 1 residue 239 PHE Chi-restraints excluded: chain 1 residue 245 ARG Chi-restraints excluded: chain 2 residue 234 ILE Chi-restraints excluded: chain 2 residue 235 HIS Chi-restraints excluded: chain 2 residue 241 ARG Chi-restraints excluded: chain 2 residue 258 LYS Chi-restraints excluded: chain 3 residue 62 SER Chi-restraints excluded: chain 3 residue 76 ARG Chi-restraints excluded: chain 3 residue 97 VAL Chi-restraints excluded: chain 3 residue 118 VAL Chi-restraints excluded: chain 3 residue 127 LEU Chi-restraints excluded: chain 3 residue 129 ASN Chi-restraints excluded: chain 3 residue 155 VAL Chi-restraints excluded: chain 3 residue 265 HIS Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 4 residue 104 ASP Chi-restraints excluded: chain 4 residue 121 GLN Chi-restraints excluded: chain 4 residue 150 ARG Chi-restraints excluded: chain 4 residue 155 VAL Chi-restraints excluded: chain 5 residue 54 MET Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 73 ASP Chi-restraints excluded: chain 6 residue 81 ARG Chi-restraints excluded: chain 6 residue 167 LEU Chi-restraints excluded: chain 6 residue 196 ASP Chi-restraints excluded: chain 6 residue 226 TYR Chi-restraints excluded: chain 6 residue 231 ARG Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 376 MET Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 337 GLU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain P residue 50 GLU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 65 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 494 optimal weight: 0.9980 chunk 336 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 441 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 506 optimal weight: 7.9990 chunk 410 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 303 optimal weight: 9.9990 chunk 532 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 200 GLN ** 1 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 133 ASN 4 213 GLN 5 46 GLN 5 129 ASN 5 138 GLN 6 36 HIS ** 6 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 229 GLN B 208 ASN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN I 27 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 104 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 50968 Z= 0.358 Angle : 0.644 14.717 69237 Z= 0.330 Chirality : 0.046 0.202 7574 Planarity : 0.005 0.057 8972 Dihedral : 8.591 174.676 7099 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.22 % Favored : 96.77 % Rotamer: Outliers : 5.11 % Allowed : 18.57 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 0.13 (0.10), residues: 6183 helix: 1.26 (0.10), residues: 2563 sheet: 0.62 (0.18), residues: 730 loop : -1.15 (0.10), residues: 2890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 215 HIS 0.013 0.002 HIS 5 16 PHE 0.032 0.002 PHE B 346 TYR 0.026 0.002 TYR 6 164 ARG 0.014 0.001 ARG O 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 522 time to evaluate : 5.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 149 ARG cc_start: 0.7803 (mmm-85) cc_final: 0.7388 (mtt-85) REVERT: 1 185 LYS cc_start: 0.7193 (mtmm) cc_final: 0.6935 (pttt) REVERT: 1 245 ARG cc_start: 0.5072 (OUTLIER) cc_final: 0.3736 (ptm-80) REVERT: 2 138 GLN cc_start: 0.7762 (pt0) cc_final: 0.7538 (pm20) REVERT: 2 241 ARG cc_start: 0.5123 (OUTLIER) cc_final: 0.3985 (ppp80) REVERT: 2 258 LYS cc_start: 0.5172 (OUTLIER) cc_final: 0.4764 (tptm) REVERT: 3 213 GLN cc_start: 0.5721 (mm-40) cc_final: 0.5422 (mm-40) REVERT: 3 236 LYS cc_start: 0.6472 (pptt) cc_final: 0.5921 (mmpt) REVERT: 3 257 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.5918 (pmtt) REVERT: 4 38 ARG cc_start: 0.5093 (OUTLIER) cc_final: 0.4305 (mmp80) REVERT: 4 150 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.5397 (ttt180) REVERT: 4 235 HIS cc_start: 0.6348 (OUTLIER) cc_final: 0.5955 (t70) REVERT: 6 62 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7834 (p) REVERT: 6 73 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7294 (m-30) REVERT: 6 87 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: 6 109 ARG cc_start: 0.5712 (OUTLIER) cc_final: 0.4999 (mtt90) REVERT: 6 226 TYR cc_start: 0.6684 (OUTLIER) cc_final: 0.6171 (t80) REVERT: 6 228 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.7088 (pt) REVERT: 6 233 PHE cc_start: 0.7862 (t80) cc_final: 0.7437 (t80) REVERT: A 89 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7413 (mm-30) REVERT: B 15 LYS cc_start: 0.8016 (tttt) cc_final: 0.7706 (ttpp) REVERT: B 303 ASP cc_start: 0.7829 (p0) cc_final: 0.7476 (t0) REVERT: C 121 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.8978 (mp) REVERT: C 132 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8026 (mtp180) REVERT: C 448 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: C 451 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8162 (mtpp) REVERT: D 120 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8507 (m) REVERT: D 361 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7150 (mtt180) REVERT: D 444 ASP cc_start: 0.7725 (t0) cc_final: 0.7364 (t0) REVERT: D 451 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7970 (mtpt) REVERT: E 89 GLU cc_start: 0.8006 (tt0) cc_final: 0.7434 (tm-30) REVERT: F 73 ASP cc_start: 0.6717 (m-30) cc_final: 0.6451 (p0) REVERT: F 132 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7594 (ptm160) REVERT: F 451 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7858 (pttp) REVERT: F 475 THR cc_start: 0.6182 (OUTLIER) cc_final: 0.5908 (p) REVERT: G 15 LYS cc_start: 0.8521 (tttt) cc_final: 0.8044 (mtpt) REVERT: G 249 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: G 467 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.6255 (mttp) REVERT: G 469 GLU cc_start: 0.6149 (mt-10) cc_final: 0.5848 (mp0) REVERT: H 15 LYS cc_start: 0.7765 (tptm) cc_final: 0.7255 (mmtt) REVERT: H 376 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8104 (mtt) REVERT: H 441 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6746 (mp0) REVERT: J 29 GLN cc_start: 0.8667 (tp-100) cc_final: 0.8412 (tp-100) REVERT: J 94 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8191 (mtmt) REVERT: K 41 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: L 20 THR cc_start: 0.7534 (OUTLIER) cc_final: 0.7135 (p) REVERT: L 49 THR cc_start: 0.8647 (m) cc_final: 0.8445 (p) REVERT: M 3 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8476 (t) REVERT: M 11 GLU cc_start: 0.7583 (mp0) cc_final: 0.7036 (mp0) REVERT: M 79 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8085 (tm-30) REVERT: N 51 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8608 (pp) REVERT: N 92 ASN cc_start: 0.8134 (p0) cc_final: 0.7722 (p0) REVERT: O 92 ASN cc_start: 0.8395 (p0) cc_final: 0.8139 (p0) REVERT: P 2 GLN cc_start: 0.7181 (mm-40) cc_final: 0.6933 (mt0) REVERT: P 51 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8485 (pp) REVERT: P 79 GLN cc_start: 0.8535 (tp40) cc_final: 0.8295 (tp40) outliers start: 266 outliers final: 112 residues processed: 725 average time/residue: 1.7466 time to fit residues: 1570.0115 Evaluate side-chains 615 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 471 time to evaluate : 5.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 62 SER Chi-restraints excluded: chain 1 residue 114 THR Chi-restraints excluded: chain 1 residue 117 THR Chi-restraints excluded: chain 1 residue 146 ASN Chi-restraints excluded: chain 1 residue 227 ASP Chi-restraints excluded: chain 1 residue 245 ARG Chi-restraints excluded: chain 2 residue 2 SER Chi-restraints excluded: chain 2 residue 234 ILE Chi-restraints excluded: chain 2 residue 235 HIS Chi-restraints excluded: chain 2 residue 241 ARG Chi-restraints excluded: chain 2 residue 258 LYS Chi-restraints excluded: chain 3 residue 62 SER Chi-restraints excluded: chain 3 residue 118 VAL Chi-restraints excluded: chain 3 residue 127 LEU Chi-restraints excluded: chain 3 residue 129 ASN Chi-restraints excluded: chain 3 residue 155 VAL Chi-restraints excluded: chain 3 residue 189 VAL Chi-restraints excluded: chain 3 residue 257 LYS Chi-restraints excluded: chain 3 residue 265 HIS Chi-restraints excluded: chain 4 residue 2 SER Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 49 LEU Chi-restraints excluded: chain 4 residue 85 THR Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 4 residue 104 ASP Chi-restraints excluded: chain 4 residue 133 ASN Chi-restraints excluded: chain 4 residue 150 ARG Chi-restraints excluded: chain 4 residue 155 VAL Chi-restraints excluded: chain 4 residue 161 SER Chi-restraints excluded: chain 4 residue 196 ASP Chi-restraints excluded: chain 4 residue 202 GLU Chi-restraints excluded: chain 4 residue 235 HIS Chi-restraints excluded: chain 5 residue 54 MET Chi-restraints excluded: chain 5 residue 117 THR Chi-restraints excluded: chain 5 residue 135 THR Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 62 SER Chi-restraints excluded: chain 6 residue 73 ASP Chi-restraints excluded: chain 6 residue 81 ARG Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 109 ARG Chi-restraints excluded: chain 6 residue 167 LEU Chi-restraints excluded: chain 6 residue 175 LYS Chi-restraints excluded: chain 6 residue 196 ASP Chi-restraints excluded: chain 6 residue 226 TYR Chi-restraints excluded: chain 6 residue 228 ILE Chi-restraints excluded: chain 6 residue 231 ARG Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 464 LYS Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain H residue 376 MET Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain P residue 50 GLU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 78 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 199 optimal weight: 0.5980 chunk 534 optimal weight: 10.0000 chunk 117 optimal weight: 0.0470 chunk 348 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 594 optimal weight: 6.9990 chunk 493 optimal weight: 10.0000 chunk 275 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 overall best weight: 2.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 200 GLN 1 248 ASN 2 23 ASN ** 2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 133 ASN 4 213 GLN 5 46 GLN 5 138 GLN 6 36 HIS ** 6 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 GLN ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 50968 Z= 0.257 Angle : 0.569 12.834 69237 Z= 0.291 Chirality : 0.043 0.185 7574 Planarity : 0.004 0.059 8972 Dihedral : 8.312 174.589 7099 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.63 % Allowed : 19.90 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 0.26 (0.10), residues: 6183 helix: 1.36 (0.10), residues: 2561 sheet: 0.69 (0.18), residues: 787 loop : -1.11 (0.10), residues: 2835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 4 178 HIS 0.011 0.001 HIS 5 16 PHE 0.033 0.002 PHE B 346 TYR 0.022 0.001 TYR 6 164 ARG 0.009 0.000 ARG 6 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 511 time to evaluate : 6.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 84 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7789 (mm-30) REVERT: 1 129 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7926 (t0) REVERT: 1 149 ARG cc_start: 0.7730 (mmm-85) cc_final: 0.7333 (mtt-85) REVERT: 1 236 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.5816 (mppt) REVERT: 2 19 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7691 (mtmt) REVERT: 2 138 GLN cc_start: 0.7821 (pt0) cc_final: 0.7514 (pm20) REVERT: 2 241 ARG cc_start: 0.5118 (OUTLIER) cc_final: 0.3858 (ppp80) REVERT: 2 258 LYS cc_start: 0.5279 (OUTLIER) cc_final: 0.4577 (tptt) REVERT: 3 213 GLN cc_start: 0.5694 (mm-40) cc_final: 0.5390 (mm-40) REVERT: 3 236 LYS cc_start: 0.6388 (pptt) cc_final: 0.5894 (mmpt) REVERT: 3 257 LYS cc_start: 0.6252 (OUTLIER) cc_final: 0.5969 (pmtt) REVERT: 3 267 ILE cc_start: 0.5149 (mp) cc_final: 0.4827 (tp) REVERT: 4 38 ARG cc_start: 0.5121 (OUTLIER) cc_final: 0.4313 (mmp80) REVERT: 4 54 MET cc_start: 0.5102 (mpt) cc_final: 0.4877 (mpt) REVERT: 4 150 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.5530 (ttt180) REVERT: 4 235 HIS cc_start: 0.6306 (OUTLIER) cc_final: 0.5942 (t70) REVERT: 5 128 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.7081 (ttp) REVERT: 6 12 LYS cc_start: 0.7570 (mmmm) cc_final: 0.7234 (tptt) REVERT: 6 73 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: 6 81 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7432 (mtt-85) REVERT: 6 87 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: 6 226 TYR cc_start: 0.6655 (OUTLIER) cc_final: 0.6133 (t80) REVERT: A 89 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: A 108 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8639 (tt) REVERT: B 15 LYS cc_start: 0.8048 (tttt) cc_final: 0.7840 (tttm) REVERT: B 303 ASP cc_start: 0.7851 (p0) cc_final: 0.7639 (t0) REVERT: B 464 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8653 (tppp) REVERT: C 121 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.8975 (mp) REVERT: C 132 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8040 (mtp180) REVERT: C 448 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: C 451 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8149 (mtpp) REVERT: D 120 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8546 (m) REVERT: D 444 ASP cc_start: 0.7756 (t0) cc_final: 0.7365 (t0) REVERT: D 451 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7945 (mtpt) REVERT: E 15 LYS cc_start: 0.8622 (tttt) cc_final: 0.7996 (tptp) REVERT: E 89 GLU cc_start: 0.7935 (tt0) cc_final: 0.7380 (tm-30) REVERT: E 447 ARG cc_start: 0.7393 (ttm110) cc_final: 0.6821 (mtm-85) REVERT: F 73 ASP cc_start: 0.6722 (m-30) cc_final: 0.6492 (p0) REVERT: F 451 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7866 (pttp) REVERT: F 475 THR cc_start: 0.6156 (OUTLIER) cc_final: 0.5937 (p) REVERT: G 15 LYS cc_start: 0.8503 (tttt) cc_final: 0.8030 (mtpt) REVERT: G 22 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7337 (ttm170) REVERT: G 249 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: G 467 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6275 (mttp) REVERT: H 15 LYS cc_start: 0.7791 (tptm) cc_final: 0.7229 (mmtt) REVERT: H 250 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7864 (mm-30) REVERT: H 303 ASP cc_start: 0.8249 (p0) cc_final: 0.7489 (t0) REVERT: H 441 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6753 (mp0) REVERT: I 98 ILE cc_start: 0.8671 (mm) cc_final: 0.8386 (pp) REVERT: J 2 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7465 (mt0) REVERT: J 29 GLN cc_start: 0.8648 (tp-100) cc_final: 0.8421 (tp-100) REVERT: J 94 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8523 (mtmt) REVERT: K 41 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: L 20 THR cc_start: 0.7532 (OUTLIER) cc_final: 0.7250 (p) REVERT: M 11 GLU cc_start: 0.7710 (mp0) cc_final: 0.7074 (mp0) REVERT: M 79 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: N 51 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8599 (pp) REVERT: N 57 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7937 (mtmt) REVERT: P 2 GLN cc_start: 0.7246 (mm-40) cc_final: 0.7027 (mt0) REVERT: P 79 GLN cc_start: 0.8502 (tp40) cc_final: 0.8284 (tp40) outliers start: 241 outliers final: 111 residues processed: 686 average time/residue: 1.7692 time to fit residues: 1493.9382 Evaluate side-chains 613 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 468 time to evaluate : 6.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 62 SER Chi-restraints excluded: chain 1 residue 117 THR Chi-restraints excluded: chain 1 residue 129 ASN Chi-restraints excluded: chain 1 residue 146 ASN Chi-restraints excluded: chain 1 residue 227 ASP Chi-restraints excluded: chain 1 residue 236 LYS Chi-restraints excluded: chain 1 residue 237 VAL Chi-restraints excluded: chain 2 residue 2 SER Chi-restraints excluded: chain 2 residue 19 LYS Chi-restraints excluded: chain 2 residue 68 SER Chi-restraints excluded: chain 2 residue 234 ILE Chi-restraints excluded: chain 2 residue 241 ARG Chi-restraints excluded: chain 2 residue 244 LEU Chi-restraints excluded: chain 2 residue 258 LYS Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain 3 residue 62 SER Chi-restraints excluded: chain 3 residue 97 VAL Chi-restraints excluded: chain 3 residue 118 VAL Chi-restraints excluded: chain 3 residue 127 LEU Chi-restraints excluded: chain 3 residue 129 ASN Chi-restraints excluded: chain 3 residue 144 ASP Chi-restraints excluded: chain 3 residue 155 VAL Chi-restraints excluded: chain 3 residue 188 ILE Chi-restraints excluded: chain 3 residue 257 LYS Chi-restraints excluded: chain 3 residue 265 HIS Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 85 THR Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 4 residue 99 MET Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 4 residue 104 ASP Chi-restraints excluded: chain 4 residue 150 ARG Chi-restraints excluded: chain 4 residue 155 VAL Chi-restraints excluded: chain 4 residue 170 ASP Chi-restraints excluded: chain 4 residue 196 ASP Chi-restraints excluded: chain 4 residue 235 HIS Chi-restraints excluded: chain 5 residue 54 MET Chi-restraints excluded: chain 5 residue 117 THR Chi-restraints excluded: chain 5 residue 128 MET Chi-restraints excluded: chain 5 residue 135 THR Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 73 ASP Chi-restraints excluded: chain 6 residue 81 ARG Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 167 LEU Chi-restraints excluded: chain 6 residue 226 TYR Chi-restraints excluded: chain 6 residue 231 ARG Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 446 ILE Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 22 ARG Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 250 GLU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 2 GLN Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain P residue 50 GLU Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 78 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 572 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 338 optimal weight: 6.9990 chunk 433 optimal weight: 6.9990 chunk 336 optimal weight: 0.2980 chunk 500 optimal weight: 0.0980 chunk 331 optimal weight: 2.9990 chunk 591 optimal weight: 6.9990 chunk 370 optimal weight: 0.9990 chunk 360 optimal weight: 0.9990 chunk 273 optimal weight: 0.0980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 200 GLN 1 248 ASN 2 115 GLN ** 3 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 213 GLN 4 265 HIS 5 46 GLN 5 138 GLN 6 16 HIS 6 36 HIS 6 124 ASN ** 6 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN F 116 ASN F 268 HIS F 414 ASN ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN L 74 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 50968 Z= 0.139 Angle : 0.506 11.186 69237 Z= 0.256 Chirality : 0.040 0.165 7574 Planarity : 0.004 0.059 8972 Dihedral : 7.765 171.267 7098 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.10 % Allowed : 21.77 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 0.63 (0.10), residues: 6183 helix: 1.70 (0.10), residues: 2545 sheet: 0.95 (0.18), residues: 804 loop : -0.96 (0.10), residues: 2834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 4 178 HIS 0.011 0.001 HIS 5 16 PHE 0.030 0.001 PHE A 346 TYR 0.024 0.001 TYR 6 164 ARG 0.013 0.000 ARG O 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 530 time to evaluate : 5.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 53 LYS cc_start: 0.7209 (mtmt) cc_final: 0.6139 (tttm) REVERT: 1 57 GLU cc_start: 0.7722 (mp0) cc_final: 0.7441 (mp0) REVERT: 1 84 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7785 (mm-30) REVERT: 1 149 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.7153 (mtp-110) REVERT: 1 236 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.5772 (mppt) REVERT: 2 138 GLN cc_start: 0.7701 (pt0) cc_final: 0.7462 (pm20) REVERT: 2 241 ARG cc_start: 0.5034 (OUTLIER) cc_final: 0.3879 (ptp90) REVERT: 3 213 GLN cc_start: 0.5729 (mm-40) cc_final: 0.5406 (mm-40) REVERT: 3 236 LYS cc_start: 0.6432 (pptt) cc_final: 0.6030 (mmpt) REVERT: 3 257 LYS cc_start: 0.6239 (OUTLIER) cc_final: 0.5968 (pmtt) REVERT: 3 267 ILE cc_start: 0.5157 (mp) cc_final: 0.4846 (tp) REVERT: 4 38 ARG cc_start: 0.4871 (OUTLIER) cc_final: 0.4151 (mmp80) REVERT: 4 150 ARG cc_start: 0.5896 (OUTLIER) cc_final: 0.5536 (ttt180) REVERT: 4 235 HIS cc_start: 0.6232 (OUTLIER) cc_final: 0.5916 (t70) REVERT: 6 5 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7654 (tp) REVERT: 6 12 LYS cc_start: 0.7555 (mmmm) cc_final: 0.7206 (tptt) REVERT: 6 73 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7240 (m-30) REVERT: 6 81 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7413 (mtm-85) REVERT: 6 226 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.6414 (t80) REVERT: B 15 LYS cc_start: 0.8008 (tttt) cc_final: 0.7793 (tttm) REVERT: B 464 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8220 (tppp) REVERT: C 132 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8008 (mtp180) REVERT: D 120 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8569 (m) REVERT: D 352 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8023 (mt-10) REVERT: D 444 ASP cc_start: 0.7707 (t0) cc_final: 0.7321 (t0) REVERT: E 15 LYS cc_start: 0.8610 (tttt) cc_final: 0.7980 (tptp) REVERT: E 89 GLU cc_start: 0.7853 (tt0) cc_final: 0.7348 (tm-30) REVERT: E 447 ARG cc_start: 0.7421 (ttm110) cc_final: 0.6862 (mtm-85) REVERT: F 73 ASP cc_start: 0.6724 (m-30) cc_final: 0.6514 (p0) REVERT: F 358 ASP cc_start: 0.7360 (t0) cc_final: 0.7070 (p0) REVERT: F 475 THR cc_start: 0.6171 (OUTLIER) cc_final: 0.5955 (p) REVERT: G 15 LYS cc_start: 0.8494 (tttt) cc_final: 0.8032 (mtpt) REVERT: G 22 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7325 (ttm170) REVERT: G 467 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6223 (mttp) REVERT: G 469 GLU cc_start: 0.6321 (mt-10) cc_final: 0.5838 (mp0) REVERT: H 15 LYS cc_start: 0.7727 (tptm) cc_final: 0.7137 (mmtt) REVERT: H 250 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7772 (mm-30) REVERT: H 303 ASP cc_start: 0.8185 (p0) cc_final: 0.7456 (t0) REVERT: H 441 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6755 (mp0) REVERT: I 98 ILE cc_start: 0.8668 (mm) cc_final: 0.8359 (pp) REVERT: I 102 ILE cc_start: 0.9164 (mt) cc_final: 0.8942 (mt) REVERT: J 2 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7479 (mt0) REVERT: J 29 GLN cc_start: 0.8458 (tp-100) cc_final: 0.8245 (tp-100) REVERT: J 94 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8514 (mtmt) REVERT: L 20 THR cc_start: 0.7497 (OUTLIER) cc_final: 0.7192 (p) REVERT: M 11 GLU cc_start: 0.7721 (mp0) cc_final: 0.7098 (mp0) REVERT: M 79 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: N 51 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8594 (pp) outliers start: 161 outliers final: 79 residues processed: 657 average time/residue: 1.8005 time to fit residues: 1453.5269 Evaluate side-chains 579 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 479 time to evaluate : 5.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 117 THR Chi-restraints excluded: chain 1 residue 146 ASN Chi-restraints excluded: chain 1 residue 196 ASP Chi-restraints excluded: chain 1 residue 236 LYS Chi-restraints excluded: chain 1 residue 239 PHE Chi-restraints excluded: chain 1 residue 272 LEU Chi-restraints excluded: chain 2 residue 68 SER Chi-restraints excluded: chain 2 residue 234 ILE Chi-restraints excluded: chain 2 residue 235 HIS Chi-restraints excluded: chain 2 residue 241 ARG Chi-restraints excluded: chain 2 residue 258 LYS Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain 3 residue 62 SER Chi-restraints excluded: chain 3 residue 97 VAL Chi-restraints excluded: chain 3 residue 118 VAL Chi-restraints excluded: chain 3 residue 127 LEU Chi-restraints excluded: chain 3 residue 129 ASN Chi-restraints excluded: chain 3 residue 155 VAL Chi-restraints excluded: chain 3 residue 257 LYS Chi-restraints excluded: chain 3 residue 265 HIS Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 85 THR Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 4 residue 104 ASP Chi-restraints excluded: chain 4 residue 121 GLN Chi-restraints excluded: chain 4 residue 150 ARG Chi-restraints excluded: chain 4 residue 155 VAL Chi-restraints excluded: chain 4 residue 170 ASP Chi-restraints excluded: chain 4 residue 235 HIS Chi-restraints excluded: chain 5 residue 54 MET Chi-restraints excluded: chain 5 residue 78 ILE Chi-restraints excluded: chain 5 residue 89 ILE Chi-restraints excluded: chain 5 residue 135 THR Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 73 ASP Chi-restraints excluded: chain 6 residue 81 ARG Chi-restraints excluded: chain 6 residue 167 LEU Chi-restraints excluded: chain 6 residue 196 ASP Chi-restraints excluded: chain 6 residue 226 TYR Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 22 ARG Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain H residue 250 GLU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain J residue 2 GLN Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 50 GLU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 366 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 353 optimal weight: 0.8980 chunk 178 optimal weight: 0.0570 chunk 116 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 376 optimal weight: 1.9990 chunk 403 optimal weight: 0.4980 chunk 292 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 465 optimal weight: 5.9990 overall best weight: 1.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 133 ASN 4 213 GLN 5 46 GLN 5 138 GLN 6 36 HIS 6 124 ASN ** 6 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN C 97 GLN C 116 ASN D 97 GLN ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN J 79 GLN ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 50968 Z= 0.185 Angle : 0.533 11.772 69237 Z= 0.269 Chirality : 0.041 0.184 7574 Planarity : 0.004 0.055 8972 Dihedral : 7.639 168.480 7098 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.21 % Allowed : 22.07 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 0.67 (0.10), residues: 6183 helix: 1.74 (0.10), residues: 2550 sheet: 0.95 (0.18), residues: 784 loop : -0.94 (0.10), residues: 2849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 4 178 HIS 0.013 0.001 HIS 5 16 PHE 0.029 0.001 PHE B 346 TYR 0.023 0.001 TYR 6 164 ARG 0.007 0.000 ARG J 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 489 time to evaluate : 6.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 53 LYS cc_start: 0.7260 (mtmt) cc_final: 0.6186 (tttm) REVERT: 1 57 GLU cc_start: 0.7657 (mp0) cc_final: 0.7362 (mp0) REVERT: 1 129 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7814 (t0) REVERT: 1 149 ARG cc_start: 0.7728 (mmm-85) cc_final: 0.7154 (mtp-110) REVERT: 1 236 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.5798 (mppt) REVERT: 2 19 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7549 (mtmt) REVERT: 2 138 GLN cc_start: 0.7801 (pt0) cc_final: 0.7523 (pm20) REVERT: 2 241 ARG cc_start: 0.5136 (OUTLIER) cc_final: 0.3971 (ptp90) REVERT: 3 213 GLN cc_start: 0.5759 (mm-40) cc_final: 0.5420 (mm-40) REVERT: 3 236 LYS cc_start: 0.6452 (pptt) cc_final: 0.6030 (mmpt) REVERT: 3 257 LYS cc_start: 0.6246 (OUTLIER) cc_final: 0.5968 (pmtt) REVERT: 3 267 ILE cc_start: 0.5177 (mp) cc_final: 0.4869 (tp) REVERT: 4 38 ARG cc_start: 0.4992 (OUTLIER) cc_final: 0.4145 (mmp80) REVERT: 4 54 MET cc_start: 0.4796 (mpt) cc_final: 0.4485 (mpt) REVERT: 4 150 ARG cc_start: 0.5917 (OUTLIER) cc_final: 0.5612 (ttt180) REVERT: 4 235 HIS cc_start: 0.6176 (OUTLIER) cc_final: 0.5841 (t70) REVERT: 6 5 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7662 (tp) REVERT: 6 12 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7175 (tptt) REVERT: 6 62 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7850 (p) REVERT: 6 81 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7390 (mtt-85) REVERT: 6 87 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: 6 226 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6553 (t80) REVERT: 6 228 ILE cc_start: 0.7190 (OUTLIER) cc_final: 0.6990 (pp) REVERT: B 303 ASP cc_start: 0.7869 (p0) cc_final: 0.7049 (t0) REVERT: C 132 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7967 (mtp180) REVERT: D 120 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8584 (m) REVERT: D 352 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8023 (mt-10) REVERT: D 444 ASP cc_start: 0.7725 (t0) cc_final: 0.7337 (t0) REVERT: E 15 LYS cc_start: 0.8621 (tttt) cc_final: 0.7995 (tptp) REVERT: E 89 GLU cc_start: 0.7901 (tt0) cc_final: 0.7385 (tm-30) REVERT: E 447 ARG cc_start: 0.7391 (ttm110) cc_final: 0.6851 (mtm-85) REVERT: F 73 ASP cc_start: 0.6726 (m-30) cc_final: 0.6506 (p0) REVERT: F 344 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7615 (mpm) REVERT: F 475 THR cc_start: 0.6189 (OUTLIER) cc_final: 0.5986 (p) REVERT: G 15 LYS cc_start: 0.8486 (tttt) cc_final: 0.8019 (mtpt) REVERT: G 22 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7323 (ttm170) REVERT: G 467 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6227 (mttp) REVERT: G 469 GLU cc_start: 0.6402 (mt-10) cc_final: 0.5905 (mp0) REVERT: H 15 LYS cc_start: 0.7718 (tptm) cc_final: 0.7139 (mmtt) REVERT: H 250 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: H 303 ASP cc_start: 0.8181 (p0) cc_final: 0.7408 (t0) REVERT: H 441 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6758 (mp0) REVERT: I 68 GLU cc_start: 0.8017 (mp0) cc_final: 0.7222 (pt0) REVERT: I 98 ILE cc_start: 0.8677 (mm) cc_final: 0.8360 (pp) REVERT: I 102 ILE cc_start: 0.9204 (mt) cc_final: 0.8990 (mt) REVERT: J 2 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7504 (mt0) REVERT: J 94 LYS cc_start: 0.8902 (mmtt) cc_final: 0.8516 (mtmt) REVERT: L 20 THR cc_start: 0.7531 (OUTLIER) cc_final: 0.7239 (p) REVERT: M 11 GLU cc_start: 0.7746 (mp0) cc_final: 0.7085 (mp0) REVERT: M 79 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8035 (tm-30) REVERT: N 51 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8632 (pp) outliers start: 167 outliers final: 98 residues processed: 611 average time/residue: 1.9251 time to fit residues: 1440.0900 Evaluate side-chains 599 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 475 time to evaluate : 6.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 117 THR Chi-restraints excluded: chain 1 residue 129 ASN Chi-restraints excluded: chain 1 residue 146 ASN Chi-restraints excluded: chain 1 residue 196 ASP Chi-restraints excluded: chain 1 residue 236 LYS Chi-restraints excluded: chain 1 residue 237 VAL Chi-restraints excluded: chain 1 residue 272 LEU Chi-restraints excluded: chain 2 residue 19 LYS Chi-restraints excluded: chain 2 residue 68 SER Chi-restraints excluded: chain 2 residue 183 ASP Chi-restraints excluded: chain 2 residue 234 ILE Chi-restraints excluded: chain 2 residue 235 HIS Chi-restraints excluded: chain 2 residue 241 ARG Chi-restraints excluded: chain 2 residue 258 LYS Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain 3 residue 62 SER Chi-restraints excluded: chain 3 residue 118 VAL Chi-restraints excluded: chain 3 residue 127 LEU Chi-restraints excluded: chain 3 residue 129 ASN Chi-restraints excluded: chain 3 residue 155 VAL Chi-restraints excluded: chain 3 residue 257 LYS Chi-restraints excluded: chain 3 residue 265 HIS Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 85 THR Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 4 residue 104 ASP Chi-restraints excluded: chain 4 residue 121 GLN Chi-restraints excluded: chain 4 residue 133 ASN Chi-restraints excluded: chain 4 residue 150 ARG Chi-restraints excluded: chain 4 residue 153 ILE Chi-restraints excluded: chain 4 residue 155 VAL Chi-restraints excluded: chain 4 residue 170 ASP Chi-restraints excluded: chain 4 residue 235 HIS Chi-restraints excluded: chain 5 residue 32 ILE Chi-restraints excluded: chain 5 residue 54 MET Chi-restraints excluded: chain 5 residue 89 ILE Chi-restraints excluded: chain 5 residue 117 THR Chi-restraints excluded: chain 5 residue 128 MET Chi-restraints excluded: chain 5 residue 135 THR Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 62 SER Chi-restraints excluded: chain 6 residue 73 ASP Chi-restraints excluded: chain 6 residue 81 ARG Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 167 LEU Chi-restraints excluded: chain 6 residue 196 ASP Chi-restraints excluded: chain 6 residue 226 TYR Chi-restraints excluded: chain 6 residue 228 ILE Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 22 ARG Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 128 PHE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain H residue 250 GLU Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 2 GLN Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain P residue 50 GLU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 538 optimal weight: 0.3980 chunk 566 optimal weight: 4.9990 chunk 517 optimal weight: 7.9990 chunk 551 optimal weight: 6.9990 chunk 331 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 433 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 498 optimal weight: 6.9990 chunk 521 optimal weight: 5.9990 chunk 549 optimal weight: 6.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 133 ASN 4 213 GLN 5 46 GLN 5 138 GLN 6 36 HIS ** 6 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 129 ASN C 97 GLN D 19 GLN D 97 GLN ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 GLN ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 50968 Z= 0.270 Angle : 0.591 11.229 69237 Z= 0.300 Chirality : 0.044 0.234 7574 Planarity : 0.005 0.085 8972 Dihedral : 7.686 166.635 7098 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.12 % Favored : 96.86 % Rotamer: Outliers : 3.50 % Allowed : 22.03 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.10), residues: 6183 helix: 1.57 (0.10), residues: 2561 sheet: 0.75 (0.18), residues: 782 loop : -1.00 (0.10), residues: 2840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP 4 178 HIS 0.014 0.001 HIS 5 16 PHE 0.031 0.002 PHE B 346 TYR 0.023 0.001 TYR 1 4 ARG 0.017 0.000 ARG O 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 481 time to evaluate : 6.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 57 GLU cc_start: 0.7600 (mp0) cc_final: 0.7132 (mp0) REVERT: 1 84 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7818 (mm-30) REVERT: 1 129 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7924 (t0) REVERT: 2 19 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7576 (mtmt) REVERT: 2 20 ASN cc_start: 0.7093 (OUTLIER) cc_final: 0.6839 (t0) REVERT: 2 54 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.6568 (tpt) REVERT: 2 138 GLN cc_start: 0.7887 (pt0) cc_final: 0.7566 (pm20) REVERT: 3 213 GLN cc_start: 0.5945 (mm-40) cc_final: 0.5590 (mm-40) REVERT: 3 236 LYS cc_start: 0.6507 (pptt) cc_final: 0.6052 (mmpt) REVERT: 3 257 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5924 (pmtt) REVERT: 4 38 ARG cc_start: 0.5018 (OUTLIER) cc_final: 0.4189 (mmp80) REVERT: 4 235 HIS cc_start: 0.6177 (OUTLIER) cc_final: 0.5844 (t70) REVERT: 5 16 HIS cc_start: 0.7057 (t70) cc_final: 0.6730 (t70) REVERT: 6 5 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7666 (tp) REVERT: 6 12 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7215 (tptt) REVERT: 6 62 SER cc_start: 0.8204 (OUTLIER) cc_final: 0.7884 (p) REVERT: 6 81 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7414 (mtt-85) REVERT: 6 87 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: 6 226 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.6655 (t80) REVERT: 6 228 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6871 (pp) REVERT: A 89 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: B 140 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.6732 (tmm160) REVERT: B 303 ASP cc_start: 0.7908 (p0) cc_final: 0.7056 (t0) REVERT: C 132 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7971 (mtp180) REVERT: C 448 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: D 120 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8571 (m) REVERT: D 444 ASP cc_start: 0.7698 (t0) cc_final: 0.7302 (t0) REVERT: D 451 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7969 (mtpt) REVERT: E 15 LYS cc_start: 0.8629 (tttt) cc_final: 0.8004 (tptp) REVERT: E 89 GLU cc_start: 0.7936 (tt0) cc_final: 0.7378 (tm-30) REVERT: F 73 ASP cc_start: 0.6695 (m-30) cc_final: 0.6477 (p0) REVERT: F 451 LYS cc_start: 0.8186 (mtmt) cc_final: 0.7818 (pttp) REVERT: G 15 LYS cc_start: 0.8437 (tttt) cc_final: 0.7980 (mtpt) REVERT: G 22 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7351 (ttm170) REVERT: G 361 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7812 (mtt90) REVERT: G 467 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6245 (mttp) REVERT: G 469 GLU cc_start: 0.6424 (mt-10) cc_final: 0.5910 (mp0) REVERT: H 15 LYS cc_start: 0.7733 (tptm) cc_final: 0.7253 (mmtt) REVERT: H 250 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7886 (mm-30) REVERT: H 303 ASP cc_start: 0.8219 (p0) cc_final: 0.7433 (t0) REVERT: H 441 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6760 (mp0) REVERT: I 98 ILE cc_start: 0.8673 (mm) cc_final: 0.8378 (pp) REVERT: J 2 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7512 (mt0) REVERT: J 94 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8512 (mtmt) REVERT: K 51 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8461 (pp) REVERT: L 20 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.7272 (p) REVERT: M 11 GLU cc_start: 0.7782 (mp0) cc_final: 0.7095 (mp0) REVERT: M 21 ASP cc_start: 0.8067 (m-30) cc_final: 0.7773 (t0) REVERT: M 79 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: N 51 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8630 (pp) outliers start: 182 outliers final: 99 residues processed: 617 average time/residue: 1.8923 time to fit residues: 1427.2653 Evaluate side-chains 592 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 464 time to evaluate : 6.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 62 SER Chi-restraints excluded: chain 1 residue 117 THR Chi-restraints excluded: chain 1 residue 122 LEU Chi-restraints excluded: chain 1 residue 129 ASN Chi-restraints excluded: chain 1 residue 146 ASN Chi-restraints excluded: chain 1 residue 196 ASP Chi-restraints excluded: chain 1 residue 237 VAL Chi-restraints excluded: chain 1 residue 272 LEU Chi-restraints excluded: chain 2 residue 19 LYS Chi-restraints excluded: chain 2 residue 20 ASN Chi-restraints excluded: chain 2 residue 54 MET Chi-restraints excluded: chain 2 residue 68 SER Chi-restraints excluded: chain 2 residue 128 MET Chi-restraints excluded: chain 2 residue 183 ASP Chi-restraints excluded: chain 2 residue 241 ARG Chi-restraints excluded: chain 2 residue 258 LYS Chi-restraints excluded: chain 3 residue 62 SER Chi-restraints excluded: chain 3 residue 97 VAL Chi-restraints excluded: chain 3 residue 118 VAL Chi-restraints excluded: chain 3 residue 127 LEU Chi-restraints excluded: chain 3 residue 128 MET Chi-restraints excluded: chain 3 residue 129 ASN Chi-restraints excluded: chain 3 residue 144 ASP Chi-restraints excluded: chain 3 residue 155 VAL Chi-restraints excluded: chain 3 residue 257 LYS Chi-restraints excluded: chain 3 residue 265 HIS Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 85 THR Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 4 residue 99 MET Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 4 residue 104 ASP Chi-restraints excluded: chain 4 residue 155 VAL Chi-restraints excluded: chain 4 residue 235 HIS Chi-restraints excluded: chain 5 residue 54 MET Chi-restraints excluded: chain 5 residue 117 THR Chi-restraints excluded: chain 5 residue 135 THR Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 62 SER Chi-restraints excluded: chain 6 residue 81 ARG Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 167 LEU Chi-restraints excluded: chain 6 residue 196 ASP Chi-restraints excluded: chain 6 residue 226 TYR Chi-restraints excluded: chain 6 residue 228 ILE Chi-restraints excluded: chain 6 residue 231 ARG Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain G residue 22 ARG Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 361 ARG Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain H residue 250 GLU Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 2 GLN Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain P residue 50 GLU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 362 optimal weight: 6.9990 chunk 583 optimal weight: 0.9980 chunk 355 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 405 optimal weight: 3.9990 chunk 611 optimal weight: 1.9990 chunk 563 optimal weight: 1.9990 chunk 487 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 376 optimal weight: 0.9980 chunk 298 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 213 GLN 5 46 GLN 5 138 GLN 6 36 HIS 6 124 ASN D 97 GLN ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 GLN ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 50968 Z= 0.179 Angle : 0.548 12.399 69237 Z= 0.276 Chirality : 0.042 0.214 7574 Planarity : 0.004 0.053 8972 Dihedral : 7.436 163.603 7098 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.88 % Allowed : 22.76 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 0.63 (0.10), residues: 6183 helix: 1.74 (0.10), residues: 2541 sheet: 0.85 (0.18), residues: 782 loop : -0.95 (0.11), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 4 178 HIS 0.012 0.001 HIS 5 16 PHE 0.029 0.001 PHE A 346 TYR 0.026 0.001 TYR 6 164 ARG 0.009 0.000 ARG F 440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 486 time to evaluate : 6.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 84 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7788 (mm-30) REVERT: 1 129 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7868 (t0) REVERT: 1 149 ARG cc_start: 0.7717 (mmm-85) cc_final: 0.7198 (mtp-110) REVERT: 1 185 LYS cc_start: 0.7138 (ptpt) cc_final: 0.6613 (pttt) REVERT: 1 204 GLU cc_start: 0.5515 (mt-10) cc_final: 0.5205 (pt0) REVERT: 2 19 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7568 (mtmt) REVERT: 2 20 ASN cc_start: 0.7013 (OUTLIER) cc_final: 0.6789 (t0) REVERT: 2 54 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.6612 (tpt) REVERT: 2 138 GLN cc_start: 0.7916 (pt0) cc_final: 0.7593 (pm20) REVERT: 2 258 LYS cc_start: 0.5257 (OUTLIER) cc_final: 0.4874 (tptt) REVERT: 3 213 GLN cc_start: 0.5960 (mm-40) cc_final: 0.5603 (mm-40) REVERT: 3 236 LYS cc_start: 0.6469 (pptt) cc_final: 0.6075 (mmpt) REVERT: 3 257 LYS cc_start: 0.6236 (OUTLIER) cc_final: 0.5960 (pmtt) REVERT: 3 267 ILE cc_start: 0.5210 (mp) cc_final: 0.4868 (tp) REVERT: 4 38 ARG cc_start: 0.4988 (OUTLIER) cc_final: 0.4174 (mmp80) REVERT: 4 235 HIS cc_start: 0.6177 (OUTLIER) cc_final: 0.5837 (t70) REVERT: 5 174 GLU cc_start: 0.6170 (tm-30) cc_final: 0.5608 (tt0) REVERT: 6 5 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7651 (tp) REVERT: 6 12 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7186 (tptt) REVERT: 6 62 SER cc_start: 0.8174 (OUTLIER) cc_final: 0.7856 (p) REVERT: 6 73 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6800 (m-30) REVERT: 6 81 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7433 (mtt-85) REVERT: 6 87 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: 6 226 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.6662 (t80) REVERT: 6 228 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6869 (pp) REVERT: B 140 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.6655 (tmm160) REVERT: B 303 ASP cc_start: 0.7909 (p0) cc_final: 0.7063 (t0) REVERT: C 132 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7996 (mtp180) REVERT: C 448 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: C 451 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8181 (mtpp) REVERT: D 120 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8564 (m) REVERT: D 352 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8052 (mt-10) REVERT: D 361 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7098 (mtt180) REVERT: D 444 ASP cc_start: 0.7679 (t0) cc_final: 0.7279 (t0) REVERT: E 15 LYS cc_start: 0.8587 (tttt) cc_final: 0.7974 (tptp) REVERT: E 89 GLU cc_start: 0.7922 (tt0) cc_final: 0.7391 (tm-30) REVERT: E 447 ARG cc_start: 0.7300 (ttm110) cc_final: 0.6774 (mtm-85) REVERT: G 15 LYS cc_start: 0.8419 (tttt) cc_final: 0.7962 (mtpt) REVERT: G 22 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7353 (ttm170) REVERT: G 361 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7799 (mtt90) REVERT: G 467 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6306 (mttp) REVERT: G 469 GLU cc_start: 0.6429 (mt-10) cc_final: 0.5927 (mp0) REVERT: H 15 LYS cc_start: 0.7649 (tptm) cc_final: 0.7129 (mmtt) REVERT: H 250 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: H 303 ASP cc_start: 0.8168 (p0) cc_final: 0.7434 (t0) REVERT: H 441 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6761 (mp0) REVERT: I 65 THR cc_start: 0.7125 (OUTLIER) cc_final: 0.6773 (p) REVERT: I 68 GLU cc_start: 0.7977 (mp0) cc_final: 0.7225 (pt0) REVERT: I 98 ILE cc_start: 0.8673 (mm) cc_final: 0.8390 (pp) REVERT: J 2 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7509 (mt0) REVERT: J 25 GLU cc_start: 0.7883 (tp30) cc_final: 0.7350 (tm-30) REVERT: J 29 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8398 (tp-100) REVERT: J 94 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8528 (mtmt) REVERT: K 51 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8367 (pp) REVERT: L 20 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7201 (p) REVERT: M 11 GLU cc_start: 0.7777 (mp0) cc_final: 0.7091 (mp0) REVERT: M 21 ASP cc_start: 0.8022 (m-30) cc_final: 0.7736 (t0) REVERT: M 79 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: N 51 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8648 (pp) outliers start: 150 outliers final: 90 residues processed: 603 average time/residue: 1.8821 time to fit residues: 1384.7526 Evaluate side-chains 594 residues out of total 5254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 472 time to evaluate : 5.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 117 THR Chi-restraints excluded: chain 1 residue 129 ASN Chi-restraints excluded: chain 1 residue 146 ASN Chi-restraints excluded: chain 1 residue 196 ASP Chi-restraints excluded: chain 1 residue 227 ASP Chi-restraints excluded: chain 1 residue 237 VAL Chi-restraints excluded: chain 2 residue 19 LYS Chi-restraints excluded: chain 2 residue 20 ASN Chi-restraints excluded: chain 2 residue 54 MET Chi-restraints excluded: chain 2 residue 68 SER Chi-restraints excluded: chain 2 residue 183 ASP Chi-restraints excluded: chain 2 residue 241 ARG Chi-restraints excluded: chain 2 residue 258 LYS Chi-restraints excluded: chain 3 residue 62 SER Chi-restraints excluded: chain 3 residue 97 VAL Chi-restraints excluded: chain 3 residue 118 VAL Chi-restraints excluded: chain 3 residue 127 LEU Chi-restraints excluded: chain 3 residue 129 ASN Chi-restraints excluded: chain 3 residue 144 ASP Chi-restraints excluded: chain 3 residue 155 VAL Chi-restraints excluded: chain 3 residue 257 LYS Chi-restraints excluded: chain 3 residue 265 HIS Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 85 THR Chi-restraints excluded: chain 4 residue 97 VAL Chi-restraints excluded: chain 4 residue 99 MET Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 4 residue 104 ASP Chi-restraints excluded: chain 4 residue 150 ARG Chi-restraints excluded: chain 4 residue 235 HIS Chi-restraints excluded: chain 5 residue 117 THR Chi-restraints excluded: chain 5 residue 135 THR Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 36 HIS Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 62 SER Chi-restraints excluded: chain 6 residue 73 ASP Chi-restraints excluded: chain 6 residue 81 ARG Chi-restraints excluded: chain 6 residue 87 GLU Chi-restraints excluded: chain 6 residue 167 LEU Chi-restraints excluded: chain 6 residue 196 ASP Chi-restraints excluded: chain 6 residue 226 TYR Chi-restraints excluded: chain 6 residue 228 ILE Chi-restraints excluded: chain 6 residue 231 ARG Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain G residue 22 ARG Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 361 ARG Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain H residue 250 GLU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 2 GLN Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 49 THR Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 614 random chunks: chunk 386 optimal weight: 10.0000 chunk 518 optimal weight: 2.9990 chunk 149 optimal weight: 0.0000 chunk 449 optimal weight: 0.0670 chunk 71 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 487 optimal weight: 0.7980 chunk 204 optimal weight: 0.5980 chunk 500 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 133 ASN 4 213 GLN 5 46 GLN 5 138 GLN ** 6 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN D 97 GLN ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN J 79 GLN ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.135128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101285 restraints weight = 81908.882| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.77 r_work: 0.3235 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 50968 Z= 0.139 Angle : 0.530 11.561 69237 Z= 0.265 Chirality : 0.040 0.273 7574 Planarity : 0.004 0.103 8972 Dihedral : 7.096 160.215 7098 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.17 % Allowed : 23.55 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % 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: 0.83 (0.10), residues: 6183 helix: 1.89 (0.10), residues: 2543 sheet: 1.03 (0.18), residues: 783 loop : -0.85 (0.11), residues: 2857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 4 178 HIS 0.019 0.001 HIS 6 36 PHE 0.029 0.001 PHE A 346 TYR 0.031 0.001 TYR 6 164 ARG 0.015 0.000 ARG O 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23009.84 seconds wall clock time: 408 minutes 39.37 seconds (24519.37 seconds total)