Starting phenix.real_space_refine (version: dev) on Wed Dec 14 22:54:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7x_9944/12_2022/6k7x_9944_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7x_9944/12_2022/6k7x_9944.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7x_9944/12_2022/6k7x_9944_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7x_9944/12_2022/6k7x_9944_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7x_9944/12_2022/6k7x_9944_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7x_9944/12_2022/6k7x_9944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7x_9944/12_2022/6k7x_9944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7x_9944/12_2022/6k7x_9944_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7x_9944/12_2022/6k7x_9944_updated.pdb" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.064 sd= 1.605 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C ASP 74": "OD1" <-> "OD2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 94": "NH1" <-> "NH2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ASP 119": "OD1" <-> "OD2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ASP 148": "OD1" <-> "OD2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A ASP 119": "OD1" <-> "OD2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 106": "OD1" <-> "OD2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 313": "OD1" <-> "OD2" Residue "D TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "H PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 69": "NH1" <-> "NH2" Residue "H ASP 96": "OD1" <-> "OD2" Residue "H GLU 101": "OE1" <-> "OE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 96": "OD1" <-> "OD2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 93": "OE1" <-> "OE2" Residue "K ASP 74": "OD1" <-> "OD2" Residue "K TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "K ARG 93": "NH1" <-> "NH2" Residue "K ARG 94": "NH1" <-> "NH2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 113": "NH1" <-> "NH2" Residue "K ASP 119": "OD1" <-> "OD2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "K ARG 134": "NH1" <-> "NH2" Residue "K ASP 148": "OD1" <-> "OD2" Residue "K ASP 155": "OD1" <-> "OD2" Residue "K ARG 161": "NH1" <-> "NH2" Residue "K ASP 166": "OD1" <-> "OD2" Residue "K ASP 178": "OD1" <-> "OD2" Residue "K GLU 193": "OE1" <-> "OE2" Residue "K ARG 201": "NH1" <-> "NH2" Residue "K ASP 209": "OD1" <-> "OD2" Residue "K GLU 223": "OE1" <-> "OE2" Residue "K ARG 226": "NH1" <-> "NH2" Residue "K PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 252": "NH1" <-> "NH2" Residue "K TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 286": "NH1" <-> "NH2" Residue "K ARG 333": "NH1" <-> "NH2" Residue "L TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 93": "NH1" <-> "NH2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "L PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 113": "NH1" <-> "NH2" Residue "L GLU 117": "OE1" <-> "OE2" Residue "L ASP 119": "OD1" <-> "OD2" Residue "L TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 147": "OD1" <-> "OD2" Residue "L ARG 165": "NH1" <-> "NH2" Residue "L ASP 166": "OD1" <-> "OD2" Residue "L ASP 178": "OD1" <-> "OD2" Residue "L GLU 205": "OE1" <-> "OE2" Residue "L ARG 206": "NH1" <-> "NH2" Residue "L ASP 209": "OD1" <-> "OD2" Residue "L ARG 226": "NH1" <-> "NH2" Residue "L PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 252": "NH1" <-> "NH2" Residue "L TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 286": "NH1" <-> "NH2" Residue "L TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 293": "OE1" <-> "OE2" Residue "L ARG 297": "NH1" <-> "NH2" Residue "L PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 322": "OD1" <-> "OD2" Residue "L ARG 345": "NH1" <-> "NH2" Residue "M ASP 74": "OD1" <-> "OD2" Residue "M ARG 93": "NH1" <-> "NH2" Residue "M ARG 113": "NH1" <-> "NH2" Residue "M TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 142": "OD1" <-> "OD2" Residue "M ASP 178": "OD1" <-> "OD2" Residue "M TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 193": "OE1" <-> "OE2" Residue "M GLU 202": "OE1" <-> "OE2" Residue "M GLU 205": "OE1" <-> "OE2" Residue "M PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 252": "NH1" <-> "NH2" Residue "M ASP 261": "OD1" <-> "OD2" Residue "M TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 286": "NH1" <-> "NH2" Residue "M TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 328": "OE1" <-> "OE2" Residue "N PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N ARG 161": "NH1" <-> "NH2" Residue "N ARG 165": "NH1" <-> "NH2" Residue "N GLU 171": "OE1" <-> "OE2" Residue "N TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 202": "OE1" <-> "OE2" Residue "N ARG 221": "NH1" <-> "NH2" Residue "N ARG 226": "NH1" <-> "NH2" Residue "N PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 252": "NH1" <-> "NH2" Residue "N TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 297": "NH1" <-> "NH2" Residue "N PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 313": "OD1" <-> "OD2" Residue "N TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 335": "NH1" <-> "NH2" Residue "N ARG 345": "NH1" <-> "NH2" Residue "O PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 69": "NH1" <-> "NH2" Residue "O ASP 96": "OD1" <-> "OD2" Residue "O GLU 101": "OE1" <-> "OE2" Residue "P ARG 52": "NH1" <-> "NH2" Residue "P PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 69": "NH1" <-> "NH2" Residue "P TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 93": "OE1" <-> "OE2" Residue "Q ARG 52": "NH1" <-> "NH2" Residue "Q PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 96": "OD1" <-> "OD2" Residue "R PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 69": "NH1" <-> "NH2" Residue "R PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 93": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 22944 Number of models: 1 Model: "" Number of chains: 24 Chain: "C" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2274 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "A" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "B" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "D" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "H" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "F" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "G" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "K" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2274 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "L" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "M" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "N" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2253 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "O" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "P" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "Q" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "R" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "C" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 186 Unusual residues: {'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 189 Unusual residues: {' CA': 3, 'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 186 Unusual residues: {'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 186 Unusual residues: {'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 188 Unusual residues: {' CA': 2, 'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 187 Unusual residues: {' CA': 1, 'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 186 Unusual residues: {'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 186 Unusual residues: {'CDL': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.86, per 1000 atoms: 0.56 Number of scatterers: 22944 At special positions: 0 Unit cell: (221.473, 101.463, 137.466, 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) Ca 6 19.99 S 72 16.00 P 32 15.00 O 4096 8.00 N 3688 7.00 C 15050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.26 Conformation dependent library (CDL) restraints added in 3.1 seconds 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 16 sheets defined 57.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 141 through 144 No H-bonds generated for 'chain 'C' and resid 141 through 144' Processing helix chain 'C' and resid 176 through 191 removed outlier: 3.565A pdb=" N GLN C 184 " --> pdb=" O LYS C 180 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 222 removed outlier: 3.786A pdb=" N GLU C 200 " --> pdb=" O GLN C 196 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Proline residue: C 216 - end of helix removed outlier: 4.168A pdb=" N LYS C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL C 220 " --> pdb=" O PRO C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 255 removed outlier: 3.675A pdb=" N THR C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 285 Proline residue: C 265 - end of helix removed outlier: 3.934A pdb=" N TYR C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C 282 " --> pdb=" O MET C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 309 removed outlier: 3.762A pdb=" N LYS C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 333 removed outlier: 3.616A pdb=" N ALA C 323 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 325 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 339 Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.572A pdb=" N ARG A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 4.269A pdb=" N LEU A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 189 removed outlier: 3.796A pdb=" N THR A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 212 removed outlier: 3.688A pdb=" N LEU A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 255 removed outlier: 4.166A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 236 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 Proline residue: A 265 - end of helix removed outlier: 3.563A pdb=" N MET A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 282 " --> pdb=" O MET A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 309 removed outlier: 3.633A pdb=" N LYS A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.615A pdb=" N ALA A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 141 through 144 No H-bonds generated for 'chain 'B' and resid 141 through 144' Processing helix chain 'B' and resid 176 through 213 removed outlier: 3.514A pdb=" N GLN B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLU B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLN B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 205 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 253 removed outlier: 4.053A pdb=" N LYS B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 285 Proline residue: B 265 - end of helix removed outlier: 3.776A pdb=" N TYR B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 282 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 306 removed outlier: 3.771A pdb=" N ASP B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 340 removed outlier: 3.881A pdb=" N GLN B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Proline residue: B 337 - end of helix Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.966A pdb=" N ASP D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 removed outlier: 4.321A pdb=" N LEU D 146 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 184 removed outlier: 3.740A pdb=" N GLN D 184 " --> pdb=" O LYS D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 189 No H-bonds generated for 'chain 'D' and resid 186 through 189' Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 215 through 255 removed outlier: 3.812A pdb=" N LYS D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL D 220 " --> pdb=" O PRO D 216 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU D 234 " --> pdb=" O LYS D 230 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 285 Proline residue: D 265 - end of helix removed outlier: 3.700A pdb=" N THR D 271 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D 282 " --> pdb=" O MET D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 309 removed outlier: 3.916A pdb=" N ASP D 296 " --> pdb=" O PRO D 292 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS D 308 " --> pdb=" O HIS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 334 removed outlier: 3.741A pdb=" N ALA D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET D 329 " --> pdb=" O ALA D 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 74 removed outlier: 4.014A pdb=" N ILE H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 95 removed outlier: 3.516A pdb=" N GLY H 81 " --> pdb=" O PHE H 77 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE H 88 " --> pdb=" O ILE H 84 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 94 removed outlier: 3.763A pdb=" N ILE E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE E 75 " --> pdb=" O PHE E 71 " (cutoff:3.500A) Proline residue: E 76 - end of helix removed outlier: 3.653A pdb=" N VAL E 80 " --> pdb=" O PRO E 76 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER E 85 " --> pdb=" O GLY E 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 94 removed outlier: 4.000A pdb=" N ILE F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE F 75 " --> pdb=" O PHE F 71 " (cutoff:3.500A) Proline residue: F 76 - end of helix Processing helix chain 'G' and resid 66 through 95 removed outlier: 3.846A pdb=" N ILE G 73 " --> pdb=" O ARG G 69 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE G 75 " --> pdb=" O PHE G 71 " (cutoff:3.500A) Proline residue: G 76 - end of helix removed outlier: 3.718A pdb=" N VAL G 80 " --> pdb=" O PRO G 76 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER G 85 " --> pdb=" O GLY G 81 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 118 Processing helix chain 'K' and resid 141 through 144 No H-bonds generated for 'chain 'K' and resid 141 through 144' Processing helix chain 'K' and resid 176 through 191 removed outlier: 3.565A pdb=" N GLN K 184 " --> pdb=" O LYS K 180 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN K 185 " --> pdb=" O THR K 181 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR K 189 " --> pdb=" O GLN K 185 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU K 190 " --> pdb=" O LEU K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 222 removed outlier: 3.786A pdb=" N GLU K 200 " --> pdb=" O GLN K 196 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU K 212 " --> pdb=" O GLU K 208 " (cutoff:3.500A) Proline residue: K 216 - end of helix removed outlier: 4.168A pdb=" N LYS K 219 " --> pdb=" O ALA K 215 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL K 220 " --> pdb=" O PRO K 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 255 removed outlier: 3.675A pdb=" N THR K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL K 235 " --> pdb=" O ARG K 231 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU K 240 " --> pdb=" O LEU K 236 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP K 255 " --> pdb=" O ALA K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 285 Proline residue: K 265 - end of helix removed outlier: 3.934A pdb=" N TYR K 279 " --> pdb=" O ALA K 275 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE K 282 " --> pdb=" O MET K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 309 removed outlier: 3.763A pdb=" N LYS K 305 " --> pdb=" O LEU K 301 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS K 308 " --> pdb=" O HIS K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 333 removed outlier: 3.616A pdb=" N ALA K 323 " --> pdb=" O GLN K 319 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE K 324 " --> pdb=" O LEU K 320 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA K 325 " --> pdb=" O LYS K 321 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU K 331 " --> pdb=" O ALA K 327 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS K 332 " --> pdb=" O GLU K 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 339 Processing helix chain 'L' and resid 108 through 119 removed outlier: 3.572A pdb=" N ARG L 113 " --> pdb=" O GLY L 109 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP L 119 " --> pdb=" O LEU L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 146 removed outlier: 4.269A pdb=" N LEU L 146 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 189 removed outlier: 3.796A pdb=" N THR L 188 " --> pdb=" O GLN L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 212 removed outlier: 3.688A pdb=" N LEU L 207 " --> pdb=" O LEU L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 255 removed outlier: 4.166A pdb=" N VAL L 220 " --> pdb=" O PRO L 216 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU L 223 " --> pdb=" O LYS L 219 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS L 227 " --> pdb=" O GLU L 223 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR L 232 " --> pdb=" O ALA L 228 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU L 234 " --> pdb=" O LYS L 230 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU L 236 " --> pdb=" O THR L 232 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR L 254 " --> pdb=" O LEU L 250 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP L 255 " --> pdb=" O ALA L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 285 Proline residue: L 265 - end of helix removed outlier: 3.563A pdb=" N MET L 278 " --> pdb=" O SER L 274 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR L 279 " --> pdb=" O ALA L 275 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE L 282 " --> pdb=" O MET L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 309 removed outlier: 3.633A pdb=" N LYS L 305 " --> pdb=" O LEU L 301 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS L 308 " --> pdb=" O HIS L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 332 removed outlier: 3.615A pdb=" N ALA L 325 " --> pdb=" O LYS L 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 115 Processing helix chain 'M' and resid 141 through 144 No H-bonds generated for 'chain 'M' and resid 141 through 144' Processing helix chain 'M' and resid 176 through 213 removed outlier: 3.514A pdb=" N GLN M 184 " --> pdb=" O LYS M 180 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU M 190 " --> pdb=" O LEU M 186 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS M 191 " --> pdb=" O TYR M 187 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLU M 193 " --> pdb=" O THR M 189 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLN M 194 " --> pdb=" O LEU M 190 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN M 198 " --> pdb=" O GLN M 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU M 202 " --> pdb=" O ASN M 198 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU M 205 " --> pdb=" O ARG M 201 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU M 208 " --> pdb=" O ILE M 204 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 253 removed outlier: 4.054A pdb=" N LYS M 219 " --> pdb=" O ALA M 215 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL M 220 " --> pdb=" O PRO M 216 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU M 223 " --> pdb=" O LYS M 219 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS M 227 " --> pdb=" O GLU M 223 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU M 229 " --> pdb=" O SER M 225 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU M 234 " --> pdb=" O LYS M 230 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE M 247 " --> pdb=" O MET M 243 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY M 248 " --> pdb=" O ALA M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 285 Proline residue: M 265 - end of helix removed outlier: 3.776A pdb=" N TYR M 279 " --> pdb=" O ALA M 275 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE M 282 " --> pdb=" O MET M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 291 through 306 removed outlier: 3.770A pdb=" N ASP M 296 " --> pdb=" O PRO M 292 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN M 298 " --> pdb=" O ALA M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 314 through 340 removed outlier: 3.882A pdb=" N GLN M 319 " --> pdb=" O GLU M 315 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP M 336 " --> pdb=" O LYS M 332 " (cutoff:3.500A) Proline residue: M 337 - end of helix Processing helix chain 'N' and resid 108 through 119 removed outlier: 3.966A pdb=" N ASP N 119 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 146 removed outlier: 4.321A pdb=" N LEU N 146 " --> pdb=" O ASP N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 184 removed outlier: 3.740A pdb=" N GLN N 184 " --> pdb=" O LYS N 180 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 189 No H-bonds generated for 'chain 'N' and resid 186 through 189' Processing helix chain 'N' and resid 192 through 210 Processing helix chain 'N' and resid 215 through 255 removed outlier: 3.812A pdb=" N LYS N 219 " --> pdb=" O ALA N 215 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL N 220 " --> pdb=" O PRO N 216 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU N 223 " --> pdb=" O LYS N 219 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG N 231 " --> pdb=" O LYS N 227 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU N 234 " --> pdb=" O LYS N 230 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL N 235 " --> pdb=" O ARG N 231 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU N 253 " --> pdb=" O ILE N 249 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR N 254 " --> pdb=" O LEU N 250 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP N 255 " --> pdb=" O ALA N 251 " (cutoff:3.500A) Processing helix chain 'N' and resid 260 through 285 Proline residue: N 265 - end of helix removed outlier: 3.700A pdb=" N THR N 271 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR N 279 " --> pdb=" O ALA N 275 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE N 282 " --> pdb=" O MET N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 309 removed outlier: 3.916A pdb=" N ASP N 296 " --> pdb=" O PRO N 292 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS N 308 " --> pdb=" O HIS N 304 " (cutoff:3.500A) Processing helix chain 'N' and resid 314 through 334 removed outlier: 3.741A pdb=" N ALA N 325 " --> pdb=" O LYS N 321 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET N 329 " --> pdb=" O ALA N 325 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 74 removed outlier: 4.014A pdb=" N ILE O 73 " --> pdb=" O ARG O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 95 removed outlier: 3.517A pdb=" N GLY O 81 " --> pdb=" O PHE O 77 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE O 88 " --> pdb=" O ILE O 84 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU O 94 " --> pdb=" O ALA O 90 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS O 95 " --> pdb=" O LEU O 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 94 removed outlier: 3.763A pdb=" N ILE P 73 " --> pdb=" O ARG P 69 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE P 75 " --> pdb=" O PHE P 71 " (cutoff:3.500A) Proline residue: P 76 - end of helix removed outlier: 3.653A pdb=" N VAL P 80 " --> pdb=" O PRO P 76 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER P 85 " --> pdb=" O GLY P 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 94 removed outlier: 4.000A pdb=" N ILE Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE Q 75 " --> pdb=" O PHE Q 71 " (cutoff:3.500A) Proline residue: Q 76 - end of helix Processing helix chain 'R' and resid 66 through 95 removed outlier: 3.846A pdb=" N ILE R 73 " --> pdb=" O ARG R 69 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) Proline residue: R 76 - end of helix removed outlier: 3.718A pdb=" N VAL R 80 " --> pdb=" O PRO R 76 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER R 85 " --> pdb=" O GLY R 81 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS R 95 " --> pdb=" O LEU R 91 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 76 through 80 removed outlier: 3.643A pdb=" N THR C 76 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 126 through 129 removed outlier: 3.615A pdb=" N PHE C 149 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.735A pdb=" N GLU A 95 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 126 through 129 Processing sheet with id= E, first strand: chain 'B' and resid 77 through 80 Processing sheet with id= F, first strand: chain 'B' and resid 125 through 128 removed outlier: 3.803A pdb=" N LYS B 150 " --> pdb=" O TYR B 128 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 76 through 80 Processing sheet with id= H, first strand: chain 'D' and resid 125 through 129 Processing sheet with id= I, first strand: chain 'K' and resid 76 through 80 removed outlier: 3.643A pdb=" N THR K 76 " --> pdb=" O SER K 87 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 126 through 129 removed outlier: 3.615A pdb=" N PHE K 149 " --> pdb=" O VAL K 160 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 76 through 80 removed outlier: 3.735A pdb=" N GLU L 95 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 126 through 129 Processing sheet with id= M, first strand: chain 'M' and resid 77 through 80 Processing sheet with id= N, first strand: chain 'M' and resid 125 through 128 removed outlier: 3.802A pdb=" N LYS M 150 " --> pdb=" O TYR M 128 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'N' and resid 76 through 80 Processing sheet with id= P, first strand: chain 'N' and resid 125 through 129 1104 hydrogen bonds defined for protein. 3234 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: 6.61 Time building geometry restraints manager: 8.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3524 1.32 - 1.44: 5873 1.44 - 1.56: 13771 1.56 - 1.68: 66 1.68 - 1.81: 128 Bond restraints: 23362 Sorted by residual: bond pdb=" O2 PLX K 404 " pdb=" P1 PLX K 404 " ideal model delta sigma weight residual 1.513 1.448 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O2 PLX C 402 " pdb=" P1 PLX C 402 " ideal model delta sigma weight residual 1.513 1.449 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O2 PLX N 402 " pdb=" P1 PLX N 402 " ideal model delta sigma weight residual 1.513 1.449 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O2 PLX D 402 " pdb=" P1 PLX D 402 " ideal model delta sigma weight residual 1.513 1.449 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O3 PLX A 405 " pdb=" P1 PLX A 405 " ideal model delta sigma weight residual 1.513 1.449 0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 23357 not shown) Histogram of bond angle deviations from ideal: 94.57 - 102.48: 116 102.48 - 110.38: 6141 110.38 - 118.29: 12104 118.29 - 126.20: 12669 126.20 - 134.10: 314 Bond angle restraints: 31344 Sorted by residual: angle pdb=" C51 CDL B 401 " pdb=" CB5 CDL B 401 " pdb=" OB6 CDL B 401 " ideal model delta sigma weight residual 111.33 128.68 -17.35 1.32e+00 5.72e-01 1.72e+02 angle pdb=" C51 CDL M 401 " pdb=" CB5 CDL M 401 " pdb=" OB6 CDL M 401 " ideal model delta sigma weight residual 111.33 128.65 -17.32 1.32e+00 5.72e-01 1.72e+02 angle pdb=" OB6 CDL B 401 " pdb=" CB5 CDL B 401 " pdb=" OB7 CDL B 401 " ideal model delta sigma weight residual 123.92 115.26 8.66 1.00e+00 9.92e-01 7.45e+01 angle pdb=" OB6 CDL M 401 " pdb=" CB5 CDL M 401 " pdb=" OB7 CDL M 401 " ideal model delta sigma weight residual 123.92 115.27 8.65 1.00e+00 9.92e-01 7.42e+01 angle pdb=" CB2 CDL N 401 " pdb=" OB2 CDL N 401 " pdb=" PB2 CDL N 401 " ideal model delta sigma weight residual 121.27 114.73 6.54 1.00e+00 1.00e+00 4.28e+01 ... (remaining 31339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 11967 15.92 - 31.83: 1544 31.83 - 47.74: 526 47.74 - 63.66: 259 63.66 - 79.57: 32 Dihedral angle restraints: 14328 sinusoidal: 6570 harmonic: 7758 Sorted by residual: dihedral pdb=" CA ASP D 155 " pdb=" C ASP D 155 " pdb=" N LEU D 156 " pdb=" CA LEU D 156 " ideal model delta harmonic sigma weight residual 180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ASP N 155 " pdb=" C ASP N 155 " pdb=" N LEU N 156 " pdb=" CA LEU N 156 " ideal model delta harmonic sigma weight residual -180.00 -153.13 -26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ILE M 153 " pdb=" C ILE M 153 " pdb=" N ASN M 154 " pdb=" CA ASN M 154 " ideal model delta harmonic sigma weight residual -180.00 -156.14 -23.86 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 14325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2800 0.075 - 0.150: 558 0.150 - 0.225: 62 0.225 - 0.300: 14 0.300 - 0.375: 4 Chirality restraints: 3438 Sorted by residual: chirality pdb=" CA4 CDL K 403 " pdb=" CA3 CDL K 403 " pdb=" CA6 CDL K 403 " pdb=" OA6 CDL K 403 " both_signs ideal model delta sigma weight residual False -2.57 -2.20 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA4 CDL C 401 " pdb=" CA3 CDL C 401 " pdb=" CA6 CDL C 401 " pdb=" OA6 CDL C 401 " both_signs ideal model delta sigma weight residual False -2.57 -2.20 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA4 CDL D 401 " pdb=" CA3 CDL D 401 " pdb=" CA6 CDL D 401 " pdb=" OA6 CDL D 401 " both_signs ideal model delta sigma weight residual False -2.57 -2.22 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 3435 not shown) Planarity restraints: 3784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 297 " -0.136 9.50e-02 1.11e+02 8.06e-02 3.67e+01 pdb=" NE ARG B 297 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG B 297 " -0.100 2.00e-02 2.50e+03 pdb=" NH1 ARG B 297 " 0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG B 297 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 297 " 0.137 9.50e-02 1.11e+02 8.05e-02 3.66e+01 pdb=" NE ARG M 297 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG M 297 " 0.100 2.00e-02 2.50e+03 pdb=" NH1 ARG M 297 " -0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG M 297 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 112 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C LEU A 112 " 0.062 2.00e-02 2.50e+03 pdb=" O LEU A 112 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 113 " -0.021 2.00e-02 2.50e+03 ... (remaining 3781 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5507 2.80 - 3.32: 19060 3.32 - 3.85: 35263 3.85 - 4.37: 41180 4.37 - 4.90: 72307 Nonbonded interactions: 173317 Sorted by model distance: nonbonded pdb=" NZ LYS G 62 " pdb=" OB3 CDL B 401 " model vdw 2.270 2.520 nonbonded pdb=" NZ LYS R 62 " pdb=" OB3 CDL M 401 " model vdw 2.275 2.520 nonbonded pdb=" OG SER B 225 " pdb=" OH TYR B 299 " model vdw 2.306 2.440 nonbonded pdb=" OG SER M 225 " pdb=" OH TYR M 299 " model vdw 2.306 2.440 nonbonded pdb=" OE2 GLU N 264 " pdb="CA CA K 401 " model vdw 2.312 2.510 ... (remaining 173312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 73 through 345) selection = (chain 'B' and resid 73 through 345) selection = (chain 'C' and resid 73 through 345) selection = (chain 'D' and resid 73 through 345) selection = (chain 'K' and resid 73 through 345) selection = (chain 'L' and resid 73 through 345) selection = (chain 'M' and resid 73 through 345) selection = (chain 'N' and resid 73 through 345) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 32 5.49 5 S 72 5.16 5 C 15050 2.51 5 N 3688 2.21 5 O 4096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.130 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: 0.020 Extract box with map and model: 12.210 Check model and map are aligned: 0.310 Convert atoms to be neutral: 0.170 Process input model: 54.980 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 0.099 23362 Z= 0.497 Angle : 1.075 17.353 31344 Z= 0.561 Chirality : 0.062 0.375 3438 Planarity : 0.008 0.081 3784 Dihedral : 17.459 79.574 9296 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.12), residues: 2590 helix: -3.03 (0.09), residues: 1586 sheet: -1.14 (0.33), residues: 198 loop : -2.68 (0.19), residues: 806 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 354 time to evaluate : 2.712 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 359 average time/residue: 0.3805 time to fit residues: 203.4859 Evaluate side-chains 249 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 2.468 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 232 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN C 185 GLN C 196 GLN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN A 196 GLN A 246 GLN B 159 HIS B 177 ASN B 213 GLN B 246 GLN D 114 GLN D 185 GLN D 194 GLN D 246 GLN D 318 ASN F 95 HIS G 95 HIS K 116 GLN K 185 GLN K 196 GLN ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 177 ASN L 196 GLN L 246 GLN M 159 HIS M 177 ASN M 213 GLN M 246 GLN N 114 GLN N 185 GLN N 194 GLN N 246 GLN N 318 ASN Q 95 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 23362 Z= 0.215 Angle : 0.554 8.672 31344 Z= 0.282 Chirality : 0.043 0.190 3438 Planarity : 0.004 0.051 3784 Dihedral : 15.656 59.961 3926 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.15), residues: 2590 helix: -0.98 (0.12), residues: 1612 sheet: -0.73 (0.36), residues: 198 loop : -2.18 (0.20), residues: 780 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 276 time to evaluate : 2.813 Fit side-chains outliers start: 43 outliers final: 30 residues processed: 301 average time/residue: 0.3395 time to fit residues: 159.5102 Evaluate side-chains 274 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 244 time to evaluate : 2.639 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1839 time to fit residues: 14.0347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 251 optimal weight: 0.0020 chunk 207 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 23362 Z= 0.206 Angle : 0.520 7.895 31344 Z= 0.264 Chirality : 0.042 0.154 3438 Planarity : 0.004 0.049 3784 Dihedral : 14.280 59.964 3926 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.17), residues: 2590 helix: -0.08 (0.13), residues: 1612 sheet: -0.52 (0.36), residues: 198 loop : -1.91 (0.21), residues: 780 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 266 time to evaluate : 2.881 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 276 average time/residue: 0.3376 time to fit residues: 145.2013 Evaluate side-chains 256 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 247 time to evaluate : 2.553 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1912 time to fit residues: 6.9675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 0.2980 chunk 233 optimal weight: 0.0570 chunk 247 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 23362 Z= 0.155 Angle : 0.491 8.485 31344 Z= 0.247 Chirality : 0.041 0.140 3438 Planarity : 0.003 0.046 3784 Dihedral : 13.352 59.824 3926 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2590 helix: 0.57 (0.14), residues: 1612 sheet: -0.75 (0.33), residues: 222 loop : -1.64 (0.22), residues: 756 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 270 time to evaluate : 2.697 Fit side-chains outliers start: 25 outliers final: 13 residues processed: 284 average time/residue: 0.3520 time to fit residues: 155.8072 Evaluate side-chains 256 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 243 time to evaluate : 2.761 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2070 time to fit residues: 8.7896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 GLN R 95 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 23362 Z= 0.331 Angle : 0.578 8.769 31344 Z= 0.290 Chirality : 0.045 0.165 3438 Planarity : 0.004 0.048 3784 Dihedral : 13.501 59.899 3926 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2590 helix: 0.64 (0.14), residues: 1632 sheet: -0.79 (0.33), residues: 222 loop : -1.71 (0.21), residues: 736 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 248 time to evaluate : 2.901 Fit side-chains outliers start: 26 outliers final: 17 residues processed: 260 average time/residue: 0.3578 time to fit residues: 144.5185 Evaluate side-chains 259 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 242 time to evaluate : 2.756 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2037 time to fit residues: 10.2371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.0870 chunk 130 optimal weight: 2.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 23362 Z= 0.199 Angle : 0.519 9.327 31344 Z= 0.258 Chirality : 0.042 0.135 3438 Planarity : 0.003 0.047 3784 Dihedral : 13.088 59.993 3926 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2590 helix: 0.96 (0.14), residues: 1624 sheet: -0.70 (0.33), residues: 222 loop : -1.58 (0.22), residues: 744 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 252 time to evaluate : 2.521 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 267 average time/residue: 0.3399 time to fit residues: 143.5317 Evaluate side-chains 258 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 242 time to evaluate : 2.699 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2016 time to fit residues: 9.7677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 208 optimal weight: 0.9980 chunk 138 optimal weight: 0.0060 chunk 246 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 23362 Z= 0.166 Angle : 0.497 9.911 31344 Z= 0.247 Chirality : 0.041 0.151 3438 Planarity : 0.003 0.042 3784 Dihedral : 12.589 59.816 3926 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2590 helix: 1.26 (0.14), residues: 1614 sheet: -0.56 (0.33), residues: 222 loop : -1.40 (0.22), residues: 754 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 254 time to evaluate : 2.542 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 260 average time/residue: 0.3332 time to fit residues: 136.3150 Evaluate side-chains 240 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 237 time to evaluate : 2.656 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2057 time to fit residues: 4.7142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 193 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 23362 Z= 0.287 Angle : 0.570 10.168 31344 Z= 0.278 Chirality : 0.044 0.223 3438 Planarity : 0.003 0.041 3784 Dihedral : 12.716 59.731 3926 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2590 helix: 1.18 (0.14), residues: 1628 sheet: -0.64 (0.33), residues: 222 loop : -1.50 (0.22), residues: 740 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 242 time to evaluate : 3.094 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 254 average time/residue: 0.3466 time to fit residues: 138.1102 Evaluate side-chains 249 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 236 time to evaluate : 2.763 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1901 time to fit residues: 8.4148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 138 optimal weight: 0.0470 chunk 100 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 23362 Z= 0.254 Angle : 0.557 10.099 31344 Z= 0.273 Chirality : 0.044 0.225 3438 Planarity : 0.003 0.040 3784 Dihedral : 12.581 59.997 3926 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2590 helix: 1.28 (0.14), residues: 1622 sheet: -0.60 (0.33), residues: 222 loop : -1.49 (0.22), residues: 746 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 248 time to evaluate : 2.825 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 254 average time/residue: 0.3248 time to fit residues: 130.3525 Evaluate side-chains 245 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 239 time to evaluate : 2.643 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1909 time to fit residues: 5.8301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 234 optimal weight: 0.7980 chunk 203 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 23362 Z= 0.244 Angle : 0.562 10.427 31344 Z= 0.274 Chirality : 0.044 0.237 3438 Planarity : 0.003 0.040 3784 Dihedral : 12.401 59.774 3926 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2590 helix: 1.34 (0.14), residues: 1620 sheet: -0.56 (0.33), residues: 222 loop : -1.43 (0.22), residues: 748 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 242 time to evaluate : 2.676 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 246 average time/residue: 0.3360 time to fit residues: 130.0917 Evaluate side-chains 241 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 236 time to evaluate : 2.525 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2010 time to fit residues: 5.3393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.102122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.082819 restraints weight = 39306.749| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.92 r_work: 0.2881 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 23362 Z= 0.243 Angle : 0.556 11.158 31344 Z= 0.273 Chirality : 0.043 0.222 3438 Planarity : 0.003 0.040 3784 Dihedral : 12.233 59.962 3926 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2590 helix: 1.37 (0.14), residues: 1624 sheet: -0.55 (0.33), residues: 222 loop : -1.41 (0.22), residues: 744 =============================================================================== Job complete usr+sys time: 4169.52 seconds wall clock time: 76 minutes 51.53 seconds (4611.53 seconds total)