Starting phenix.real_space_refine (version: dev) on Thu Dec 22 02:42:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9i_5623/12_2022/3j9i_5623.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9i_5623/12_2022/3j9i_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_5623/12_2022/3j9i_5623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9i_5623/12_2022/3j9i_5623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9i_5623/12_2022/3j9i_5623.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9i_5623/12_2022/3j9i_5623.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.008 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 Convert atoms to be neutral 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: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 26.60, per 1000 atoms: 0.58 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: 19.70 Conformation dependent library (CDL) restraints added in 7.3 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: 2.57 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: 19.11 Time building geometry restraints manager: 21.06 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 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. 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 8.080 Check model and map are aligned: 0.700 Convert atoms to be neutral: 0.410 Process input model: 120.630 Find NCS groups from input model: 3.370 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 3.608 15.454 63182 Z= 2.425 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 % 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 *********************** 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 : 6.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 462 outliers final: 194 residues processed: 2210 average time/residue: 0.5904 time to fit residues: 2095.9443 Evaluate side-chains 1509 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1315 time to evaluate : 5.750 Switching outliers to nearest non-outliers outliers start: 194 outliers final: 0 residues processed: 194 average time/residue: 0.4297 time to fit residues: 165.8546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 496 optimal weight: 3.9990 chunk 445 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 460 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 343 optimal weight: 2.9990 chunk 533 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 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 85 ASN ** 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 V 98 GLN B 121 GLN B 158 ASN B 219 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 85 ASN ** 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 L 98 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 46816 Z= 0.343 Angle : 0.833 17.029 63182 Z= 0.446 Chirality : 0.051 0.272 7406 Planarity : 0.006 0.065 8106 Dihedral : 6.913 82.131 6566 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.50 % Favored : 96.03 % Rotamer Outliers : 5.24 % 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: -1.15 (0.10), residues: 5922 helix: 0.86 (0.10), residues: 2366 sheet: -0.31 (0.12), residues: 1344 loop : -2.95 (0.10), residues: 2212 *********************** 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 1518 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1257 time to evaluate : 5.941 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 outliers start: 261 outliers final: 128 residues processed: 1458 average time/residue: 0.5557 time to fit residues: 1344.2280 Evaluate side-chains 1206 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1078 time to evaluate : 5.714 Switching outliers to nearest non-outliers outliers start: 128 outliers final: 0 residues processed: 128 average time/residue: 0.4069 time to fit residues: 107.9898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 296 optimal weight: 9.9990 chunk 165 optimal weight: 0.9990 chunk 444 optimal weight: 5.9990 chunk 363 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 534 optimal weight: 0.6980 chunk 577 optimal weight: 0.5980 chunk 476 optimal weight: 6.9990 chunk 530 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 429 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 186 GLN Z 191 GLN F 44 ASN F 122 GLN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 122 GLN ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 186 GLN 1 191 GLN G 122 GLN G 219 ASN N 141 GLN U 119 GLN U 219 ASN H 141 GLN O 122 GLN O 219 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 186 GLN J 191 GLN Q 122 GLN Q 219 ASN X 141 GLN D 119 GLN D 219 ASN K 98 GLN E 122 GLN E 219 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 46816 Z= 0.210 Angle : 0.697 15.014 63182 Z= 0.371 Chirality : 0.046 0.286 7406 Planarity : 0.005 0.055 8106 Dihedral : 6.086 58.184 6566 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.75 % Favored : 95.95 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.65 % 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: -0.32 (0.10), residues: 5922 helix: 1.91 (0.11), residues: 2324 sheet: -0.26 (0.12), residues: 1372 loop : -2.60 (0.10), residues: 2226 *********************** 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 1345 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1196 time to evaluate : 5.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 149 outliers final: 87 residues processed: 1286 average time/residue: 0.5487 time to fit residues: 1169.3860 Evaluate side-chains 1149 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1062 time to evaluate : 5.444 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 0.3929 time to fit residues: 72.9729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 528 optimal weight: 5.9990 chunk 402 optimal weight: 0.8980 chunk 277 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 255 optimal weight: 9.9990 chunk 359 optimal weight: 3.9990 chunk 536 optimal weight: 0.0470 chunk 568 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 508 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 85 ASN 1 85 ASN G 122 GLN A 226 GLN O 122 GLN I 85 ASN J 85 ASN Q 122 GLN R 226 GLN E 122 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 46816 Z= 0.214 Angle : 0.666 14.849 63182 Z= 0.351 Chirality : 0.046 0.331 7406 Planarity : 0.004 0.048 8106 Dihedral : 5.779 55.591 6566 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.43 % Favored : 96.34 % Rotamer Outliers : 3.29 % 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: -0.07 (0.10), residues: 5922 helix: 2.17 (0.11), residues: 2324 sheet: -0.35 (0.12), residues: 1372 loop : -2.37 (0.10), residues: 2226 *********************** 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 1288 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1124 time to evaluate : 6.320 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 outliers start: 164 outliers final: 82 residues processed: 1231 average time/residue: 0.5510 time to fit residues: 1134.1060 Evaluate side-chains 1118 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1036 time to evaluate : 5.695 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 0 residues processed: 82 average time/residue: 0.4078 time to fit residues: 71.1986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 473 optimal weight: 6.9990 chunk 322 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 423 optimal weight: 3.9990 chunk 234 optimal weight: 0.0670 chunk 485 optimal weight: 2.9990 chunk 392 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 290 optimal weight: 0.9990 chunk 510 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 186 GLN T 111 ASN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN O 122 GLN V 186 GLN I 186 GLN ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 GLN E 122 GLN L 186 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 46816 Z= 0.230 Angle : 0.665 15.114 63182 Z= 0.349 Chirality : 0.046 0.465 7406 Planarity : 0.004 0.045 8106 Dihedral : 5.616 54.118 6566 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.41 % Favored : 96.35 % Rotamer Outliers : 2.77 % 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: 0.05 (0.11), residues: 5922 helix: 2.27 (0.11), residues: 2324 sheet: -0.38 (0.12), residues: 1372 loop : -2.23 (0.11), residues: 2226 *********************** 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 1240 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1102 time to evaluate : 5.585 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 outliers start: 138 outliers final: 64 residues processed: 1181 average time/residue: 0.5736 time to fit residues: 1129.6991 Evaluate side-chains 1095 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1031 time to evaluate : 5.687 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.4127 time to fit residues: 58.1647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 1.9990 chunk 511 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 333 optimal weight: 0.7980 chunk 140 optimal weight: 0.0570 chunk 568 optimal weight: 0.9980 chunk 472 optimal weight: 7.9990 chunk 263 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 298 optimal weight: 0.0170 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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** ** T 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 ASN G 111 ASN G 122 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 164 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN Q 111 ASN Q 122 GLN ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 46816 Z= 0.181 Angle : 0.647 14.839 63182 Z= 0.339 Chirality : 0.045 0.385 7406 Planarity : 0.004 0.048 8106 Dihedral : 5.483 51.929 6566 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.39 % Favored : 96.37 % Rotamer Outliers : 2.27 % 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: 2.31 (0.11), residues: 2380 sheet: -0.30 (0.12), residues: 1372 loop : -2.20 (0.11), residues: 2170 *********************** 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 1265 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1152 time to evaluate : 6.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 43 residues processed: 1209 average time/residue: 0.5646 time to fit residues: 1140.3977 Evaluate side-chains 1112 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1069 time to evaluate : 5.815 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4471 time to fit residues: 43.2341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 324 optimal weight: 3.9990 chunk 415 optimal weight: 1.9990 chunk 321 optimal weight: 0.8980 chunk 478 optimal weight: 6.9990 chunk 317 optimal weight: 5.9990 chunk 566 optimal weight: 0.0020 chunk 354 optimal weight: 7.9990 chunk 345 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- 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** M 164 GLN ** 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 A 111 ASN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 23 GLN ** O 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 46816 Z= 0.250 Angle : 0.684 15.612 63182 Z= 0.355 Chirality : 0.046 0.421 7406 Planarity : 0.004 0.049 8106 Dihedral : 5.420 51.011 6566 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.55 % Favored : 96.22 % Rotamer Outliers : 1.95 % 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: 2.30 (0.11), residues: 2366 sheet: -0.20 (0.13), residues: 1330 loop : -2.20 (0.11), residues: 2226 *********************** 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 1182 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1085 time to evaluate : 5.808 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 outliers start: 97 outliers final: 53 residues processed: 1137 average time/residue: 0.5577 time to fit residues: 1051.9846 Evaluate side-chains 1071 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1018 time to evaluate : 5.736 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.4175 time to fit residues: 49.2798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 350 optimal weight: 0.4980 chunk 226 optimal weight: 5.9990 chunk 338 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 360 optimal weight: 0.0980 chunk 386 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 445 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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** M 141 GLN ** 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 A 226 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 141 GLN ** 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 R 226 GLN ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 46816 Z= 0.207 Angle : 0.685 15.448 63182 Z= 0.355 Chirality : 0.046 0.418 7406 Planarity : 0.004 0.051 8106 Dihedral : 5.390 49.806 6566 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.29 % Favored : 96.44 % Rotamer Outliers : 1.30 % 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: 0.26 (0.11), residues: 5922 helix: 2.34 (0.11), residues: 2366 sheet: -0.15 (0.13), residues: 1330 loop : -2.13 (0.11), residues: 2226 *********************** 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 1147 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1082 time to evaluate : 6.216 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 outliers start: 65 outliers final: 19 residues processed: 1114 average time/residue: 0.5682 time to fit residues: 1052.2311 Evaluate side-chains 1051 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1032 time to evaluate : 6.230 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4442 time to fit residues: 23.5824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 515 optimal weight: 5.9990 chunk 542 optimal weight: 0.8980 chunk 495 optimal weight: 0.2980 chunk 528 optimal weight: 0.0670 chunk 317 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 414 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 477 optimal weight: 2.9990 chunk 499 optimal weight: 2.9990 chunk 526 optimal weight: 0.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- 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** M 141 GLN ** 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 ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN W 141 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 GLN Q 111 ASN Q 122 GLN X 164 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 E 23 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 46816 Z= 0.211 Angle : 0.690 14.848 63182 Z= 0.358 Chirality : 0.046 0.428 7406 Planarity : 0.004 0.051 8106 Dihedral : 5.321 49.466 6566 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.23 % Favored : 96.42 % Rotamer Outliers : 1.08 % 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: 0.28 (0.11), residues: 5922 helix: 2.33 (0.11), residues: 2366 sheet: -0.27 (0.12), residues: 1372 loop : -2.02 (0.12), residues: 2184 *********************** 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 1121 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1067 time to evaluate : 6.100 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 outliers start: 54 outliers final: 30 residues processed: 1082 average time/residue: 0.5663 time to fit residues: 1016.0492 Evaluate side-chains 1033 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1003 time to evaluate : 5.997 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4209 time to fit residues: 31.4578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 346 optimal weight: 0.9990 chunk 558 optimal weight: 0.9980 chunk 340 optimal weight: 4.9990 chunk 264 optimal weight: 0.9980 chunk 388 optimal weight: 5.9990 chunk 585 optimal weight: 9.9990 chunk 539 optimal weight: 0.5980 chunk 466 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 360 optimal weight: 7.9990 chunk 286 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 GLN G 98 GLN G 122 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 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 B 122 GLN P 111 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 61 GLN Q 98 GLN Q 122 GLN ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 46816 Z= 0.220 Angle : 0.701 14.575 63182 Z= 0.363 Chirality : 0.047 0.410 7406 Planarity : 0.004 0.043 8106 Dihedral : 5.315 49.048 6566 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.11 % Favored : 96.56 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.65 % 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: 0.26 (0.11), residues: 5922 helix: 2.26 (0.11), residues: 2408 sheet: -0.32 (0.13), residues: 1372 loop : -2.01 (0.12), residues: 2142 ********************** 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 1090 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1061 time to evaluate : 5.708 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 outliers start: 29 outliers final: 16 residues processed: 1074 average time/residue: 0.5777 time to fit residues: 1023.6261 Evaluate side-chains 1035 residues out of total 4984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1019 time to evaluate : 5.637 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4191 time to fit residues: 19.8675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 370 optimal weight: 4.9990 chunk 496 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 430 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 467 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 479 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 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 122 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN P 62 ASN 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** ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 GLN R 111 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.085529 restraints weight = 70556.290| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.30 r_work: 0.2797 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 46816 Z= 0.297 Angle : 0.732 15.985 63182 Z= 0.378 Chirality : 0.048 0.463 7406 Planarity : 0.004 0.044 8106 Dihedral : 5.365 49.603 6566 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.31 % Favored : 96.42 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 1.30 % 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: 0.26 (0.11), residues: 5922 helix: 2.33 (0.11), residues: 2338 sheet: -0.19 (0.13), residues: 1330 loop : -2.03 (0.11), residues: 2254 =============================================================================== Job complete usr+sys time: 17311.99 seconds wall clock time: 306 minutes 5.76 seconds (18365.76 seconds total)