Starting phenix.real_space_refine on Mon Mar 25 04:22:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9i_5623/03_2024/3j9i_5623.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9i_5623/03_2024/3j9i_5623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9i_5623/03_2024/3j9i_5623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9i_5623/03_2024/3j9i_5623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9i_5623/03_2024/3j9i_5623.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9i_5623/03_2024/3j9i_5623.pdb" } resolution = 3.3 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= -0.008 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 29288 2.51 5 N 7840 2.21 5 O 8904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 25": "OE1" <-> "OE2" Residue "S GLU 29": "OE1" <-> "OE2" Residue "S GLU 60": "OE1" <-> "OE2" Residue "S GLU 110": "OE1" <-> "OE2" Residue "S GLU 177": "OE1" <-> "OE2" Residue "S GLU 179": "OE1" <-> "OE2" Residue "S GLU 186": "OE1" <-> "OE2" Residue "S GLU 188": "OE1" <-> "OE2" Residue "S GLU 202": "OE1" <-> "OE2" Residue "S GLU 205": "OE1" <-> "OE2" Residue "S GLU 211": "OE1" <-> "OE2" Residue "S GLU 227": "OE1" <-> "OE2" Residue "S GLU 228": "OE1" <-> "OE2" Residue "Z GLU 17": "OE1" <-> "OE2" Residue "Z PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 121": "OE1" <-> "OE2" Residue "Z ASP 182": "OD1" <-> "OD2" Residue "Z GLU 193": "OE1" <-> "OE2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 25": "OE1" <-> "OE2" Residue "F GLU 29": "OE1" <-> "OE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F GLU 177": "OE1" <-> "OE2" Residue "F GLU 179": "OE1" <-> "OE2" Residue "F GLU 186": "OE1" <-> "OE2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 121": "OE1" <-> "OE2" Residue "M ASP 182": "OD1" <-> "OD2" Residue "M GLU 193": "OE1" <-> "OE2" Residue "T PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "T GLU 29": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T GLU 110": "OE1" <-> "OE2" Residue "T GLU 177": "OE1" <-> "OE2" Residue "T GLU 179": "OE1" <-> "OE2" Residue "T GLU 186": "OE1" <-> "OE2" Residue "T GLU 188": "OE1" <-> "OE2" Residue "T GLU 202": "OE1" <-> "OE2" Residue "T GLU 205": "OE1" <-> "OE2" Residue "T GLU 211": "OE1" <-> "OE2" Residue "T GLU 227": "OE1" <-> "OE2" Residue "T GLU 228": "OE1" <-> "OE2" Residue "1 GLU 17": "OE1" <-> "OE2" Residue "1 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 121": "OE1" <-> "OE2" Residue "1 ASP 182": "OD1" <-> "OD2" Residue "1 GLU 193": "OE1" <-> "OE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 25": "OE1" <-> "OE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 177": "OE1" <-> "OE2" Residue "G GLU 179": "OE1" <-> "OE2" Residue "G GLU 186": "OE1" <-> "OE2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "G GLU 211": "OE1" <-> "OE2" Residue "G GLU 227": "OE1" <-> "OE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 121": "OE1" <-> "OE2" Residue "N ASP 182": "OD1" <-> "OD2" Residue "N GLU 193": "OE1" <-> "OE2" Residue "U PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 25": "OE1" <-> "OE2" Residue "U GLU 29": "OE1" <-> "OE2" Residue "U GLU 60": "OE1" <-> "OE2" Residue "U GLU 110": "OE1" <-> "OE2" Residue "U GLU 177": "OE1" <-> "OE2" Residue "U GLU 179": "OE1" <-> "OE2" Residue "U GLU 186": "OE1" <-> "OE2" Residue "U GLU 188": "OE1" <-> "OE2" Residue "U GLU 202": "OE1" <-> "OE2" Residue "U GLU 205": "OE1" <-> "OE2" Residue "U GLU 211": "OE1" <-> "OE2" Residue "U GLU 227": "OE1" <-> "OE2" Residue "U GLU 228": "OE1" <-> "OE2" Residue "2 GLU 17": "OE1" <-> "OE2" Residue "2 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 121": "OE1" <-> "OE2" Residue "2 ASP 182": "OD1" <-> "OD2" Residue "2 GLU 193": "OE1" <-> "OE2" Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 121": "OE1" <-> "OE2" Residue "H ASP 182": "OD1" <-> "OD2" Residue "H GLU 193": "OE1" <-> "OE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 25": "OE1" <-> "OE2" Residue "O GLU 29": "OE1" <-> "OE2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O GLU 110": "OE1" <-> "OE2" Residue "O GLU 177": "OE1" <-> "OE2" Residue "O GLU 179": "OE1" <-> "OE2" Residue "O GLU 186": "OE1" <-> "OE2" Residue "O GLU 188": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "O GLU 205": "OE1" <-> "OE2" Residue "O GLU 211": "OE1" <-> "OE2" Residue "O GLU 227": "OE1" <-> "OE2" Residue "O GLU 228": "OE1" <-> "OE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 121": "OE1" <-> "OE2" Residue "V ASP 182": "OD1" <-> "OD2" Residue "V GLU 193": "OE1" <-> "OE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I ASP 182": "OD1" <-> "OD2" Residue "I GLU 193": "OE1" <-> "OE2" Residue "P PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 25": "OE1" <-> "OE2" Residue "P GLU 29": "OE1" <-> "OE2" Residue "P GLU 60": "OE1" <-> "OE2" Residue "P GLU 110": "OE1" <-> "OE2" Residue "P GLU 177": "OE1" <-> "OE2" Residue "P GLU 179": "OE1" <-> "OE2" Residue "P GLU 186": "OE1" <-> "OE2" Residue "P GLU 188": "OE1" <-> "OE2" Residue "P GLU 202": "OE1" <-> "OE2" Residue "P GLU 205": "OE1" <-> "OE2" Residue "P GLU 211": "OE1" <-> "OE2" Residue "P GLU 227": "OE1" <-> "OE2" Residue "P GLU 228": "OE1" <-> "OE2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 121": "OE1" <-> "OE2" Residue "W ASP 182": "OD1" <-> "OD2" Residue "W GLU 193": "OE1" <-> "OE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 25": "OE1" <-> "OE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "J GLU 17": "OE1" <-> "OE2" Residue "J PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J ASP 182": "OD1" <-> "OD2" Residue "J GLU 193": "OE1" <-> "OE2" Residue "Q PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 25": "OE1" <-> "OE2" Residue "Q GLU 29": "OE1" <-> "OE2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "Q GLU 110": "OE1" <-> "OE2" Residue "Q GLU 177": "OE1" <-> "OE2" Residue "Q GLU 179": "OE1" <-> "OE2" Residue "Q GLU 186": "OE1" <-> "OE2" Residue "Q GLU 188": "OE1" <-> "OE2" Residue "Q GLU 202": "OE1" <-> "OE2" Residue "Q GLU 205": "OE1" <-> "OE2" Residue "Q GLU 211": "OE1" <-> "OE2" Residue "Q GLU 227": "OE1" <-> "OE2" Residue "Q GLU 228": "OE1" <-> "OE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 121": "OE1" <-> "OE2" Residue "X ASP 182": "OD1" <-> "OD2" Residue "X GLU 193": "OE1" <-> "OE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 177": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "K ASP 182": "OD1" <-> "OD2" Residue "K GLU 193": "OE1" <-> "OE2" Residue "R PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 25": "OE1" <-> "OE2" Residue "R GLU 29": "OE1" <-> "OE2" Residue "R GLU 60": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R GLU 177": "OE1" <-> "OE2" Residue "R GLU 179": "OE1" <-> "OE2" Residue "R GLU 186": "OE1" <-> "OE2" Residue "R GLU 188": "OE1" <-> "OE2" Residue "R GLU 202": "OE1" <-> "OE2" Residue "R GLU 205": "OE1" <-> "OE2" Residue "R GLU 211": "OE1" <-> "OE2" Residue "R GLU 227": "OE1" <-> "OE2" Residue "R GLU 228": "OE1" <-> "OE2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 121": "OE1" <-> "OE2" Residue "Y ASP 182": "OD1" <-> "OD2" Residue "Y GLU 193": "OE1" <-> "OE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "E GLU 179": "OE1" <-> "OE2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "E GLU 188": "OE1" <-> "OE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E GLU 228": "OE1" <-> "OE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L ASP 182": "OD1" <-> "OD2" Residue "L GLU 193": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46228 Number of models: 1 Model: "" Number of chains: 28 Chain: "S" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "Z" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "F" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "M" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "T" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "1" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "G" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "N" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "U" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "2" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "A" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "H" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "O" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "V" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "B" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "I" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "P" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "W" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "C" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "J" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "Q" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "X" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "D" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "K" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "R" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "Y" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "L" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Time building chain proxies: 24.79, per 1000 atoms: 0.54 Number of scatterers: 46228 At special positions: 0 Unit cell: (128.854, 130.069, 166.537, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 8904 8.00 N 7840 7.00 C 29288 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: 19.47 Conformation dependent library (CDL) restraints added in 9.3 seconds 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11004 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 56 sheets defined 43.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.48 Creating SS restraints... Processing helix chain 'S' and resid 21 through 33 Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 81 through 104 Processing helix chain 'S' and resid 108 through 126 removed outlier: 3.630A pdb=" N LEU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL S 116 " --> pdb=" O LEU S 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR S 123 " --> pdb=" O GLN S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 180 Processing helix chain 'S' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER S 200 " --> pdb=" O ALA S 196 " (cutoff:3.500A) Processing helix chain 'S' and resid 225 through 233 removed outlier: 3.684A pdb=" N LYS S 230 " --> pdb=" O GLN S 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS S 231 " --> pdb=" O GLU S 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE S 232 " --> pdb=" O GLU S 228 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL Z 134 " --> pdb=" O GLY Z 130 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 166 Processing helix chain 'Z' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE Z 192 " --> pdb=" O PRO Z 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 33 Processing helix chain 'F' and resid 60 through 64 Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.631A pdb=" N LEU F 112 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 180 Processing helix chain 'F' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 233 removed outlier: 3.684A pdb=" N LYS F 230 " --> pdb=" O GLN F 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 71 Processing helix chain 'M' and resid 75 through 90 removed outlier: 3.766A pdb=" N VAL M 90 " --> pdb=" O MET M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 removed outlier: 3.638A pdb=" N VAL M 134 " --> pdb=" O GLY M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 166 Processing helix chain 'M' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE M 192 " --> pdb=" O PRO M 188 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 33 Processing helix chain 'T' and resid 60 through 64 Processing helix chain 'T' and resid 81 through 104 Processing helix chain 'T' and resid 108 through 126 removed outlier: 3.631A pdb=" N LEU T 112 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL T 116 " --> pdb=" O LEU T 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR T 123 " --> pdb=" O GLN T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 180 Processing helix chain 'T' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER T 200 " --> pdb=" O ALA T 196 " (cutoff:3.500A) Processing helix chain 'T' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS T 230 " --> pdb=" O GLN T 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS T 231 " --> pdb=" O GLU T 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE T 232 " --> pdb=" O GLU T 228 " (cutoff:3.500A) Processing helix chain '1' and resid 48 through 71 Processing helix chain '1' and resid 75 through 90 removed outlier: 3.766A pdb=" N VAL 1 90 " --> pdb=" O MET 1 86 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL 1 134 " --> pdb=" O GLY 1 130 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 166 Processing helix chain '1' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE 1 192 " --> pdb=" O PRO 1 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.630A pdb=" N LEU G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 180 Processing helix chain 'G' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS G 230 " --> pdb=" O GLN G 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS G 231 " --> pdb=" O GLU G 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL N 134 " --> pdb=" O GLY N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 166 Processing helix chain 'N' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE N 192 " --> pdb=" O PRO N 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 33 Processing helix chain 'U' and resid 60 through 64 Processing helix chain 'U' and resid 81 through 104 Processing helix chain 'U' and resid 108 through 126 removed outlier: 3.630A pdb=" N LEU U 112 " --> pdb=" O ASN U 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL U 116 " --> pdb=" O LEU U 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR U 123 " --> pdb=" O GLN U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 180 Processing helix chain 'U' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER U 200 " --> pdb=" O ALA U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS U 230 " --> pdb=" O GLN U 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS U 231 " --> pdb=" O GLU U 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE U 232 " --> pdb=" O GLU U 228 " (cutoff:3.500A) Processing helix chain '2' and resid 48 through 71 Processing helix chain '2' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL 2 90 " --> pdb=" O MET 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL 2 134 " --> pdb=" O GLY 2 130 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 166 Processing helix chain '2' and resid 188 through 200 removed outlier: 3.502A pdb=" N ILE 2 192 " --> pdb=" O PRO 2 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 33 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 81 through 104 Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.631A pdb=" N LEU A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.766A pdb=" N VAL H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL H 134 " --> pdb=" O GLY H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 166 Processing helix chain 'H' and resid 188 through 200 removed outlier: 3.502A pdb=" N ILE H 192 " --> pdb=" O PRO H 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 33 Processing helix chain 'O' and resid 60 through 64 Processing helix chain 'O' and resid 81 through 104 Processing helix chain 'O' and resid 108 through 126 removed outlier: 3.631A pdb=" N LEU O 112 " --> pdb=" O ASN O 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL O 116 " --> pdb=" O LEU O 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 180 Processing helix chain 'O' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER O 200 " --> pdb=" O ALA O 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS O 230 " --> pdb=" O GLN O 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS O 231 " --> pdb=" O GLU O 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE O 232 " --> pdb=" O GLU O 228 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.766A pdb=" N VAL V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL V 134 " --> pdb=" O GLY V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 166 Processing helix chain 'V' and resid 188 through 200 removed outlier: 3.502A pdb=" N ILE V 192 " --> pdb=" O PRO V 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 81 through 104 Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.630A pdb=" N LEU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 removed outlier: 3.684A pdb=" N LYS B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'I' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE I 192 " --> pdb=" O PRO I 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 33 Processing helix chain 'P' and resid 60 through 64 Processing helix chain 'P' and resid 81 through 104 Processing helix chain 'P' and resid 108 through 126 removed outlier: 3.630A pdb=" N LEU P 112 " --> pdb=" O ASN P 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL P 116 " --> pdb=" O LEU P 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 180 Processing helix chain 'P' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER P 200 " --> pdb=" O ALA P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 233 removed outlier: 3.684A pdb=" N LYS P 230 " --> pdb=" O GLN P 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS P 231 " --> pdb=" O GLU P 227 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE P 232 " --> pdb=" O GLU P 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL W 134 " --> pdb=" O GLY W 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 166 Processing helix chain 'W' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE W 192 " --> pdb=" O PRO W 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 81 through 104 Processing helix chain 'C' and resid 108 through 126 removed outlier: 3.631A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS C 230 " --> pdb=" O GLN C 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 71 Processing helix chain 'J' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL J 90 " --> pdb=" O MET J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 removed outlier: 3.636A pdb=" N VAL J 134 " --> pdb=" O GLY J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 166 Processing helix chain 'J' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE J 192 " --> pdb=" O PRO J 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 33 Processing helix chain 'Q' and resid 60 through 64 Processing helix chain 'Q' and resid 81 through 104 Processing helix chain 'Q' and resid 108 through 126 removed outlier: 3.630A pdb=" N LEU Q 112 " --> pdb=" O ASN Q 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL Q 116 " --> pdb=" O LEU Q 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR Q 123 " --> pdb=" O GLN Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 180 Processing helix chain 'Q' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER Q 200 " --> pdb=" O ALA Q 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS Q 230 " --> pdb=" O GLN Q 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS Q 231 " --> pdb=" O GLU Q 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE Q 232 " --> pdb=" O GLU Q 228 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 71 Processing helix chain 'X' and resid 75 through 90 removed outlier: 3.766A pdb=" N VAL X 90 " --> pdb=" O MET X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL X 134 " --> pdb=" O GLY X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 166 Processing helix chain 'X' and resid 188 through 200 removed outlier: 3.502A pdb=" N ILE X 192 " --> pdb=" O PRO X 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.630A pdb=" N LEU D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 180 Processing helix chain 'D' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS D 230 " --> pdb=" O GLN D 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL K 134 " --> pdb=" O GLY K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 166 Processing helix chain 'K' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE K 192 " --> pdb=" O PRO K 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 33 Processing helix chain 'R' and resid 60 through 64 Processing helix chain 'R' and resid 81 through 104 Processing helix chain 'R' and resid 108 through 126 removed outlier: 3.631A pdb=" N LEU R 112 " --> pdb=" O ASN R 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL R 116 " --> pdb=" O LEU R 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 180 Processing helix chain 'R' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER R 200 " --> pdb=" O ALA R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 233 removed outlier: 3.684A pdb=" N LYS R 230 " --> pdb=" O GLN R 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS R 231 " --> pdb=" O GLU R 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE R 232 " --> pdb=" O GLU R 228 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 90 removed outlier: 3.766A pdb=" N VAL Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL Y 134 " --> pdb=" O GLY Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 166 Processing helix chain 'Y' and resid 188 through 200 removed outlier: 3.502A pdb=" N ILE Y 192 " --> pdb=" O PRO Y 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 33 Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.631A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'E' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 233 removed outlier: 3.684A pdb=" N LYS E 230 " --> pdb=" O GLN E 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 166 Processing helix chain 'L' and resid 188 through 200 removed outlier: 3.502A pdb=" N ILE L 192 " --> pdb=" O PRO L 188 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'S' and resid 162 through 165 Processing sheet with id= B, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN S 158 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'Z' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR Z 127 " --> pdb=" O THR Z 3 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL Z 120 " --> pdb=" O SER Z 112 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 162 through 165 Processing sheet with id= F, first strand: chain 'F' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN F 158 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'M' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR M 127 " --> pdb=" O THR M 3 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'M' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR M 41 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL M 120 " --> pdb=" O SER M 112 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'T' and resid 162 through 165 Processing sheet with id= J, first strand: chain 'T' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL T 74 " --> pdb=" O ILE T 70 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN T 158 " --> pdb=" O ASP T 150 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '1' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR 1 127 " --> pdb=" O THR 1 3 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '1' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR 1 41 " --> pdb=" O ILE 1 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL 1 120 " --> pdb=" O SER 1 112 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 162 through 165 Processing sheet with id= N, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL G 74 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN G 158 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'N' and resid 124 through 128 removed outlier: 3.517A pdb=" N THR N 127 " --> pdb=" O THR N 3 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'N' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL N 120 " --> pdb=" O SER N 112 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'U' and resid 162 through 165 Processing sheet with id= R, first strand: chain 'U' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL U 74 " --> pdb=" O ILE U 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN U 158 " --> pdb=" O ASP U 150 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '2' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR 2 127 " --> pdb=" O THR 2 3 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '2' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR 2 41 " --> pdb=" O ILE 2 37 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 162 through 165 Processing sheet with id= V, first strand: chain 'A' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 158 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR H 127 " --> pdb=" O THR H 3 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL H 120 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 162 through 165 Processing sheet with id= Z, first strand: chain 'O' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL O 74 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN O 158 " --> pdb=" O ASP O 150 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'V' and resid 124 through 128 removed outlier: 3.519A pdb=" N THR V 127 " --> pdb=" O THR V 3 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 162 through 165 Processing sheet with id= AD, first strand: chain 'B' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 158 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR I 127 " --> pdb=" O THR I 3 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL I 120 " --> pdb=" O SER I 112 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'P' and resid 162 through 165 Processing sheet with id= AH, first strand: chain 'P' and resid 67 through 71 removed outlier: 6.541A pdb=" N VAL P 74 " --> pdb=" O ILE P 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN P 158 " --> pdb=" O ASP P 150 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'W' and resid 124 through 128 removed outlier: 3.517A pdb=" N THR W 127 " --> pdb=" O THR W 3 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL W 120 " --> pdb=" O SER W 112 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 162 through 165 Processing sheet with id= AL, first strand: chain 'C' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL C 74 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN C 158 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'J' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR J 127 " --> pdb=" O THR J 3 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL J 120 " --> pdb=" O SER J 112 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Q' and resid 162 through 165 Processing sheet with id= AP, first strand: chain 'Q' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL Q 74 " --> pdb=" O ILE Q 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN Q 158 " --> pdb=" O ASP Q 150 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'X' and resid 124 through 128 removed outlier: 3.517A pdb=" N THR X 127 " --> pdb=" O THR X 3 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'X' and resid 34 through 38 removed outlier: 6.445A pdb=" N THR X 41 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL X 120 " --> pdb=" O SER X 112 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'D' and resid 162 through 165 Processing sheet with id= AT, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN D 158 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'K' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR K 127 " --> pdb=" O THR K 3 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL K 120 " --> pdb=" O SER K 112 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'R' and resid 162 through 165 Processing sheet with id= AX, first strand: chain 'R' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN R 158 " --> pdb=" O ASP R 150 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Y' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR Y 127 " --> pdb=" O THR Y 3 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'E' and resid 162 through 165 Processing sheet with id= BB, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN E 158 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'L' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR L 127 " --> pdb=" O THR L 3 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL L 120 " --> pdb=" O SER L 112 " (cutoff:3.500A) 2733 hydrogen bonds defined for protein. 7821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.15 Time building geometry restraints manager: 20.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 8219 1.31 - 1.45: 14535 1.45 - 1.59: 22567 1.59 - 1.73: 1131 1.73 - 1.86: 364 Bond restraints: 46816 Sorted by residual: bond pdb=" CA PHE 2 111 " pdb=" C PHE 2 111 " ideal model delta sigma weight residual 1.522 1.375 0.147 1.20e-02 6.94e+03 1.51e+02 bond pdb=" CA PHE M 111 " pdb=" C PHE M 111 " ideal model delta sigma weight residual 1.522 1.375 0.147 1.20e-02 6.94e+03 1.51e+02 bond pdb=" CA PHE L 111 " pdb=" C PHE L 111 " ideal model delta sigma weight residual 1.522 1.375 0.147 1.20e-02 6.94e+03 1.50e+02 bond pdb=" CA PHE N 111 " pdb=" C PHE N 111 " ideal model delta sigma weight residual 1.522 1.376 0.147 1.20e-02 6.94e+03 1.50e+02 bond pdb=" CA PHE X 111 " pdb=" C PHE X 111 " ideal model delta sigma weight residual 1.522 1.376 0.147 1.20e-02 6.94e+03 1.50e+02 ... (remaining 46811 not shown) Histogram of bond angle deviations from ideal: 91.75 - 100.86: 527 100.86 - 109.96: 10997 109.96 - 119.07: 28874 119.07 - 128.18: 21828 128.18 - 137.29: 956 Bond angle restraints: 63182 Sorted by residual: angle pdb=" CA ASN N 24 " pdb=" C ASN N 24 " pdb=" N PHE N 25 " ideal model delta sigma weight residual 118.82 131.20 -12.38 1.26e+00 6.30e-01 9.65e+01 angle pdb=" CA ASN 1 24 " pdb=" C ASN 1 24 " pdb=" N PHE 1 25 " ideal model delta sigma weight residual 118.82 131.18 -12.36 1.26e+00 6.30e-01 9.63e+01 angle pdb=" CA ASN J 24 " pdb=" C ASN J 24 " pdb=" N PHE J 25 " ideal model delta sigma weight residual 118.82 131.18 -12.36 1.26e+00 6.30e-01 9.63e+01 angle pdb=" CA ASN W 24 " pdb=" C ASN W 24 " pdb=" N PHE W 25 " ideal model delta sigma weight residual 118.82 131.18 -12.36 1.26e+00 6.30e-01 9.62e+01 angle pdb=" CA ASN Y 24 " pdb=" C ASN Y 24 " pdb=" N PHE Y 25 " ideal model delta sigma weight residual 118.82 131.17 -12.35 1.26e+00 6.30e-01 9.61e+01 ... (remaining 63177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.48: 27020 25.48 - 50.96: 1071 50.96 - 76.44: 481 76.44 - 101.91: 100 101.91 - 127.39: 14 Dihedral angle restraints: 28686 sinusoidal: 11466 harmonic: 17220 Sorted by residual: dihedral pdb=" CA ASN N 24 " pdb=" C ASN N 24 " pdb=" N PHE N 25 " pdb=" CA PHE N 25 " ideal model delta harmonic sigma weight residual 180.00 52.61 127.39 0 5.00e+00 4.00e-02 6.49e+02 dihedral pdb=" CA ASN W 24 " pdb=" C ASN W 24 " pdb=" N PHE W 25 " pdb=" CA PHE W 25 " ideal model delta harmonic sigma weight residual 180.00 52.65 127.35 0 5.00e+00 4.00e-02 6.49e+02 dihedral pdb=" CA ASN H 24 " pdb=" C ASN H 24 " pdb=" N PHE H 25 " pdb=" CA PHE H 25 " ideal model delta harmonic sigma weight residual 180.00 52.66 127.34 0 5.00e+00 4.00e-02 6.49e+02 ... (remaining 28683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.205: 4706 0.205 - 0.411: 2126 0.411 - 0.616: 518 0.616 - 0.821: 42 0.821 - 1.027: 14 Chirality restraints: 7406 Sorted by residual: chirality pdb=" CB ILE W 178 " pdb=" CA ILE W 178 " pdb=" CG1 ILE W 178 " pdb=" CG2 ILE W 178 " both_signs ideal model delta sigma weight residual False 2.64 1.62 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CB ILE M 178 " pdb=" CA ILE M 178 " pdb=" CG1 ILE M 178 " pdb=" CG2 ILE M 178 " both_signs ideal model delta sigma weight residual False 2.64 1.62 1.03 2.00e-01 2.50e+01 2.63e+01 chirality pdb=" CB ILE V 178 " pdb=" CA ILE V 178 " pdb=" CG1 ILE V 178 " pdb=" CG2 ILE V 178 " both_signs ideal model delta sigma weight residual False 2.64 1.62 1.03 2.00e-01 2.50e+01 2.63e+01 ... (remaining 7403 not shown) Planarity restraints: 8106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 124 " -0.151 2.00e-02 2.50e+03 1.18e-01 2.76e+02 pdb=" CG TYR 2 124 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 124 " 0.093 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 124 " 0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 124 " 0.093 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 124 " 0.096 2.00e-02 2.50e+03 pdb=" CZ TYR 2 124 " 0.070 2.00e-02 2.50e+03 pdb=" OH TYR 2 124 " -0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 124 " -0.151 2.00e-02 2.50e+03 1.17e-01 2.76e+02 pdb=" CG TYR K 124 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR K 124 " 0.093 2.00e-02 2.50e+03 pdb=" CD2 TYR K 124 " 0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR K 124 " 0.093 2.00e-02 2.50e+03 pdb=" CE2 TYR K 124 " 0.096 2.00e-02 2.50e+03 pdb=" CZ TYR K 124 " 0.070 2.00e-02 2.50e+03 pdb=" OH TYR K 124 " -0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR X 124 " 0.150 2.00e-02 2.50e+03 1.17e-01 2.76e+02 pdb=" CG TYR X 124 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR X 124 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 TYR X 124 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR X 124 " -0.093 2.00e-02 2.50e+03 pdb=" CE2 TYR X 124 " -0.095 2.00e-02 2.50e+03 pdb=" CZ TYR X 124 " -0.070 2.00e-02 2.50e+03 pdb=" OH TYR X 124 " 0.220 2.00e-02 2.50e+03 ... (remaining 8103 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 487 2.52 - 3.11: 31577 3.11 - 3.71: 70632 3.71 - 4.30: 106955 4.30 - 4.90: 178413 Nonbonded interactions: 388064 Sorted by model distance: nonbonded pdb=" OXT LEU Z 203 " pdb=" OXT LEU M 203 " model vdw 1.922 3.040 nonbonded pdb=" OXT LEU I 203 " pdb=" OXT LEU W 203 " model vdw 1.922 3.040 nonbonded pdb=" OXT LEU N 203 " pdb=" OXT LEU Y 203 " model vdw 1.923 3.040 nonbonded pdb=" OXT LEU 2 203 " pdb=" OXT LEU K 203 " model vdw 1.923 3.040 nonbonded pdb=" OXT LEU V 203 " pdb=" OXT LEU J 203 " model vdw 1.923 3.040 ... (remaining 388059 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' selection = chain '2' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 6.620 Check model and map are aligned: 0.720 Set scattering table: 0.420 Process input model: 124.360 Find NCS groups from input model: 3.740 Set up NCS constraints: 0.480 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.034 0.147 46816 Z= 2.243 Angle : 3.609 15.587 63182 Z= 2.428 Chirality : 0.229 1.027 7406 Planarity : 0.030 0.246 8106 Dihedral : 18.099 127.392 17682 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 1.89 % Allowed : 8.04 % Favored : 90.07 % Rotamer: Outliers : 9.27 % Allowed : 12.08 % Favored : 78.65 % Cbeta Deviations : 10.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.61 (0.09), residues: 5922 helix: -2.41 (0.09), residues: 2226 sheet: -0.96 (0.14), residues: 1302 loop : -3.12 (0.10), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.020 0.009 HIS J 109 PHE 0.146 0.046 PHE T 91 TYR 0.220 0.047 TYR 2 124 ARG 0.065 0.011 ARG O 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2360 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 462 poor density : 1898 time to evaluate : 5.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 76 ILE cc_start: 0.9082 (mm) cc_final: 0.8878 (mm) REVERT: Z 149 ASP cc_start: 0.5737 (m-30) cc_final: 0.5456 (m-30) REVERT: Z 203 LEU cc_start: 0.1995 (OUTLIER) cc_final: 0.1620 (tp) REVERT: F 221 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.5884 (t80) REVERT: T 53 LYS cc_start: 0.4769 (OUTLIER) cc_final: 0.4557 (mmmt) REVERT: T 221 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.6951 (t80) REVERT: 1 45 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7779 (mp) REVERT: 1 85 ASN cc_start: 0.8506 (m110) cc_final: 0.8145 (m110) REVERT: 1 149 ASP cc_start: 0.6079 (m-30) cc_final: 0.5773 (m-30) REVERT: 1 203 LEU cc_start: 0.2339 (OUTLIER) cc_final: 0.2068 (tp) REVERT: G 53 LYS cc_start: 0.5176 (OUTLIER) cc_final: 0.4920 (mmmt) REVERT: G 158 ASN cc_start: 0.7970 (m110) cc_final: 0.7725 (m-40) REVERT: N 112 SER cc_start: 0.8544 (t) cc_final: 0.8333 (p) REVERT: N 131 SER cc_start: 0.8699 (t) cc_final: 0.8427 (t) REVERT: N 149 ASP cc_start: 0.5982 (m-30) cc_final: 0.5585 (m-30) REVERT: N 203 LEU cc_start: 0.0891 (OUTLIER) cc_final: 0.0664 (tp) REVERT: U 225 ASP cc_start: 0.4295 (OUTLIER) cc_final: 0.2920 (p0) REVERT: 2 203 LEU cc_start: 0.1751 (OUTLIER) cc_final: 0.1331 (tp) REVERT: A 225 ASP cc_start: 0.4182 (OUTLIER) cc_final: 0.3348 (p0) REVERT: H 112 SER cc_start: 0.8587 (t) cc_final: 0.8301 (p) REVERT: H 114 ASP cc_start: 0.8079 (p0) cc_final: 0.7785 (p0) REVERT: O 90 ASP cc_start: 0.6558 (m-30) cc_final: 0.6344 (m-30) REVERT: O 221 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.6922 (t80) REVERT: O 225 ASP cc_start: 0.4272 (OUTLIER) cc_final: 0.2798 (p0) REVERT: V 120 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8584 (t) REVERT: V 149 ASP cc_start: 0.5939 (m-30) cc_final: 0.5673 (m-30) REVERT: I 149 ASP cc_start: 0.5734 (m-30) cc_final: 0.5449 (m-30) REVERT: I 203 LEU cc_start: 0.2009 (OUTLIER) cc_final: 0.1621 (tp) REVERT: P 221 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.5854 (t80) REVERT: C 53 LYS cc_start: 0.4750 (OUTLIER) cc_final: 0.4531 (mmmt) REVERT: C 221 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.6964 (t80) REVERT: J 45 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7763 (mp) REVERT: J 85 ASN cc_start: 0.8460 (m110) cc_final: 0.8119 (m110) REVERT: J 149 ASP cc_start: 0.6090 (m-30) cc_final: 0.5767 (m-30) REVERT: J 203 LEU cc_start: 0.2336 (OUTLIER) cc_final: 0.2078 (tp) REVERT: Q 53 LYS cc_start: 0.5184 (OUTLIER) cc_final: 0.4928 (mmmt) REVERT: Q 118 ASP cc_start: 0.7535 (m-30) cc_final: 0.7308 (m-30) REVERT: Q 158 ASN cc_start: 0.7956 (m110) cc_final: 0.7721 (m-40) REVERT: X 112 SER cc_start: 0.8537 (t) cc_final: 0.8325 (p) REVERT: X 131 SER cc_start: 0.8711 (t) cc_final: 0.8447 (t) REVERT: X 149 ASP cc_start: 0.5987 (m-30) cc_final: 0.5591 (m-30) REVERT: X 203 LEU cc_start: 0.0900 (OUTLIER) cc_final: 0.0669 (tp) REVERT: D 225 ASP cc_start: 0.4306 (OUTLIER) cc_final: 0.2999 (p0) REVERT: K 203 LEU cc_start: 0.1758 (OUTLIER) cc_final: 0.1334 (tp) REVERT: R 225 ASP cc_start: 0.4154 (OUTLIER) cc_final: 0.3349 (p0) REVERT: Y 112 SER cc_start: 0.8576 (t) cc_final: 0.8291 (p) REVERT: Y 114 ASP cc_start: 0.8053 (p0) cc_final: 0.7767 (p0) REVERT: E 221 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.6944 (t80) REVERT: L 120 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8582 (t) REVERT: L 149 ASP cc_start: 0.5916 (m-30) cc_final: 0.5663 (m-30) outliers start: 462 outliers final: 194 residues processed: 2210 average time/residue: 0.6518 time to fit residues: 2321.0642 Evaluate side-chains 1526 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1305 time to evaluate : 5.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 136 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 137 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 53 LYS Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 136 LEU Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain T residue 224 TYR Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 37 ILE Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 1 residue 49 VAL Chi-restraints excluded: chain 1 residue 79 VAL Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 137 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 179 THR Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 136 LEU Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 224 TYR Chi-restraints excluded: chain U residue 225 ASP Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 137 VAL Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 179 THR Chi-restraints excluded: chain 2 residue 203 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 225 ASP Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 179 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain Q residue 53 LYS Chi-restraints excluded: chain Q residue 136 LEU Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 79 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 179 THR Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 224 TYR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 137 VAL Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 496 optimal weight: 4.9990 chunk 445 optimal weight: 0.9980 chunk 247 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 300 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 460 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 chunk 533 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 121 GLN S 158 ASN S 219 ASN Z 73 ASN Z 85 ASN Z 89 GLN Z 141 GLN Z 191 GLN F 119 GLN F 121 GLN F 219 ASN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 191 GLN T 121 GLN ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN G 122 GLN N 191 GLN U 121 GLN 2 191 GLN A 121 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN ** O 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 119 GLN O 121 GLN O 158 ASN O 219 ASN V 98 GLN B 121 GLN B 158 ASN B 219 ASN I 73 ASN I 85 ASN I 89 GLN I 141 GLN I 191 GLN P 119 GLN P 121 GLN P 219 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 191 GLN C 121 GLN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 GLN Q 122 GLN X 191 GLN D 121 GLN K 191 GLN R 121 GLN Y 191 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN E 121 GLN E 158 ASN E 219 ASN L 98 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 46816 Z= 0.276 Angle : 0.792 9.907 63182 Z= 0.438 Chirality : 0.050 0.195 7406 Planarity : 0.006 0.065 8106 Dihedral : 9.728 102.810 6922 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.93 % Favored : 95.59 % Rotamer: Outliers : 6.96 % Allowed : 18.90 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.10), residues: 5922 helix: 0.91 (0.10), residues: 2324 sheet: -0.25 (0.12), residues: 1344 loop : -2.94 (0.10), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.005 HIS Y 28 PHE 0.019 0.002 PHE R 42 TYR 0.026 0.002 TYR W 92 ARG 0.005 0.001 ARG W 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1617 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 1270 time to evaluate : 5.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 103 TYR cc_start: 0.8645 (m-80) cc_final: 0.8394 (m-80) REVERT: S 221 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7020 (t80) REVERT: Z 17 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7599 (pp20) REVERT: Z 51 ASP cc_start: 0.7123 (m-30) cc_final: 0.6887 (m-30) REVERT: Z 96 MET cc_start: 0.7960 (mpp) cc_final: 0.7429 (mpp) REVERT: F 221 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.5909 (t80) REVERT: M 30 ASN cc_start: 0.8091 (t0) cc_final: 0.7877 (t0) REVERT: T 123 TYR cc_start: 0.8132 (m-80) cc_final: 0.7915 (m-80) REVERT: T 221 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.6787 (t80) REVERT: 1 51 ASP cc_start: 0.7021 (m-30) cc_final: 0.6777 (m-30) REVERT: 1 123 ILE cc_start: 0.8482 (pt) cc_final: 0.8278 (pt) REVERT: G 221 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.6907 (t80) REVERT: 2 153 ASP cc_start: 0.7004 (m-30) cc_final: 0.6597 (m-30) REVERT: A 132 TYR cc_start: 0.8636 (m-80) cc_final: 0.8426 (m-80) REVERT: A 221 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7183 (t80) REVERT: H 51 ASP cc_start: 0.7135 (m-30) cc_final: 0.6638 (m-30) REVERT: H 55 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8143 (mm) REVERT: H 96 MET cc_start: 0.7782 (mpp) cc_final: 0.7543 (mpp) REVERT: O 221 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.6748 (t80) REVERT: V 96 MET cc_start: 0.7803 (mpp) cc_final: 0.7532 (mtm) REVERT: V 120 VAL cc_start: 0.9420 (OUTLIER) cc_final: 0.9209 (p) REVERT: V 153 ASP cc_start: 0.7267 (m-30) cc_final: 0.7025 (m-30) REVERT: B 103 TYR cc_start: 0.8644 (m-80) cc_final: 0.8393 (m-80) REVERT: B 221 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7037 (t80) REVERT: I 17 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7609 (pp20) REVERT: I 51 ASP cc_start: 0.7149 (m-30) cc_final: 0.6871 (m-30) REVERT: I 96 MET cc_start: 0.7978 (mpp) cc_final: 0.7428 (mpp) REVERT: P 221 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.5899 (t80) REVERT: W 30 ASN cc_start: 0.8090 (t0) cc_final: 0.7877 (t0) REVERT: C 123 TYR cc_start: 0.8124 (m-80) cc_final: 0.7921 (m-80) REVERT: C 221 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.6801 (t80) REVERT: Q 118 ASP cc_start: 0.7426 (m-30) cc_final: 0.7132 (m-30) REVERT: Q 221 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.6892 (t80) REVERT: K 153 ASP cc_start: 0.6995 (m-30) cc_final: 0.6613 (m-30) REVERT: R 132 TYR cc_start: 0.8645 (m-80) cc_final: 0.8434 (m-80) REVERT: R 221 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7168 (t80) REVERT: Y 51 ASP cc_start: 0.7119 (m-30) cc_final: 0.6661 (m-30) REVERT: Y 55 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8139 (mm) REVERT: E 221 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.6958 (t80) REVERT: L 96 MET cc_start: 0.7801 (mpp) cc_final: 0.7544 (mtm) REVERT: L 153 ASP cc_start: 0.7260 (m-30) cc_final: 0.6994 (m-30) outliers start: 347 outliers final: 203 residues processed: 1538 average time/residue: 0.5601 time to fit residues: 1426.1482 Evaluate side-chains 1314 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1094 time to evaluate : 5.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 55 LEU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 112 SER Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 137 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 79 VAL Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 137 VAL Chi-restraints excluded: chain 1 residue 143 SER Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 179 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 165 ILE Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 2 residue 137 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 179 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 129 SER Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 179 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 216 THR Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 55 LEU Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 124 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 79 VAL Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 179 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 137 VAL Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 296 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 444 optimal weight: 1.9990 chunk 363 optimal weight: 0.8980 chunk 147 optimal weight: 0.0050 chunk 534 optimal weight: 0.0770 chunk 577 optimal weight: 0.7980 chunk 476 optimal weight: 6.9990 chunk 530 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 429 optimal weight: 0.8980 overall best weight: 0.5352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 125 GLN Z 85 ASN Z 186 GLN Z 191 GLN F 122 GLN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 191 GLN N 141 GLN N 191 GLN U 119 GLN 2 98 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN O 122 GLN I 85 ASN I 186 GLN I 191 GLN P 122 GLN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN Q 122 GLN X 141 GLN X 191 GLN D 119 GLN K 98 GLN Y 191 GLN E 122 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 46816 Z= 0.190 Angle : 0.664 11.672 63182 Z= 0.365 Chirality : 0.045 0.193 7406 Planarity : 0.005 0.056 8106 Dihedral : 7.771 57.011 6776 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.20 % Favored : 95.56 % Rotamer: Outliers : 5.40 % Allowed : 21.47 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.10), residues: 5922 helix: 2.01 (0.11), residues: 2324 sheet: -0.18 (0.12), residues: 1372 loop : -2.61 (0.10), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS H 28 PHE 0.015 0.002 PHE R 42 TYR 0.017 0.001 TYR W 92 ARG 0.007 0.000 ARG F 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1482 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1213 time to evaluate : 5.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 221 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.6909 (t80) REVERT: Z 51 ASP cc_start: 0.6914 (m-30) cc_final: 0.6607 (m-30) REVERT: Z 96 MET cc_start: 0.7906 (mpp) cc_final: 0.7395 (mpp) REVERT: F 221 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.5937 (t80) REVERT: T 221 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.6753 (t80) REVERT: G 221 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.6815 (t80) REVERT: N 139 GLU cc_start: 0.7392 (tp30) cc_final: 0.7165 (tp30) REVERT: 2 14 MET cc_start: 0.8467 (mtp) cc_final: 0.8259 (mtp) REVERT: 2 139 GLU cc_start: 0.6979 (tp30) cc_final: 0.6769 (tp30) REVERT: A 221 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7127 (t80) REVERT: H 55 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.7986 (mm) REVERT: H 139 GLU cc_start: 0.7215 (tp30) cc_final: 0.7014 (tp30) REVERT: O 221 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7029 (t80) REVERT: O 225 ASP cc_start: 0.4943 (OUTLIER) cc_final: 0.4441 (p0) REVERT: V 120 VAL cc_start: 0.9427 (OUTLIER) cc_final: 0.9173 (p) REVERT: V 139 GLU cc_start: 0.7655 (tp30) cc_final: 0.7170 (tp30) REVERT: B 221 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.6915 (t80) REVERT: I 51 ASP cc_start: 0.6925 (m-30) cc_final: 0.6601 (m-30) REVERT: I 96 MET cc_start: 0.7924 (mpp) cc_final: 0.7377 (mpp) REVERT: P 221 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.5925 (t80) REVERT: C 221 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.6753 (t80) REVERT: Q 221 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.6790 (t80) REVERT: X 139 GLU cc_start: 0.7391 (tp30) cc_final: 0.7150 (tp30) REVERT: K 14 MET cc_start: 0.8466 (mtp) cc_final: 0.8254 (mtp) REVERT: R 221 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7113 (t80) REVERT: Y 55 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8098 (mm) REVERT: E 221 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7111 (t80) REVERT: E 225 ASP cc_start: 0.4349 (p0) cc_final: 0.2508 (p0) REVERT: L 120 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.9010 (p) REVERT: L 139 GLU cc_start: 0.7655 (tp30) cc_final: 0.7185 (tp30) outliers start: 269 outliers final: 167 residues processed: 1417 average time/residue: 0.5675 time to fit residues: 1336.3551 Evaluate side-chains 1254 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1070 time to evaluate : 5.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 173 ILE Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 186 GLN Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 59 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 137 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 137 ILE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 2 residue 137 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 225 ASP Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 186 GLN Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 100 LEU Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 137 VAL Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 528 optimal weight: 0.0060 chunk 402 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 359 optimal weight: 1.9990 chunk 536 optimal weight: 0.7980 chunk 568 optimal weight: 0.9990 chunk 280 optimal weight: 0.9990 chunk 508 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 85 ASN F 122 GLN G 122 GLN N 191 GLN A 226 GLN H 85 ASN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN O 122 GLN I 85 ASN P 122 GLN Q 122 GLN X 191 GLN R 226 GLN Y 85 ASN Y 191 GLN E 122 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 46816 Z= 0.204 Angle : 0.641 9.180 63182 Z= 0.350 Chirality : 0.044 0.182 7406 Planarity : 0.004 0.060 8106 Dihedral : 6.965 56.774 6680 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.70 % Favored : 96.07 % Rotamer: Outliers : 5.88 % Allowed : 22.01 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.11), residues: 5922 helix: 2.25 (0.11), residues: 2324 sheet: -0.21 (0.12), residues: 1372 loop : -2.43 (0.10), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS H 28 PHE 0.021 0.002 PHE T 42 TYR 0.020 0.001 TYR Y 95 ARG 0.008 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1125 time to evaluate : 5.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 221 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.6938 (t80) REVERT: Z 96 MET cc_start: 0.7964 (mpp) cc_final: 0.7468 (mpp) REVERT: Z 139 GLU cc_start: 0.6862 (tp30) cc_final: 0.6651 (tp30) REVERT: F 221 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.5923 (t80) REVERT: T 221 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.6811 (t80) REVERT: 1 139 GLU cc_start: 0.7075 (tp30) cc_final: 0.6735 (tp30) REVERT: G 221 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.6842 (t80) REVERT: 2 14 MET cc_start: 0.8516 (mtp) cc_final: 0.8299 (mtp) REVERT: 2 139 GLU cc_start: 0.7072 (tp30) cc_final: 0.6808 (tp30) REVERT: A 221 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7296 (t80) REVERT: H 55 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7998 (mm) REVERT: O 221 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7188 (t80) REVERT: V 120 VAL cc_start: 0.9393 (OUTLIER) cc_final: 0.9103 (p) REVERT: B 221 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.6952 (t80) REVERT: I 51 ASP cc_start: 0.6858 (m-30) cc_final: 0.6588 (m-30) REVERT: I 96 MET cc_start: 0.7978 (mpp) cc_final: 0.7452 (mpp) REVERT: I 139 GLU cc_start: 0.6866 (tp30) cc_final: 0.6665 (tp30) REVERT: P 221 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.5903 (t80) REVERT: C 221 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.6875 (t80) REVERT: J 139 GLU cc_start: 0.7076 (tp30) cc_final: 0.6756 (tp30) REVERT: Q 221 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.6827 (t80) REVERT: K 14 MET cc_start: 0.8520 (mtp) cc_final: 0.8289 (mtp) REVERT: R 221 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7273 (t80) REVERT: Y 55 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8142 (mm) REVERT: E 221 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7220 (t80) REVERT: L 120 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9100 (p) outliers start: 293 outliers final: 186 residues processed: 1332 average time/residue: 0.5544 time to fit residues: 1230.9829 Evaluate side-chains 1272 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1070 time to evaluate : 5.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 ILE Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 190 ASP Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 123 ILE Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 138 LEU Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 179 THR Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 137 ILE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain U residue 225 ASP Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 74 MET Chi-restraints excluded: chain 2 residue 86 MET Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 123 ILE Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 59 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 149 ASP Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 190 ASP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 100 LEU Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 179 THR Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 74 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 121 GLU Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 473 optimal weight: 7.9990 chunk 322 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 423 optimal weight: 2.9990 chunk 234 optimal weight: 0.0870 chunk 485 optimal weight: 1.9990 chunk 392 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 chunk 510 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 73 ASN ** F 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 ASN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 141 GLN H 191 GLN O 122 GLN V 186 GLN I 73 ASN ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 GLN E 122 GLN L 186 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 46816 Z= 0.277 Angle : 0.666 9.952 63182 Z= 0.361 Chirality : 0.045 0.267 7406 Planarity : 0.004 0.055 8106 Dihedral : 6.886 57.385 6663 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.61 % Favored : 96.15 % Rotamer: Outliers : 6.76 % Allowed : 21.57 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.10), residues: 5922 helix: 2.22 (0.11), residues: 2324 sheet: -0.25 (0.12), residues: 1372 loop : -2.30 (0.11), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS Y 28 PHE 0.017 0.002 PHE B 232 TYR 0.027 0.002 TYR X 92 ARG 0.005 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1419 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 1082 time to evaluate : 5.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 221 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.6850 (t80) REVERT: Z 96 MET cc_start: 0.7939 (mpp) cc_final: 0.7622 (mpt) REVERT: Z 139 GLU cc_start: 0.6958 (tp30) cc_final: 0.6754 (tp30) REVERT: F 221 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.5955 (t80) REVERT: T 221 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.6895 (t80) REVERT: G 221 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.6936 (t80) REVERT: N 191 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7236 (tm-30) REVERT: A 221 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7370 (t80) REVERT: A 232 PHE cc_start: 0.6590 (m-80) cc_final: 0.6164 (t80) REVERT: H 51 ASP cc_start: 0.7064 (m-30) cc_final: 0.6508 (m-30) REVERT: H 55 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8127 (mm) REVERT: H 91 LYS cc_start: 0.7943 (pttp) cc_final: 0.7717 (pttm) REVERT: O 221 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7245 (t80) REVERT: V 26 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8473 (pp) REVERT: V 120 VAL cc_start: 0.9411 (OUTLIER) cc_final: 0.9153 (p) REVERT: V 139 GLU cc_start: 0.7480 (tp30) cc_final: 0.7075 (tp30) REVERT: B 221 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.6859 (t80) REVERT: I 96 MET cc_start: 0.7962 (mpp) cc_final: 0.7616 (mpt) REVERT: P 221 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.5931 (t80) REVERT: C 221 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.6896 (t80) REVERT: Q 221 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.6918 (t80) REVERT: X 8 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8532 (pp) REVERT: X 139 GLU cc_start: 0.6985 (tp30) cc_final: 0.6771 (tp30) REVERT: X 191 GLN cc_start: 0.7565 (tm-30) cc_final: 0.7217 (tm-30) REVERT: R 221 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7352 (t80) REVERT: R 232 PHE cc_start: 0.6587 (m-80) cc_final: 0.6187 (t80) REVERT: Y 51 ASP cc_start: 0.7050 (m-30) cc_final: 0.6578 (m-30) REVERT: Y 55 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8159 (mm) REVERT: Y 91 LYS cc_start: 0.7959 (pttp) cc_final: 0.7720 (pttm) REVERT: E 221 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7221 (t80) REVERT: L 26 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8481 (pp) REVERT: L 120 VAL cc_start: 0.9390 (OUTLIER) cc_final: 0.9090 (p) REVERT: L 139 GLU cc_start: 0.7483 (tp30) cc_final: 0.7076 (tp30) outliers start: 337 outliers final: 235 residues processed: 1325 average time/residue: 0.5528 time to fit residues: 1226.0193 Evaluate side-chains 1277 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1023 time to evaluate : 5.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 93 MET Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 ILE Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 190 ASP Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 179 THR Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 1 residue 190 ASP Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 137 ILE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain U residue 225 ASP Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain 2 residue 190 ASP Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 179 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 59 MET Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 149 ASP Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 190 ASP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 59 MET Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 100 LEU Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 179 THR Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 86 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 4.9990 chunk 511 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 333 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 568 optimal weight: 0.9990 chunk 472 optimal weight: 0.9980 chunk 263 optimal weight: 5.9990 chunk 47 optimal weight: 0.0170 chunk 188 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 ASN G 98 GLN G 111 ASN G 122 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN Q 98 GLN Q 111 ASN Q 122 GLN ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN R 226 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 46816 Z= 0.214 Angle : 0.642 10.580 63182 Z= 0.346 Chirality : 0.044 0.233 7406 Planarity : 0.004 0.050 8106 Dihedral : 6.738 57.574 6663 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.43 % Favored : 96.34 % Rotamer: Outliers : 5.80 % Allowed : 23.52 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.11), residues: 5922 helix: 2.41 (0.11), residues: 2352 sheet: -0.25 (0.12), residues: 1372 loop : -2.31 (0.11), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS V 28 PHE 0.020 0.002 PHE P 232 TYR 0.029 0.001 TYR J 58 ARG 0.005 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1388 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1099 time to evaluate : 5.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 221 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.6857 (t80) REVERT: Z 145 LYS cc_start: 0.6899 (mmtt) cc_final: 0.6537 (mmtm) REVERT: F 221 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.5967 (t80) REVERT: M 139 GLU cc_start: 0.6982 (tp30) cc_final: 0.6643 (tp30) REVERT: T 221 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.6898 (t80) REVERT: 1 26 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8491 (pp) REVERT: G 221 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.6940 (t80) REVERT: A 221 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7297 (t80) REVERT: H 55 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8022 (mm) REVERT: H 91 LYS cc_start: 0.7905 (pttp) cc_final: 0.7604 (pttm) REVERT: O 13 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.7992 (p) REVERT: O 221 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7492 (t80) REVERT: V 120 VAL cc_start: 0.9379 (OUTLIER) cc_final: 0.9169 (p) REVERT: V 123 ILE cc_start: 0.8625 (pt) cc_final: 0.8373 (pt) REVERT: V 139 GLU cc_start: 0.7459 (tp30) cc_final: 0.6966 (tp30) REVERT: B 221 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.6857 (t80) REVERT: I 145 LYS cc_start: 0.6891 (mmtt) cc_final: 0.6549 (mmtm) REVERT: P 221 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.5947 (t80) REVERT: W 139 GLU cc_start: 0.6990 (tp30) cc_final: 0.6644 (tp30) REVERT: C 221 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7074 (t80) REVERT: J 26 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8473 (pp) REVERT: Q 221 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.6922 (t80) REVERT: X 139 GLU cc_start: 0.7010 (tp30) cc_final: 0.6759 (tp30) REVERT: R 221 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7279 (t80) REVERT: Y 55 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8132 (mm) REVERT: Y 91 LYS cc_start: 0.7922 (pttp) cc_final: 0.7610 (pttm) REVERT: E 221 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.7503 (t80) REVERT: L 139 GLU cc_start: 0.7481 (tp30) cc_final: 0.7025 (tp30) outliers start: 289 outliers final: 207 residues processed: 1290 average time/residue: 0.5424 time to fit residues: 1164.4299 Evaluate side-chains 1286 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1061 time to evaluate : 5.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 36 THR Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 112 SER Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 190 ASP Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain 1 residue 8 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 179 THR Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 172 MET Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain U residue 225 ASP Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 141 GLN Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 179 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 59 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain P residue 216 THR Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 149 ASP Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 190 ASP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 100 LEU Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 172 MET Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 179 THR Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 86 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 149 ASP Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 324 optimal weight: 0.8980 chunk 415 optimal weight: 0.9980 chunk 321 optimal weight: 4.9990 chunk 478 optimal weight: 5.9990 chunk 317 optimal weight: 4.9990 chunk 566 optimal weight: 10.0000 chunk 354 optimal weight: 5.9990 chunk 345 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 23 GLN ** F 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 ASN G 98 GLN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN H 191 GLN O 23 GLN ** O 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 GLN ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN Y 191 GLN E 23 GLN ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 46816 Z= 0.331 Angle : 0.687 11.331 63182 Z= 0.370 Chirality : 0.046 0.237 7406 Planarity : 0.004 0.049 8106 Dihedral : 6.752 58.367 6658 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.36 % Favored : 96.37 % Rotamer: Outliers : 6.12 % Allowed : 23.25 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.11), residues: 5922 helix: 2.22 (0.11), residues: 2352 sheet: -0.24 (0.12), residues: 1372 loop : -2.22 (0.11), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS K 28 PHE 0.025 0.002 PHE F 232 TYR 0.025 0.002 TYR J 58 ARG 0.004 0.000 ARG K 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1041 time to evaluate : 6.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 221 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.6907 (t80) REVERT: F 221 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.5917 (t80) REVERT: M 96 MET cc_start: 0.7802 (mpp) cc_final: 0.7427 (mmm) REVERT: T 221 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.7050 (t80) REVERT: 1 30 ASN cc_start: 0.8242 (t0) cc_final: 0.8033 (t0) REVERT: G 221 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7026 (t80) REVERT: A 221 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.7343 (t80) REVERT: A 232 PHE cc_start: 0.6657 (m-80) cc_final: 0.6344 (t80) REVERT: H 51 ASP cc_start: 0.7091 (m-30) cc_final: 0.6653 (m-30) REVERT: H 55 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8087 (mm) REVERT: H 91 LYS cc_start: 0.7994 (pttp) cc_final: 0.7718 (pttm) REVERT: O 13 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8031 (p) REVERT: O 221 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7386 (t80) REVERT: V 26 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8502 (pp) REVERT: B 221 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.6914 (t80) REVERT: P 221 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.5903 (t80) REVERT: W 96 MET cc_start: 0.7822 (mpp) cc_final: 0.7399 (mmm) REVERT: C 221 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7059 (t80) REVERT: Q 221 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7009 (t80) REVERT: X 139 GLU cc_start: 0.7205 (tp30) cc_final: 0.6742 (tp30) REVERT: R 221 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.7323 (t80) REVERT: R 232 PHE cc_start: 0.6633 (m-80) cc_final: 0.6370 (t80) REVERT: Y 91 LYS cc_start: 0.7996 (pttp) cc_final: 0.7693 (pttm) REVERT: E 13 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8002 (p) REVERT: E 221 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7405 (t80) REVERT: L 26 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8510 (pp) REVERT: L 139 GLU cc_start: 0.7819 (tp30) cc_final: 0.7420 (mm-30) outliers start: 305 outliers final: 245 residues processed: 1251 average time/residue: 0.5499 time to fit residues: 1137.3958 Evaluate side-chains 1253 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 991 time to evaluate : 5.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 112 SER Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 190 ASP Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain 1 residue 8 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 179 THR Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 172 MET Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain U residue 225 ASP Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 141 GLN Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 179 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 59 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain P residue 216 THR Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 149 ASP Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain W residue 190 ASP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 124 THR Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 100 LEU Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 172 MET Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 179 THR Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 86 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 350 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 338 optimal weight: 0.0670 chunk 170 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 360 optimal weight: 0.8980 chunk 386 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 445 optimal weight: 5.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 ASN G 98 GLN G 111 ASN G 122 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN A 111 ASN ** O 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN Q 98 GLN Q 111 ASN Q 122 GLN ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 GLN R 111 ASN ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 46816 Z= 0.205 Angle : 0.653 11.616 63182 Z= 0.351 Chirality : 0.044 0.225 7406 Planarity : 0.004 0.052 8106 Dihedral : 6.661 58.854 6657 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.33 % Favored : 96.44 % Rotamer: Outliers : 5.52 % Allowed : 24.22 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.11), residues: 5922 helix: 2.48 (0.11), residues: 2338 sheet: -0.17 (0.12), residues: 1372 loop : -2.17 (0.11), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS 2 28 PHE 0.020 0.001 PHE S 232 TYR 0.032 0.001 TYR 1 58 ARG 0.004 0.000 ARG K 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1069 time to evaluate : 5.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 221 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.6870 (t80) REVERT: F 221 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.5907 (t80) REVERT: M 26 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8382 (pp) REVERT: M 96 MET cc_start: 0.7699 (mpp) cc_final: 0.7307 (mmm) REVERT: T 221 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7071 (t80) REVERT: 1 26 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8468 (pp) REVERT: 1 30 ASN cc_start: 0.8153 (t0) cc_final: 0.7928 (t0) REVERT: G 186 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6817 (tm-30) REVERT: G 221 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7009 (t80) REVERT: U 226 GLN cc_start: 0.6037 (mm-40) cc_final: 0.5798 (mm110) REVERT: 2 185 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8591 (m) REVERT: A 132 TYR cc_start: 0.8549 (m-80) cc_final: 0.8347 (m-10) REVERT: A 221 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7183 (t80) REVERT: A 232 PHE cc_start: 0.6496 (m-80) cc_final: 0.6291 (t80) REVERT: O 13 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.7965 (p) REVERT: O 221 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7424 (t80) REVERT: V 26 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8480 (pp) REVERT: V 139 GLU cc_start: 0.7334 (tp30) cc_final: 0.7002 (mm-30) REVERT: B 221 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.6866 (t80) REVERT: P 221 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.5910 (t80) REVERT: W 26 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8408 (pp) REVERT: W 96 MET cc_start: 0.7722 (mpp) cc_final: 0.7289 (mmm) REVERT: C 221 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7111 (t80) REVERT: J 26 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8501 (pp) REVERT: Q 186 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: Q 221 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.6989 (t80) REVERT: X 139 GLU cc_start: 0.7026 (tp30) cc_final: 0.6663 (tp30) REVERT: D 226 GLN cc_start: 0.6070 (mm-40) cc_final: 0.5845 (mm110) REVERT: K 185 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8588 (m) REVERT: R 221 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7176 (t80) REVERT: E 13 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7924 (p) REVERT: E 221 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7439 (t80) REVERT: L 26 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8484 (pp) REVERT: L 139 GLU cc_start: 0.7610 (tp30) cc_final: 0.7205 (tp30) outliers start: 275 outliers final: 188 residues processed: 1253 average time/residue: 0.5519 time to fit residues: 1149.6229 Evaluate side-chains 1214 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1002 time to evaluate : 5.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 112 SER Chi-restraints excluded: chain Z residue 139 GLU Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 190 ASP Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain T residue 225 ASP Chi-restraints excluded: chain 1 residue 8 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 179 THR Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 225 ASP Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 60 LYS Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 141 GLN Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 179 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain P residue 216 THR Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 149 ASP Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain W residue 190 ASP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 179 THR Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 86 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain L residue 121 GLU Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 515 optimal weight: 6.9990 chunk 542 optimal weight: 0.9980 chunk 495 optimal weight: 0.0050 chunk 528 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 414 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 477 optimal weight: 8.9990 chunk 499 optimal weight: 0.9990 chunk 526 optimal weight: 0.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 122 GLN ** F 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN G 111 ASN G 122 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN H 191 GLN B 122 GLN ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 61 GLN Q 98 GLN Q 111 ASN Q 122 GLN ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN Y 191 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46816 Z= 0.224 Angle : 0.674 12.191 63182 Z= 0.361 Chirality : 0.044 0.218 7406 Planarity : 0.004 0.051 8106 Dihedral : 6.622 59.602 6657 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.43 % Favored : 96.34 % Rotamer: Outliers : 5.18 % Allowed : 24.46 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.11), residues: 5922 helix: 2.48 (0.11), residues: 2338 sheet: -0.14 (0.13), residues: 1372 loop : -2.10 (0.11), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS K 28 PHE 0.028 0.002 PHE F 232 TYR 0.032 0.002 TYR J 58 ARG 0.004 0.000 ARG 2 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1053 time to evaluate : 5.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 221 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7004 (t80) REVERT: S 232 PHE cc_start: 0.6230 (OUTLIER) cc_final: 0.5967 (t80) REVERT: Z 144 GLU cc_start: 0.6333 (pm20) cc_final: 0.6107 (pm20) REVERT: F 221 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.5917 (t80) REVERT: M 26 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8368 (pp) REVERT: M 96 MET cc_start: 0.7729 (mpp) cc_final: 0.7333 (mmm) REVERT: T 221 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7051 (t80) REVERT: 1 26 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8454 (pp) REVERT: G 186 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: G 221 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7019 (t80) REVERT: 2 185 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8604 (m) REVERT: A 221 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7201 (t80) REVERT: O 13 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.7911 (p) REVERT: O 221 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7430 (t80) REVERT: V 26 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8402 (pp) REVERT: V 139 GLU cc_start: 0.7327 (tp30) cc_final: 0.7009 (mm-30) REVERT: B 221 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7025 (t80) REVERT: B 232 PHE cc_start: 0.6218 (OUTLIER) cc_final: 0.5950 (t80) REVERT: I 26 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8371 (pp) REVERT: I 144 GLU cc_start: 0.6320 (pm20) cc_final: 0.6118 (pm20) REVERT: P 221 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.5933 (t80) REVERT: W 26 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8416 (pp) REVERT: W 96 MET cc_start: 0.7762 (mpp) cc_final: 0.7312 (mmm) REVERT: C 221 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7059 (t80) REVERT: J 26 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8472 (pp) REVERT: Q 221 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.7011 (t80) REVERT: X 14 MET cc_start: 0.8369 (mtp) cc_final: 0.8060 (mmm) REVERT: X 139 GLU cc_start: 0.6974 (tp30) cc_final: 0.6581 (tp30) REVERT: K 185 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8606 (m) REVERT: R 221 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7185 (t80) REVERT: Y 21 THR cc_start: 0.6378 (OUTLIER) cc_final: 0.6172 (t) REVERT: E 13 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7866 (p) REVERT: E 221 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7439 (t80) REVERT: L 26 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8417 (pp) REVERT: L 139 GLU cc_start: 0.7612 (tp30) cc_final: 0.7180 (mm-30) outliers start: 258 outliers final: 203 residues processed: 1225 average time/residue: 0.5595 time to fit residues: 1141.1899 Evaluate side-chains 1249 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1019 time to evaluate : 5.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain S residue 232 PHE Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 112 SER Chi-restraints excluded: chain Z residue 139 GLU Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 190 ASP Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain T residue 225 ASP Chi-restraints excluded: chain 1 residue 8 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 179 THR Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain U residue 225 ASP Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 141 GLN Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 179 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain P residue 216 THR Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 225 ASP Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 149 ASP Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain W residue 190 ASP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 179 THR Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 86 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain L residue 121 GLU Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 346 optimal weight: 0.7980 chunk 558 optimal weight: 5.9990 chunk 340 optimal weight: 0.7980 chunk 264 optimal weight: 2.9990 chunk 388 optimal weight: 5.9990 chunk 585 optimal weight: 2.9990 chunk 539 optimal weight: 0.6980 chunk 466 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 360 optimal weight: 0.3980 chunk 286 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 GLN ** F 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 ASN T 122 GLN ** G 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN G 122 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 73 ASN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN H 191 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 122 GLN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 GLN Q 122 GLN ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 ASN ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 46816 Z= 0.222 Angle : 0.681 12.704 63182 Z= 0.364 Chirality : 0.045 0.312 7406 Planarity : 0.004 0.051 8106 Dihedral : 6.582 59.392 6657 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.24 % Favored : 96.52 % Rotamer: Outliers : 4.92 % Allowed : 24.88 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.11), residues: 5922 helix: 2.48 (0.11), residues: 2338 sheet: -0.13 (0.13), residues: 1372 loop : -2.05 (0.11), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS 2 109 PHE 0.024 0.002 PHE T 42 TYR 0.036 0.002 TYR J 58 ARG 0.004 0.000 ARG K 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1320 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1075 time to evaluate : 5.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 221 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7024 (t80) REVERT: Z 26 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8398 (pp) REVERT: F 221 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.5915 (t80) REVERT: M 26 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8366 (pp) REVERT: M 96 MET cc_start: 0.7729 (mpp) cc_final: 0.7331 (mmm) REVERT: M 124 TYR cc_start: 0.8690 (p90) cc_final: 0.8170 (p90) REVERT: M 139 GLU cc_start: 0.6909 (tp30) cc_final: 0.6617 (tp30) REVERT: T 221 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7022 (t80) REVERT: 1 26 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8465 (pp) REVERT: 1 191 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7587 (tp40) REVERT: G 221 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.7034 (t80) REVERT: 2 185 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8595 (m) REVERT: A 221 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.7182 (t80) REVERT: O 13 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7929 (p) REVERT: O 221 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7434 (t80) REVERT: V 26 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8435 (pp) REVERT: V 139 GLU cc_start: 0.7369 (tp30) cc_final: 0.7066 (mm-30) REVERT: B 221 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7048 (t80) REVERT: I 26 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8480 (pp) REVERT: P 221 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.5935 (t80) REVERT: W 26 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8417 (pp) REVERT: W 96 MET cc_start: 0.7768 (mpp) cc_final: 0.7321 (mmm) REVERT: W 124 TYR cc_start: 0.8688 (p90) cc_final: 0.8154 (p90) REVERT: W 139 GLU cc_start: 0.6886 (tp30) cc_final: 0.6578 (tp30) REVERT: C 221 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7024 (t80) REVERT: J 26 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8600 (pp) REVERT: Q 221 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7033 (t80) REVERT: X 90 VAL cc_start: 0.7704 (p) cc_final: 0.7268 (m) REVERT: X 139 GLU cc_start: 0.7053 (tp30) cc_final: 0.6695 (tp30) REVERT: K 185 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8597 (m) REVERT: R 221 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7177 (t80) REVERT: Y 21 THR cc_start: 0.6309 (OUTLIER) cc_final: 0.6072 (t) REVERT: E 13 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7874 (p) REVERT: E 221 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7492 (t80) REVERT: L 26 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8460 (pp) REVERT: L 139 GLU cc_start: 0.7569 (tp30) cc_final: 0.7243 (mm-30) outliers start: 245 outliers final: 204 residues processed: 1228 average time/residue: 0.5392 time to fit residues: 1104.2585 Evaluate side-chains 1229 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1000 time to evaluate : 5.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 139 GLU Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 190 ASP Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain 1 residue 8 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 179 THR Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 59 MET Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain U residue 225 ASP Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 86 MET Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 60 LYS Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 141 GLN Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 179 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain P residue 216 THR Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 225 ASP Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 149 ASP Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain W residue 190 ASP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 59 MET Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 59 MET Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 179 THR Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 86 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain L residue 121 GLU Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 370 optimal weight: 6.9990 chunk 496 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 430 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 467 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 479 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 122 GLN ** F 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN T 23 GLN ** T 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 ASN ** G 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN G 122 GLN ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 GLN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN H 191 GLN B 122 GLN ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 ASN ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 GLN Q 122 GLN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 GLN ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.083578 restraints weight = 70059.205| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.32 r_work: 0.2741 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 46816 Z= 0.355 Angle : 0.734 12.712 63182 Z= 0.391 Chirality : 0.047 0.325 7406 Planarity : 0.004 0.050 8106 Dihedral : 6.716 59.645 6655 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.46 % Favored : 96.30 % Rotamer: Outliers : 4.92 % Allowed : 25.12 % Favored : 69.96 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.11), residues: 5922 helix: 2.27 (0.11), residues: 2338 sheet: -0.19 (0.13), residues: 1372 loop : -2.04 (0.11), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS 2 28 PHE 0.029 0.002 PHE S 232 TYR 0.037 0.002 TYR 1 58 ARG 0.008 0.001 ARG H 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18024.89 seconds wall clock time: 319 minutes 0.19 seconds (19140.19 seconds total)