Starting phenix.real_space_refine on Thu Mar 14 18:55:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dhx_27437/03_2024/8dhx_27437_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dhx_27437/03_2024/8dhx_27437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dhx_27437/03_2024/8dhx_27437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dhx_27437/03_2024/8dhx_27437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dhx_27437/03_2024/8dhx_27437_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dhx_27437/03_2024/8dhx_27437_neut.pdb" } resolution = 2.92 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= 0.002 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 33936 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 21504 2.51 5 N 5976 2.21 5 O 6600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 27": "OE1" <-> "OE2" Residue "1 GLU 62": "OE1" <-> "OE2" Residue "1 GLU 64": "OE1" <-> "OE2" Residue "1 GLU 116": "OE1" <-> "OE2" Residue "1 GLU 167": "OE1" <-> "OE2" Residue "2 GLU 27": "OE1" <-> "OE2" Residue "2 GLU 62": "OE1" <-> "OE2" Residue "2 GLU 64": "OE1" <-> "OE2" Residue "2 GLU 116": "OE1" <-> "OE2" Residue "2 GLU 167": "OE1" <-> "OE2" Residue "4 GLU 27": "OE1" <-> "OE2" Residue "4 GLU 62": "OE1" <-> "OE2" Residue "4 GLU 64": "OE1" <-> "OE2" Residue "4 GLU 116": "OE1" <-> "OE2" Residue "4 GLU 167": "OE1" <-> "OE2" Residue "6 GLU 27": "OE1" <-> "OE2" Residue "6 GLU 62": "OE1" <-> "OE2" Residue "6 GLU 64": "OE1" <-> "OE2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "6 GLU 167": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K GLU 62": "OE1" <-> "OE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M GLU 62": "OE1" <-> "OE2" Residue "M GLU 64": "OE1" <-> "OE2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O GLU 62": "OE1" <-> "OE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "O GLU 167": "OE1" <-> "OE2" Residue "P GLU 27": "OE1" <-> "OE2" Residue "P GLU 62": "OE1" <-> "OE2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "P GLU 167": "OE1" <-> "OE2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q GLU 62": "OE1" <-> "OE2" Residue "Q GLU 64": "OE1" <-> "OE2" Residue "Q GLU 116": "OE1" <-> "OE2" Residue "Q GLU 167": "OE1" <-> "OE2" Residue "S GLU 27": "OE1" <-> "OE2" Residue "S GLU 62": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S GLU 116": "OE1" <-> "OE2" Residue "S GLU 167": "OE1" <-> "OE2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U GLU 62": "OE1" <-> "OE2" Residue "U GLU 64": "OE1" <-> "OE2" Residue "U GLU 116": "OE1" <-> "OE2" Residue "U GLU 167": "OE1" <-> "OE2" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W GLU 62": "OE1" <-> "OE2" Residue "W GLU 64": "OE1" <-> "OE2" Residue "W GLU 116": "OE1" <-> "OE2" Residue "W GLU 167": "OE1" <-> "OE2" Residue "X GLU 27": "OE1" <-> "OE2" Residue "X GLU 62": "OE1" <-> "OE2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "X GLU 116": "OE1" <-> "OE2" Residue "X GLU 167": "OE1" <-> "OE2" Residue "Y GLU 27": "OE1" <-> "OE2" Residue "Y GLU 62": "OE1" <-> "OE2" Residue "Y GLU 64": "OE1" <-> "OE2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Y GLU 167": "OE1" <-> "OE2" Residue "a GLU 27": "OE1" <-> "OE2" Residue "a GLU 62": "OE1" <-> "OE2" Residue "a GLU 64": "OE1" <-> "OE2" Residue "a GLU 116": "OE1" <-> "OE2" Residue "a GLU 167": "OE1" <-> "OE2" Residue "e GLU 27": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 167": "OE1" <-> "OE2" Residue "r GLU 27": "OE1" <-> "OE2" Residue "r GLU 62": "OE1" <-> "OE2" Residue "r GLU 64": "OE1" <-> "OE2" Residue "r GLU 116": "OE1" <-> "OE2" Residue "r GLU 167": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34200 Number of models: 1 Model: "" Number of chains: 24 Chain: "1" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "2" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "4" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "6" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "A" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "B" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "E" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "F" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "G" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "H" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "I" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "K" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "M" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "O" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "P" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "Q" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "S" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "U" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "W" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "X" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "Y" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "a" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "e" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Chain: "r" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Time building chain proxies: 23.52, per 1000 atoms: 0.69 Number of scatterers: 34200 At special positions: 0 Unit cell: (137.16, 137.16, 137.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 6600 8.00 N 5976 7.00 C 21504 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: 9.71 Conformation dependent library (CDL) restraints added in 8.3 seconds 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain '1' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE 1 20 " --> pdb=" O SER 1 16 " (cutoff:3.500A) Processing helix chain '1' and resid 48 through 76 Processing helix chain '1' and resid 95 through 124 Processing helix chain '1' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS 1 130 " --> pdb=" O ASP 1 126 " (cutoff:3.500A) Processing helix chain '1' and resid 137 through 159 Processing helix chain '1' and resid 162 through 174 Processing helix chain '2' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE 2 20 " --> pdb=" O SER 2 16 " (cutoff:3.500A) Processing helix chain '2' and resid 48 through 76 Processing helix chain '2' and resid 95 through 124 Processing helix chain '2' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS 2 130 " --> pdb=" O ASP 2 126 " (cutoff:3.500A) Processing helix chain '2' and resid 137 through 159 Processing helix chain '2' and resid 162 through 174 Processing helix chain '4' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE 4 20 " --> pdb=" O SER 4 16 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 76 Processing helix chain '4' and resid 95 through 124 Processing helix chain '4' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS 4 130 " --> pdb=" O ASP 4 126 " (cutoff:3.500A) Processing helix chain '4' and resid 137 through 159 Processing helix chain '4' and resid 162 through 174 Processing helix chain '6' and resid 13 through 42 removed outlier: 3.510A pdb=" N ILE 6 20 " --> pdb=" O SER 6 16 " (cutoff:3.500A) Processing helix chain '6' and resid 48 through 76 Processing helix chain '6' and resid 95 through 124 Processing helix chain '6' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS 6 130 " --> pdb=" O ASP 6 126 " (cutoff:3.500A) Processing helix chain '6' and resid 137 through 159 Processing helix chain '6' and resid 162 through 174 Processing helix chain 'A' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'B' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE B 20 " --> pdb=" O SER B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'E' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'F' and resid 13 through 42 removed outlier: 3.510A pdb=" N ILE F 20 " --> pdb=" O SER F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'G' and resid 13 through 42 removed outlier: 3.510A pdb=" N ILE G 20 " --> pdb=" O SER G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS G 130 " --> pdb=" O ASP G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 162 through 174 Processing helix chain 'H' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS H 130 " --> pdb=" O ASP H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 162 through 174 Processing helix chain 'I' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE I 20 " --> pdb=" O SER I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS I 130 " --> pdb=" O ASP I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 162 through 174 Processing helix chain 'K' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE K 20 " --> pdb=" O SER K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS K 130 " --> pdb=" O ASP K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 162 through 174 Processing helix chain 'M' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE M 20 " --> pdb=" O SER M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS M 130 " --> pdb=" O ASP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 162 through 174 Processing helix chain 'O' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE O 20 " --> pdb=" O SER O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS O 130 " --> pdb=" O ASP O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 162 through 174 Processing helix chain 'P' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE P 20 " --> pdb=" O SER P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS P 130 " --> pdb=" O ASP P 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 162 through 174 Processing helix chain 'Q' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE Q 20 " --> pdb=" O SER Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS Q 130 " --> pdb=" O ASP Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 162 through 174 Processing helix chain 'S' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE S 20 " --> pdb=" O SER S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 removed outlier: 3.515A pdb=" N CYS S 130 " --> pdb=" O ASP S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 162 through 174 Processing helix chain 'U' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE U 20 " --> pdb=" O SER U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS U 130 " --> pdb=" O ASP U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 162 through 174 Processing helix chain 'W' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE W 20 " --> pdb=" O SER W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS W 130 " --> pdb=" O ASP W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 162 through 174 Processing helix chain 'X' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE X 20 " --> pdb=" O SER X 16 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 removed outlier: 3.515A pdb=" N CYS X 130 " --> pdb=" O ASP X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 162 through 174 Processing helix chain 'Y' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE Y 20 " --> pdb=" O SER Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 76 Processing helix chain 'Y' and resid 95 through 124 Processing helix chain 'Y' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS Y 130 " --> pdb=" O ASP Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 137 through 159 Processing helix chain 'Y' and resid 162 through 174 Processing helix chain 'a' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE a 20 " --> pdb=" O SER a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 76 Processing helix chain 'a' and resid 95 through 124 Processing helix chain 'a' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS a 130 " --> pdb=" O ASP a 126 " (cutoff:3.500A) Processing helix chain 'a' and resid 137 through 159 Processing helix chain 'a' and resid 162 through 174 Processing helix chain 'e' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE e 20 " --> pdb=" O SER e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 76 Processing helix chain 'e' and resid 95 through 124 Processing helix chain 'e' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) Processing helix chain 'e' and resid 137 through 159 Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'r' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE r 20 " --> pdb=" O SER r 16 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 76 Processing helix chain 'r' and resid 95 through 124 Processing helix chain 'r' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS r 130 " --> pdb=" O ASP r 126 " (cutoff:3.500A) Processing helix chain 'r' and resid 137 through 159 Processing helix chain 'r' and resid 162 through 174 2664 hydrogen bonds defined for protein. 7944 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: 7.83 Time building geometry restraints manager: 10.69 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: 6748 1.32 - 1.45: 8650 1.45 - 1.57: 19330 1.57 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 34944 Sorted by residual: bond pdb=" C SER F 163 " pdb=" O SER F 163 " ideal model delta sigma weight residual 1.237 1.204 0.033 1.17e-02 7.31e+03 7.87e+00 bond pdb=" C SER O 163 " pdb=" O SER O 163 " ideal model delta sigma weight residual 1.237 1.204 0.033 1.17e-02 7.31e+03 7.84e+00 bond pdb=" C SER 4 163 " pdb=" O SER 4 163 " ideal model delta sigma weight residual 1.237 1.204 0.033 1.17e-02 7.31e+03 7.84e+00 bond pdb=" C SER M 163 " pdb=" O SER M 163 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.17e-02 7.31e+03 7.51e+00 bond pdb=" C SER W 163 " pdb=" O SER W 163 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.17e-02 7.31e+03 7.51e+00 ... (remaining 34939 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.38: 984 107.38 - 114.02: 19224 114.02 - 120.66: 15591 120.66 - 127.30: 10977 127.30 - 133.94: 384 Bond angle restraints: 47160 Sorted by residual: angle pdb=" C GLN A 14 " pdb=" N ASP A 15 " pdb=" CA ASP A 15 " ideal model delta sigma weight residual 120.44 131.69 -11.25 1.30e+00 5.92e-01 7.49e+01 angle pdb=" C GLN Y 14 " pdb=" N ASP Y 15 " pdb=" CA ASP Y 15 " ideal model delta sigma weight residual 120.44 131.68 -11.24 1.30e+00 5.92e-01 7.48e+01 angle pdb=" C GLN X 14 " pdb=" N ASP X 15 " pdb=" CA ASP X 15 " ideal model delta sigma weight residual 120.44 131.66 -11.22 1.30e+00 5.92e-01 7.45e+01 angle pdb=" C GLN Q 14 " pdb=" N ASP Q 15 " pdb=" CA ASP Q 15 " ideal model delta sigma weight residual 120.44 131.65 -11.21 1.30e+00 5.92e-01 7.44e+01 angle pdb=" C GLN I 14 " pdb=" N ASP I 15 " pdb=" CA ASP I 15 " ideal model delta sigma weight residual 120.44 131.65 -11.21 1.30e+00 5.92e-01 7.44e+01 ... (remaining 47155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 18236 17.41 - 34.83: 2092 34.83 - 52.24: 648 52.24 - 69.65: 168 69.65 - 87.06: 96 Dihedral angle restraints: 21240 sinusoidal: 8736 harmonic: 12504 Sorted by residual: dihedral pdb=" CA TYR r 39 " pdb=" C TYR r 39 " pdb=" N TYR r 40 " pdb=" CA TYR r 40 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA TYR A 39 " pdb=" C TYR A 39 " pdb=" N TYR A 40 " pdb=" CA TYR A 40 " ideal model delta harmonic sigma weight residual 180.00 164.13 15.87 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA TYR S 39 " pdb=" C TYR S 39 " pdb=" N TYR S 40 " pdb=" CA TYR S 40 " ideal model delta harmonic sigma weight residual 180.00 164.14 15.86 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 21237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4234 0.047 - 0.094: 421 0.094 - 0.141: 268 0.141 - 0.188: 45 0.188 - 0.234: 24 Chirality restraints: 4992 Sorted by residual: chirality pdb=" CG LEU W 97 " pdb=" CB LEU W 97 " pdb=" CD1 LEU W 97 " pdb=" CD2 LEU W 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CG LEU I 97 " pdb=" CB LEU I 97 " pdb=" CD1 LEU I 97 " pdb=" CD2 LEU I 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CG LEU Y 97 " pdb=" CB LEU Y 97 " pdb=" CD1 LEU Y 97 " pdb=" CD2 LEU Y 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 4989 not shown) Planarity restraints: 6216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER M 95 " 0.005 2.00e-02 2.50e+03 1.06e-02 1.13e+00 pdb=" C SER M 95 " -0.018 2.00e-02 2.50e+03 pdb=" O SER M 95 " 0.007 2.00e-02 2.50e+03 pdb=" N GLY M 96 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 95 " 0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C SER F 95 " -0.018 2.00e-02 2.50e+03 pdb=" O SER F 95 " 0.007 2.00e-02 2.50e+03 pdb=" N GLY F 96 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER U 95 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C SER U 95 " 0.018 2.00e-02 2.50e+03 pdb=" O SER U 95 " -0.007 2.00e-02 2.50e+03 pdb=" N GLY U 96 " -0.006 2.00e-02 2.50e+03 ... (remaining 6213 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4885 2.75 - 3.29: 33685 3.29 - 3.83: 58947 3.83 - 4.36: 69949 4.36 - 4.90: 120726 Nonbonded interactions: 288192 Sorted by model distance: nonbonded pdb=" ND2 ASN X 50 " pdb=" OD1 ASP X 171 " model vdw 2.218 2.520 nonbonded pdb=" ND2 ASN I 50 " pdb=" OD1 ASP I 171 " model vdw 2.218 2.520 nonbonded pdb=" ND2 ASN F 50 " pdb=" OD1 ASP F 171 " model vdw 2.218 2.520 nonbonded pdb=" ND2 ASN H 50 " pdb=" OD1 ASP H 171 " model vdw 2.218 2.520 nonbonded pdb=" ND2 ASN E 50 " pdb=" OD1 ASP E 171 " model vdw 2.219 2.520 ... (remaining 288187 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 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain '2' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain '4' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain '6' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'A' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'B' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'E' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'F' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'G' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'H' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'I' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'K' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'M' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'O' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'P' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'Q' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'S' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'U' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'W' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'X' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'Y' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'a' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'e' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'r' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) } 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=0.00 max=1.00 mean=0.99 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.300 Construct map_model_manager: 0.010 Extract box with map and model: 6.550 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 78.550 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.150 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:9.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2119 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 : 0.004 0.033 34944 Z= 0.254 Angle : 0.819 11.251 47160 Z= 0.517 Chirality : 0.043 0.234 4992 Planarity : 0.003 0.016 6216 Dihedral : 17.606 87.065 13176 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.58 % Allowed : 1.75 % Favored : 97.66 % Rotamer: Outliers : 1.95 % Allowed : 19.48 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.13), residues: 4152 helix: 3.21 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -1.37 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 2 93 HIS 0.007 0.001 HIS U 13 PHE 0.011 0.001 PHE O 132 TYR 0.012 0.002 TYR Q 137 ARG 0.002 0.000 ARG F 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 639 time to evaluate : 3.023 Fit side-chains REVERT: 2 153 THR cc_start: 0.3586 (OUTLIER) cc_final: 0.3232 (t) REVERT: 4 153 THR cc_start: 0.3585 (OUTLIER) cc_final: 0.3227 (t) REVERT: 6 153 THR cc_start: 0.3584 (OUTLIER) cc_final: 0.3184 (t) REVERT: F 153 THR cc_start: 0.3578 (OUTLIER) cc_final: 0.3209 (t) REVERT: H 153 THR cc_start: 0.3579 (OUTLIER) cc_final: 0.3181 (t) REVERT: I 153 THR cc_start: 0.3583 (OUTLIER) cc_final: 0.3224 (t) REVERT: M 153 THR cc_start: 0.3583 (OUTLIER) cc_final: 0.3225 (t) REVERT: O 153 THR cc_start: 0.3582 (OUTLIER) cc_final: 0.3223 (t) REVERT: P 153 THR cc_start: 0.3605 (OUTLIER) cc_final: 0.3210 (t) REVERT: Q 153 THR cc_start: 0.3583 (OUTLIER) cc_final: 0.3226 (t) REVERT: S 153 THR cc_start: 0.3586 (OUTLIER) cc_final: 0.3230 (t) REVERT: U 153 THR cc_start: 0.3583 (OUTLIER) cc_final: 0.3228 (t) REVERT: W 153 THR cc_start: 0.3585 (OUTLIER) cc_final: 0.3224 (t) REVERT: X 153 THR cc_start: 0.3583 (OUTLIER) cc_final: 0.3223 (t) REVERT: Y 153 THR cc_start: 0.3587 (OUTLIER) cc_final: 0.3230 (t) outliers start: 72 outliers final: 24 residues processed: 687 average time/residue: 1.1577 time to fit residues: 948.5491 Evaluate side-chains 580 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 541 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 89 ASP Chi-restraints excluded: chain 2 residue 89 ASP Chi-restraints excluded: chain 2 residue 153 THR Chi-restraints excluded: chain 4 residue 89 ASP Chi-restraints excluded: chain 4 residue 153 THR Chi-restraints excluded: chain 6 residue 89 ASP Chi-restraints excluded: chain 6 residue 153 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain Q residue 153 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain S residue 153 THR Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 153 THR Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 153 THR Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain X residue 153 THR Chi-restraints excluded: chain Y residue 89 ASP Chi-restraints excluded: chain Y residue 153 THR Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain e residue 89 ASP Chi-restraints excluded: chain r residue 89 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 6.9990 chunk 309 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 319 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2127 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 34944 Z= 0.317 Angle : 0.648 6.917 47160 Z= 0.334 Chirality : 0.040 0.124 4992 Planarity : 0.003 0.024 6216 Dihedral : 5.992 58.894 4671 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.68 % Allowed : 20.37 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.17 (0.13), residues: 4152 helix: 3.61 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -1.32 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP S 93 HIS 0.004 0.001 HIS P 151 PHE 0.019 0.002 PHE 1 41 TYR 0.027 0.003 TYR G 39 ARG 0.006 0.001 ARG K 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 646 time to evaluate : 3.035 Fit side-chains outliers start: 173 outliers final: 63 residues processed: 741 average time/residue: 1.1516 time to fit residues: 1020.5844 Evaluate side-chains 641 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 578 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 89 ASP Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 89 ASP Chi-restraints excluded: chain 2 residue 153 THR Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 89 ASP Chi-restraints excluded: chain 4 residue 153 THR Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 89 ASP Chi-restraints excluded: chain 6 residue 153 THR Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain Q residue 153 THR Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain S residue 153 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 153 THR Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 153 THR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain X residue 153 THR Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 89 ASP Chi-restraints excluded: chain Y residue 153 THR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 89 ASP Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 89 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 371 optimal weight: 3.9990 chunk 400 optimal weight: 6.9990 chunk 330 optimal weight: 0.9990 chunk 368 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 297 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2129 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 34944 Z= 0.304 Angle : 0.616 8.980 47160 Z= 0.321 Chirality : 0.038 0.124 4992 Planarity : 0.003 0.020 6216 Dihedral : 5.101 34.685 4671 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.46 % Allowed : 19.59 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.52 (0.13), residues: 4152 helix: 3.79 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.84 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP e 93 HIS 0.003 0.001 HIS U 151 PHE 0.016 0.002 PHE O 132 TYR 0.023 0.002 TYR a 39 ARG 0.006 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 587 time to evaluate : 2.919 Fit side-chains outliers start: 165 outliers final: 96 residues processed: 681 average time/residue: 1.0732 time to fit residues: 885.5057 Evaluate side-chains 669 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 573 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 1 residue 64 GLU Chi-restraints excluded: chain 1 residue 89 ASP Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 SER Chi-restraints excluded: chain 2 residue 64 GLU Chi-restraints excluded: chain 2 residue 89 ASP Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 64 GLU Chi-restraints excluded: chain 4 residue 89 ASP Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 89 ASP Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 SER Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 89 ASP Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 64 GLU Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 89 ASP Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 SER Chi-restraints excluded: chain r residue 64 GLU Chi-restraints excluded: chain r residue 89 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 249 optimal weight: 4.9990 chunk 372 optimal weight: 0.8980 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 353 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 73 GLN 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 73 GLN B 109 ASN E 73 GLN E 109 ASN F 109 ASN G 73 GLN G 109 ASN H 109 ASN I 109 ASN K 73 GLN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 73 GLN a 109 ASN e 73 GLN e 109 ASN r 73 GLN r 109 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2129 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 34944 Z= 0.285 Angle : 0.599 8.060 47160 Z= 0.313 Chirality : 0.038 0.121 4992 Planarity : 0.003 0.022 6216 Dihedral : 5.092 36.547 4656 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 5.44 % Allowed : 19.43 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.64 (0.13), residues: 4152 helix: 3.84 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.60 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 93 HIS 0.003 0.001 HIS F 151 PHE 0.016 0.002 PHE r 132 TYR 0.023 0.002 TYR P 39 ARG 0.007 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 570 time to evaluate : 3.536 Fit side-chains outliers start: 201 outliers final: 96 residues processed: 701 average time/residue: 1.0870 time to fit residues: 919.0359 Evaluate side-chains 658 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 562 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 1 residue 64 GLU Chi-restraints excluded: chain 1 residue 89 ASP Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 SER Chi-restraints excluded: chain 2 residue 64 GLU Chi-restraints excluded: chain 2 residue 89 ASP Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 64 GLU Chi-restraints excluded: chain 4 residue 89 ASP Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 89 ASP Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 SER Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 89 ASP Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 64 GLU Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 89 ASP Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 SER Chi-restraints excluded: chain r residue 64 GLU Chi-restraints excluded: chain r residue 89 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 293 optimal weight: 0.3980 chunk 162 optimal weight: 0.9990 chunk 336 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 201 optimal weight: 0.9990 chunk 353 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 73 GLN 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 73 GLN B 109 ASN E 73 GLN E 109 ASN F 109 ASN G 73 GLN G 109 ASN H 109 ASN I 109 ASN K 73 GLN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 73 GLN a 109 ASN e 73 GLN e 109 ASN r 73 GLN r 109 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2135 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34944 Z= 0.188 Angle : 0.555 8.427 47160 Z= 0.289 Chirality : 0.035 0.123 4992 Planarity : 0.003 0.023 6216 Dihedral : 4.806 34.053 4656 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.71 % Allowed : 22.08 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.18 (0.13), residues: 4152 helix: 4.20 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.34 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 6 93 HIS 0.002 0.000 HIS S 151 PHE 0.012 0.001 PHE B 132 TYR 0.025 0.002 TYR P 29 ARG 0.007 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 540 time to evaluate : 2.975 Fit side-chains outliers start: 137 outliers final: 58 residues processed: 617 average time/residue: 1.1710 time to fit residues: 861.7773 Evaluate side-chains 595 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 537 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 89 ASP Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 SER Chi-restraints excluded: chain 2 residue 89 ASP Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 89 ASP Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 89 ASP Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 22 ARG Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 89 ASP Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 89 ASP Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 89 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 5.9990 chunk 355 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 231 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 394 optimal weight: 4.9990 chunk 327 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2140 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34944 Z= 0.218 Angle : 0.569 8.330 47160 Z= 0.297 Chirality : 0.035 0.120 4992 Planarity : 0.003 0.031 6216 Dihedral : 4.818 33.107 4656 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.92 % Allowed : 23.51 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.27 (0.13), residues: 4152 helix: 4.26 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.34 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 93 HIS 0.003 0.001 HIS M 151 PHE 0.014 0.002 PHE K 132 TYR 0.025 0.002 TYR P 39 ARG 0.005 0.001 ARG M 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 534 time to evaluate : 2.943 Fit side-chains outliers start: 108 outliers final: 77 residues processed: 587 average time/residue: 1.1107 time to fit residues: 783.9791 Evaluate side-chains 606 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 529 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 1 residue 89 ASP Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 SER Chi-restraints excluded: chain 2 residue 89 ASP Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 89 ASP Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 89 ASP Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 SER Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 89 ASP Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 89 ASP Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 SER Chi-restraints excluded: chain r residue 89 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 288 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 332 optimal weight: 0.0040 chunk 220 optimal weight: 9.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 2 112 GLN 4 109 ASN 6 109 ASN 6 112 GLN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN H 112 GLN I 109 ASN I 112 GLN K 109 ASN M 109 ASN O 109 ASN O 112 GLN P 109 ASN Q 109 ASN Q 112 GLN S 109 ASN U 109 ASN U 112 GLN W 109 ASN X 109 ASN X 112 GLN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2134 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34944 Z= 0.182 Angle : 0.572 8.331 47160 Z= 0.294 Chirality : 0.034 0.123 4992 Planarity : 0.003 0.033 6216 Dihedral : 4.656 30.599 4656 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.27 % Allowed : 23.54 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.55 (0.13), residues: 4152 helix: 4.46 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.23 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Y 93 HIS 0.003 0.000 HIS H 151 PHE 0.012 0.001 PHE 1 132 TYR 0.029 0.002 TYR 4 39 ARG 0.006 0.000 ARG H 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 529 time to evaluate : 2.905 Fit side-chains REVERT: A 156 ARG cc_start: 0.5494 (tpp-160) cc_final: 0.5279 (tpp80) REVERT: K 156 ARG cc_start: 0.5664 (tpp-160) cc_final: 0.5444 (tpp80) REVERT: a 156 ARG cc_start: 0.5569 (tpp-160) cc_final: 0.5356 (tpp80) outliers start: 84 outliers final: 70 residues processed: 580 average time/residue: 1.2234 time to fit residues: 861.1844 Evaluate side-chains 597 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 527 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 1 residue 89 ASP Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 SER Chi-restraints excluded: chain 2 residue 89 ASP Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 89 ASP Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 89 ASP Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 SER Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 89 ASP Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 89 ASP Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 SER Chi-restraints excluded: chain r residue 89 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 267 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 309 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 4 112 GLN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN S 112 GLN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN Y 112 GLN a 109 ASN a 112 GLN e 109 ASN r 109 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2139 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34944 Z= 0.221 Angle : 0.591 8.383 47160 Z= 0.304 Chirality : 0.035 0.121 4992 Planarity : 0.003 0.029 6216 Dihedral : 4.762 30.823 4656 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.52 % Allowed : 23.05 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.33 (0.13), residues: 4152 helix: 4.31 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.31 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 1 93 HIS 0.003 0.001 HIS 6 151 PHE 0.014 0.002 PHE G 132 TYR 0.026 0.002 TYR Q 39 ARG 0.003 0.000 ARG H 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 549 time to evaluate : 2.992 Fit side-chains REVERT: E 156 ARG cc_start: 0.5659 (tpp-160) cc_final: 0.5457 (tpp80) REVERT: a 156 ARG cc_start: 0.5660 (tpp-160) cc_final: 0.5452 (tpp80) REVERT: e 156 ARG cc_start: 0.5665 (tpp-160) cc_final: 0.5459 (tpp80) outliers start: 130 outliers final: 75 residues processed: 635 average time/residue: 1.1058 time to fit residues: 844.7882 Evaluate side-chains 620 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 545 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 1 residue 89 ASP Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 SER Chi-restraints excluded: chain 2 residue 89 ASP Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 89 ASP Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 89 ASP Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 SER Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 89 ASP Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 89 ASP Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 SER Chi-restraints excluded: chain r residue 89 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.9990 chunk 376 optimal weight: 2.9990 chunk 343 optimal weight: 0.9980 chunk 366 optimal weight: 0.2980 chunk 220 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 287 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 331 optimal weight: 0.0570 chunk 346 optimal weight: 2.9990 chunk 365 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN F 112 GLN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN M 112 GLN O 109 ASN P 109 ASN P 112 GLN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN W 112 GLN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2131 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34944 Z= 0.150 Angle : 0.569 8.387 47160 Z= 0.291 Chirality : 0.033 0.127 4992 Planarity : 0.003 0.029 6216 Dihedral : 4.405 24.632 4656 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.08 % Allowed : 24.22 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.72 (0.13), residues: 4152 helix: 4.59 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.20 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 93 HIS 0.003 0.000 HIS K 151 PHE 0.009 0.001 PHE e 132 TYR 0.026 0.001 TYR A 29 ARG 0.007 0.000 ARG K 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 564 time to evaluate : 2.918 Fit side-chains REVERT: E 156 ARG cc_start: 0.5478 (tpp-160) cc_final: 0.5227 (tpp80) REVERT: H 156 ARG cc_start: 0.5448 (tpp-160) cc_final: 0.5238 (tpp80) REVERT: a 156 ARG cc_start: 0.5510 (tpp-160) cc_final: 0.5253 (tpp80) REVERT: e 156 ARG cc_start: 0.5477 (tpp-160) cc_final: 0.5223 (tpp80) outliers start: 77 outliers final: 20 residues processed: 622 average time/residue: 1.1555 time to fit residues: 859.2029 Evaluate side-chains 580 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 560 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain W residue 6 SER Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 7.9990 chunk 387 optimal weight: 5.9990 chunk 236 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 269 optimal weight: 2.9990 chunk 406 optimal weight: 0.0170 chunk 374 optimal weight: 3.9990 chunk 323 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2134 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34944 Z= 0.192 Angle : 0.570 8.058 47160 Z= 0.295 Chirality : 0.034 0.119 4992 Planarity : 0.003 0.031 6216 Dihedral : 4.071 20.310 4608 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.35 % Allowed : 25.08 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.58 (0.13), residues: 4152 helix: 4.49 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.25 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 93 HIS 0.003 0.001 HIS H 151 PHE 0.012 0.001 PHE a 132 TYR 0.032 0.002 TYR E 39 ARG 0.005 0.000 ARG K 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 547 time to evaluate : 3.049 Fit side-chains REVERT: E 156 ARG cc_start: 0.5567 (tpp-160) cc_final: 0.5313 (tpp80) REVERT: H 156 ARG cc_start: 0.5440 (tpp-160) cc_final: 0.5235 (tpp80) REVERT: e 156 ARG cc_start: 0.5507 (tpp-160) cc_final: 0.5249 (tpp80) outliers start: 50 outliers final: 35 residues processed: 565 average time/residue: 1.1637 time to fit residues: 791.3487 Evaluate side-chains 582 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 547 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 SER Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 6.9990 chunk 344 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 324 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 332 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 1 112 GLN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN E 112 GLN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN K 112 GLN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN e 112 GLN r 109 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.137952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122288 restraints weight = 181217.445| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 4.41 r_work: 0.3429 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34944 Z= 0.163 Angle : 0.557 8.418 47160 Z= 0.288 Chirality : 0.033 0.120 4992 Planarity : 0.003 0.031 6216 Dihedral : 4.040 20.520 4608 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.46 % Allowed : 25.35 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.72 (0.13), residues: 4152 helix: 4.57 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.15 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP W 93 HIS 0.003 0.000 HIS P 151 PHE 0.012 0.001 PHE a 132 TYR 0.027 0.002 TYR S 29 ARG 0.002 0.000 ARG K 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12882.15 seconds wall clock time: 224 minutes 5.55 seconds (13445.55 seconds total)