Starting phenix.real_space_refine (version: dev) on Mon Dec 19 15:36:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj5_12938/12_2022/7oj5_12938.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj5_12938/12_2022/7oj5_12938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj5_12938/12_2022/7oj5_12938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj5_12938/12_2022/7oj5_12938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj5_12938/12_2022/7oj5_12938.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oj5_12938/12_2022/7oj5_12938.pdb" } resolution = 2.4 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= 0.000 sd= 0.017 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 "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 258": "OD1" <-> "OD2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 258": "OD1" <-> "OD2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 258": "OD1" <-> "OD2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 258": "OD1" <-> "OD2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 258": "OD1" <-> "OD2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H GLU 212": "OE1" <-> "OE2" Residue "H TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 258": "OD1" <-> "OD2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "I GLU 212": "OE1" <-> "OE2" Residue "I TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 258": "OD1" <-> "OD2" Residue "J GLU 82": "OE1" <-> "OE2" Residue "J GLU 212": "OE1" <-> "OE2" Residue "J TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 258": "OD1" <-> "OD2" Residue "K GLU 82": "OE1" <-> "OE2" Residue "K GLU 212": "OE1" <-> "OE2" Residue "K TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 258": "OD1" <-> "OD2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L GLU 212": "OE1" <-> "OE2" Residue "L TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 258": "OD1" <-> "OD2" Residue "M GLU 82": "OE1" <-> "OE2" Residue "M GLU 212": "OE1" <-> "OE2" Residue "M TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 258": "OD1" <-> "OD2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N GLU 212": "OE1" <-> "OE2" Residue "N TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 258": "OD1" <-> "OD2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O GLU 212": "OE1" <-> "OE2" Residue "O TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 258": "OD1" <-> "OD2" Residue "P GLU 82": "OE1" <-> "OE2" Residue "P GLU 212": "OE1" <-> "OE2" Residue "P TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 258": "OD1" <-> "OD2" Residue "Q GLU 82": "OE1" <-> "OE2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "Q TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 258": "OD1" <-> "OD2" Residue "R GLU 82": "OE1" <-> "OE2" Residue "R GLU 212": "OE1" <-> "OE2" Residue "R TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 258": "OD1" <-> "OD2" Residue "S GLU 82": "OE1" <-> "OE2" Residue "S GLU 212": "OE1" <-> "OE2" Residue "S TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 258": "OD1" <-> "OD2" Residue "T GLU 82": "OE1" <-> "OE2" Residue "T GLU 212": "OE1" <-> "OE2" Residue "T TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 258": "OD1" <-> "OD2" Residue "V GLU 82": "OE1" <-> "OE2" Residue "V GLU 212": "OE1" <-> "OE2" Residue "V TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 258": "OD1" <-> "OD2" Residue "W GLU 82": "OE1" <-> "OE2" Residue "W GLU 212": "OE1" <-> "OE2" Residue "W TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 258": "OD1" <-> "OD2" Residue "X GLU 82": "OE1" <-> "OE2" Residue "X GLU 212": "OE1" <-> "OE2" Residue "X TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 258": "OD1" <-> "OD2" Residue "Y GLU 82": "OE1" <-> "OE2" Residue "Y GLU 212": "OE1" <-> "OE2" Residue "Y TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 258": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 35323 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "B" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "D" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "E" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "F" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "G" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "H" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "I" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "J" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "K" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "L" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "M" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "N" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "O" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "P" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "Q" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "R" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "S" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "T" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "V" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "W" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "X" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "Y" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Time building chain proxies: 18.91, per 1000 atoms: 0.54 Number of scatterers: 35323 At special positions: 0 Unit cell: (129.86, 129.86, 129.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 48 24.99 S 72 16.00 O 7483 8.00 N 6336 7.00 C 21384 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: 14.38 Conformation dependent library (CDL) restraints added in 4.9 seconds 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8112 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 48 sheets defined 40.2% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN A 119 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 160 Processing helix chain 'A' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 256 Processing helix chain 'B' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN B 119 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 120 " --> pdb=" O MET B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 160 Processing helix chain 'B' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 256 Processing helix chain 'C' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN C 119 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 120 " --> pdb=" O MET C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 160 Processing helix chain 'C' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 256 Processing helix chain 'D' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN D 119 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 120 " --> pdb=" O MET D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 160 Processing helix chain 'D' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 256 Processing helix chain 'E' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN E 119 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 120 " --> pdb=" O MET E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 160 Processing helix chain 'E' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 256 Processing helix chain 'F' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN F 119 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 120 " --> pdb=" O MET F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 160 Processing helix chain 'F' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 256 Processing helix chain 'G' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN G 119 " --> pdb=" O HIS G 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU G 120 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 160 Processing helix chain 'G' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS G 213 " --> pdb=" O GLN G 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 256 Processing helix chain 'H' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN H 119 " --> pdb=" O HIS H 115 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 120 " --> pdb=" O MET H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 160 Processing helix chain 'H' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS H 213 " --> pdb=" O GLN H 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 256 Processing helix chain 'I' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU I 120 " --> pdb=" O MET I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 160 Processing helix chain 'I' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS I 213 " --> pdb=" O GLN I 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR I 221 " --> pdb=" O SER I 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 256 Processing helix chain 'J' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN J 119 " --> pdb=" O HIS J 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU J 120 " --> pdb=" O MET J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 160 Processing helix chain 'J' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS J 213 " --> pdb=" O GLN J 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR J 221 " --> pdb=" O SER J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 235 through 256 Processing helix chain 'K' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN K 119 " --> pdb=" O HIS K 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU K 120 " --> pdb=" O MET K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 160 Processing helix chain 'K' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS K 213 " --> pdb=" O GLN K 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR K 221 " --> pdb=" O SER K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 256 Processing helix chain 'L' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN L 119 " --> pdb=" O HIS L 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU L 120 " --> pdb=" O MET L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 160 Processing helix chain 'L' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS L 213 " --> pdb=" O GLN L 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR L 221 " --> pdb=" O SER L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 235 through 256 Processing helix chain 'M' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN M 119 " --> pdb=" O HIS M 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU M 120 " --> pdb=" O MET M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 160 Processing helix chain 'M' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS M 213 " --> pdb=" O GLN M 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR M 221 " --> pdb=" O SER M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 256 Processing helix chain 'N' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN N 119 " --> pdb=" O HIS N 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU N 120 " --> pdb=" O MET N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 160 Processing helix chain 'N' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS N 213 " --> pdb=" O GLN N 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR N 221 " --> pdb=" O SER N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 235 through 256 Processing helix chain 'O' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN O 119 " --> pdb=" O HIS O 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU O 120 " --> pdb=" O MET O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 160 Processing helix chain 'O' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS O 213 " --> pdb=" O GLN O 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR O 221 " --> pdb=" O SER O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 235 through 256 Processing helix chain 'P' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN P 119 " --> pdb=" O HIS P 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU P 120 " --> pdb=" O MET P 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 160 Processing helix chain 'P' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS P 213 " --> pdb=" O GLN P 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR P 221 " --> pdb=" O SER P 217 " (cutoff:3.500A) Processing helix chain 'P' and resid 235 through 256 Processing helix chain 'Q' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN Q 119 " --> pdb=" O HIS Q 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU Q 120 " --> pdb=" O MET Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 160 Processing helix chain 'Q' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS Q 213 " --> pdb=" O GLN Q 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR Q 221 " --> pdb=" O SER Q 217 " (cutoff:3.500A) Processing helix chain 'Q' and resid 235 through 256 Processing helix chain 'R' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN R 119 " --> pdb=" O HIS R 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU R 120 " --> pdb=" O MET R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 160 Processing helix chain 'R' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS R 213 " --> pdb=" O GLN R 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 256 Processing helix chain 'S' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN S 119 " --> pdb=" O HIS S 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU S 120 " --> pdb=" O MET S 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 140 through 160 Processing helix chain 'S' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS S 213 " --> pdb=" O GLN S 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR S 221 " --> pdb=" O SER S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 235 through 256 Processing helix chain 'T' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN T 119 " --> pdb=" O HIS T 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU T 120 " --> pdb=" O MET T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 160 Processing helix chain 'T' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS T 213 " --> pdb=" O GLN T 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR T 221 " --> pdb=" O SER T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 235 through 256 Processing helix chain 'V' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN V 119 " --> pdb=" O HIS V 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU V 120 " --> pdb=" O MET V 116 " (cutoff:3.500A) Processing helix chain 'V' and resid 140 through 160 Processing helix chain 'V' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS V 213 " --> pdb=" O GLN V 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR V 221 " --> pdb=" O SER V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 235 through 256 Processing helix chain 'W' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN W 119 " --> pdb=" O HIS W 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU W 120 " --> pdb=" O MET W 116 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 160 Processing helix chain 'W' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS W 213 " --> pdb=" O GLN W 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR W 221 " --> pdb=" O SER W 217 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 256 Processing helix chain 'X' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN X 119 " --> pdb=" O HIS X 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU X 120 " --> pdb=" O MET X 116 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 160 Processing helix chain 'X' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS X 213 " --> pdb=" O GLN X 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR X 221 " --> pdb=" O SER X 217 " (cutoff:3.500A) Processing helix chain 'X' and resid 235 through 256 Processing helix chain 'Y' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN Y 119 " --> pdb=" O HIS Y 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU Y 120 " --> pdb=" O MET Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 140 through 160 Processing helix chain 'Y' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS Y 213 " --> pdb=" O GLN Y 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR Y 221 " --> pdb=" O SER Y 217 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 256 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 86 Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU A 179 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS A 191 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE A 228 " --> pdb=" O HIS A 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY A 193 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN A 230 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP A 195 " --> pdb=" O GLN A 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER A 232 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 86 Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU B 179 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS B 191 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE B 228 " --> pdb=" O HIS B 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY B 193 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN B 230 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP B 195 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER B 232 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 80 through 86 Processing sheet with id=AA6, first strand: chain 'C' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU C 179 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS C 191 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE C 228 " --> pdb=" O HIS C 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY C 193 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN C 230 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP C 195 " --> pdb=" O GLN C 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER C 232 " --> pdb=" O ASP C 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 80 through 86 Processing sheet with id=AA8, first strand: chain 'D' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU D 179 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS D 191 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE D 228 " --> pdb=" O HIS D 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY D 193 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN D 230 " --> pdb=" O GLY D 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP D 195 " --> pdb=" O GLN D 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER D 232 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 80 through 86 Processing sheet with id=AB1, first strand: chain 'E' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU E 179 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS E 191 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE E 228 " --> pdb=" O HIS E 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY E 193 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN E 230 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP E 195 " --> pdb=" O GLN E 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER E 232 " --> pdb=" O ASP E 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 80 through 86 Processing sheet with id=AB3, first strand: chain 'F' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU F 179 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS F 191 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE F 228 " --> pdb=" O HIS F 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY F 193 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN F 230 " --> pdb=" O GLY F 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP F 195 " --> pdb=" O GLN F 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER F 232 " --> pdb=" O ASP F 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 80 through 86 Processing sheet with id=AB5, first strand: chain 'G' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU G 179 " --> pdb=" O PHE G 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS G 191 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE G 228 " --> pdb=" O HIS G 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY G 193 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN G 230 " --> pdb=" O GLY G 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP G 195 " --> pdb=" O GLN G 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER G 232 " --> pdb=" O ASP G 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 80 through 86 Processing sheet with id=AB7, first strand: chain 'H' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU H 179 " --> pdb=" O PHE H 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS H 191 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE H 228 " --> pdb=" O HIS H 191 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLY H 193 " --> pdb=" O ILE H 228 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLN H 230 " --> pdb=" O GLY H 193 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASP H 195 " --> pdb=" O GLN H 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER H 232 " --> pdb=" O ASP H 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 80 through 86 Processing sheet with id=AB9, first strand: chain 'I' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU I 179 " --> pdb=" O PHE I 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS I 191 " --> pdb=" O LEU I 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE I 228 " --> pdb=" O HIS I 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY I 193 " --> pdb=" O ILE I 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN I 230 " --> pdb=" O GLY I 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP I 195 " --> pdb=" O GLN I 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER I 232 " --> pdb=" O ASP I 195 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 80 through 86 Processing sheet with id=AC2, first strand: chain 'J' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU J 179 " --> pdb=" O PHE J 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS J 191 " --> pdb=" O LEU J 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE J 228 " --> pdb=" O HIS J 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY J 193 " --> pdb=" O ILE J 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN J 230 " --> pdb=" O GLY J 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP J 195 " --> pdb=" O GLN J 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER J 232 " --> pdb=" O ASP J 195 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 80 through 86 Processing sheet with id=AC4, first strand: chain 'K' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU K 179 " --> pdb=" O PHE K 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS K 191 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE K 228 " --> pdb=" O HIS K 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY K 193 " --> pdb=" O ILE K 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN K 230 " --> pdb=" O GLY K 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP K 195 " --> pdb=" O GLN K 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER K 232 " --> pdb=" O ASP K 195 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 80 through 86 Processing sheet with id=AC6, first strand: chain 'L' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU L 179 " --> pdb=" O PHE L 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS L 191 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE L 228 " --> pdb=" O HIS L 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY L 193 " --> pdb=" O ILE L 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN L 230 " --> pdb=" O GLY L 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP L 195 " --> pdb=" O GLN L 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER L 232 " --> pdb=" O ASP L 195 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 80 through 86 Processing sheet with id=AC8, first strand: chain 'M' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU M 179 " --> pdb=" O PHE M 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS M 191 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE M 228 " --> pdb=" O HIS M 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY M 193 " --> pdb=" O ILE M 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN M 230 " --> pdb=" O GLY M 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP M 195 " --> pdb=" O GLN M 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER M 232 " --> pdb=" O ASP M 195 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 80 through 86 Processing sheet with id=AD1, first strand: chain 'N' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU N 179 " --> pdb=" O PHE N 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS N 191 " --> pdb=" O LEU N 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE N 228 " --> pdb=" O HIS N 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY N 193 " --> pdb=" O ILE N 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN N 230 " --> pdb=" O GLY N 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP N 195 " --> pdb=" O GLN N 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER N 232 " --> pdb=" O ASP N 195 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 80 through 86 Processing sheet with id=AD3, first strand: chain 'O' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU O 179 " --> pdb=" O PHE O 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS O 191 " --> pdb=" O LEU O 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE O 228 " --> pdb=" O HIS O 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY O 193 " --> pdb=" O ILE O 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN O 230 " --> pdb=" O GLY O 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP O 195 " --> pdb=" O GLN O 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER O 232 " --> pdb=" O ASP O 195 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 80 through 86 Processing sheet with id=AD5, first strand: chain 'P' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU P 179 " --> pdb=" O PHE P 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS P 191 " --> pdb=" O LEU P 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE P 228 " --> pdb=" O HIS P 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY P 193 " --> pdb=" O ILE P 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN P 230 " --> pdb=" O GLY P 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP P 195 " --> pdb=" O GLN P 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER P 232 " --> pdb=" O ASP P 195 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 80 through 86 Processing sheet with id=AD7, first strand: chain 'Q' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU Q 179 " --> pdb=" O PHE Q 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS Q 191 " --> pdb=" O LEU Q 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE Q 228 " --> pdb=" O HIS Q 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY Q 193 " --> pdb=" O ILE Q 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN Q 230 " --> pdb=" O GLY Q 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP Q 195 " --> pdb=" O GLN Q 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER Q 232 " --> pdb=" O ASP Q 195 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 80 through 86 Processing sheet with id=AD9, first strand: chain 'R' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU R 179 " --> pdb=" O PHE R 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS R 191 " --> pdb=" O LEU R 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE R 228 " --> pdb=" O HIS R 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY R 193 " --> pdb=" O ILE R 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN R 230 " --> pdb=" O GLY R 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP R 195 " --> pdb=" O GLN R 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER R 232 " --> pdb=" O ASP R 195 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 80 through 86 Processing sheet with id=AE2, first strand: chain 'S' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU S 179 " --> pdb=" O PHE S 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS S 191 " --> pdb=" O LEU S 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE S 228 " --> pdb=" O HIS S 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY S 193 " --> pdb=" O ILE S 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN S 230 " --> pdb=" O GLY S 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP S 195 " --> pdb=" O GLN S 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER S 232 " --> pdb=" O ASP S 195 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 80 through 86 Processing sheet with id=AE4, first strand: chain 'T' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU T 179 " --> pdb=" O PHE T 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS T 191 " --> pdb=" O LEU T 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE T 228 " --> pdb=" O HIS T 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY T 193 " --> pdb=" O ILE T 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN T 230 " --> pdb=" O GLY T 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP T 195 " --> pdb=" O GLN T 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER T 232 " --> pdb=" O ASP T 195 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 80 through 86 Processing sheet with id=AE6, first strand: chain 'V' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU V 179 " --> pdb=" O PHE V 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS V 191 " --> pdb=" O LEU V 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE V 228 " --> pdb=" O HIS V 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY V 193 " --> pdb=" O ILE V 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN V 230 " --> pdb=" O GLY V 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP V 195 " --> pdb=" O GLN V 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER V 232 " --> pdb=" O ASP V 195 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 80 through 86 Processing sheet with id=AE8, first strand: chain 'W' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU W 179 " --> pdb=" O PHE W 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS W 191 " --> pdb=" O LEU W 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE W 228 " --> pdb=" O HIS W 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY W 193 " --> pdb=" O ILE W 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN W 230 " --> pdb=" O GLY W 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP W 195 " --> pdb=" O GLN W 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER W 232 " --> pdb=" O ASP W 195 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 80 through 86 Processing sheet with id=AF1, first strand: chain 'X' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU X 179 " --> pdb=" O PHE X 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS X 191 " --> pdb=" O LEU X 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE X 228 " --> pdb=" O HIS X 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY X 193 " --> pdb=" O ILE X 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN X 230 " --> pdb=" O GLY X 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP X 195 " --> pdb=" O GLN X 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER X 232 " --> pdb=" O ASP X 195 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 80 through 86 Processing sheet with id=AF3, first strand: chain 'Y' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU Y 179 " --> pdb=" O PHE Y 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS Y 191 " --> pdb=" O LEU Y 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE Y 228 " --> pdb=" O HIS Y 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY Y 193 " --> pdb=" O ILE Y 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN Y 230 " --> pdb=" O GLY Y 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP Y 195 " --> pdb=" O GLN Y 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER Y 232 " --> pdb=" O ASP Y 195 " (cutoff:3.500A) 2088 hydrogen bonds defined for protein. 6120 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: 13.65 Time building geometry restraints manager: 15.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12000 1.34 - 1.46: 7223 1.46 - 1.58: 15625 1.58 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 34992 Sorted by residual: bond pdb=" CB MET H 116 " pdb=" CG MET H 116 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.51e-01 bond pdb=" CB MET Y 116 " pdb=" CG MET Y 116 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 bond pdb=" CB MET K 116 " pdb=" CG MET K 116 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 bond pdb=" CB MET J 116 " pdb=" CG MET J 116 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 bond pdb=" CB MET R 116 " pdb=" CG MET R 116 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 ... (remaining 34987 not shown) Histogram of bond angle deviations from ideal: 100.83 - 106.94: 720 106.94 - 113.05: 19249 113.05 - 119.15: 9191 119.15 - 125.26: 17760 125.26 - 131.37: 432 Bond angle restraints: 47352 Sorted by residual: angle pdb=" CA GLU K 241 " pdb=" CB GLU K 241 " pdb=" CG GLU K 241 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.97e+00 angle pdb=" CA GLU J 241 " pdb=" CB GLU J 241 " pdb=" CG GLU J 241 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.97e+00 angle pdb=" CA GLU I 241 " pdb=" CB GLU I 241 " pdb=" CG GLU I 241 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.97e+00 angle pdb=" CA GLU C 241 " pdb=" CB GLU C 241 " pdb=" CG GLU C 241 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.97e+00 angle pdb=" CA GLU P 241 " pdb=" CB GLU P 241 " pdb=" CG GLU P 241 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.97e+00 ... (remaining 47347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 18072 17.45 - 34.90: 1896 34.90 - 52.36: 504 52.36 - 69.81: 144 69.81 - 87.26: 72 Dihedral angle restraints: 20688 sinusoidal: 8112 harmonic: 12576 Sorted by residual: dihedral pdb=" CA GLY H 204 " pdb=" C GLY H 204 " pdb=" N LYS H 205 " pdb=" CA LYS H 205 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA GLY L 204 " pdb=" C GLY L 204 " pdb=" N LYS L 205 " pdb=" CA LYS L 205 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA GLY Y 204 " pdb=" C GLY Y 204 " pdb=" N LYS Y 205 " pdb=" CA LYS Y 205 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 20685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2805 0.025 - 0.050: 1612 0.050 - 0.074: 526 0.074 - 0.099: 121 0.099 - 0.124: 336 Chirality restraints: 5400 Sorted by residual: chirality pdb=" CA ILE H 228 " pdb=" N ILE H 228 " pdb=" C ILE H 228 " pdb=" CB ILE H 228 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ARG P 167 " pdb=" N ARG P 167 " pdb=" C ARG P 167 " pdb=" CB ARG P 167 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ARG C 167 " pdb=" N ARG C 167 " pdb=" C ARG C 167 " pdb=" CB ARG C 167 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 5397 not shown) Planarity restraints: 6240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE X 198 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO X 199 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO X 199 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO X 199 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE T 198 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO T 199 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO T 199 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO T 199 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE Q 198 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO Q 199 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO Q 199 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO Q 199 " -0.016 5.00e-02 4.00e+02 ... (remaining 6237 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1194 2.72 - 3.27: 32251 3.27 - 3.81: 57475 3.81 - 4.36: 77663 4.36 - 4.90: 125243 Nonbonded interactions: 293826 Sorted by model distance: nonbonded pdb=" OE1 GLU Q 241 " pdb="MN MN Q 302 " model vdw 2.177 2.320 nonbonded pdb=" OE1 GLU X 241 " pdb="MN MN X 302 " model vdw 2.177 2.320 nonbonded pdb=" OE1 GLU B 241 " pdb="MN MN B 302 " model vdw 2.177 2.320 nonbonded pdb=" OE1 GLU N 241 " pdb="MN MN N 302 " model vdw 2.177 2.320 nonbonded pdb=" OE1 GLU T 241 " pdb="MN MN T 302 " model vdw 2.177 2.320 ... (remaining 293821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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: 5 Type Number sf(0) Gaussians Mn 48 7.51 5 S 72 5.16 5 C 21384 2.51 5 N 6336 2.21 5 O 7483 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: 2.030 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: 0.030 Extract box with map and model: 12.900 Check model and map are aligned: 0.540 Convert atoms to be neutral: 0.310 Process input model: 89.300 Find NCS groups from input model: 3.180 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 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 : 0.002 0.030 34992 Z= 0.132 Angle : 0.531 7.305 47352 Z= 0.282 Chirality : 0.043 0.124 5400 Planarity : 0.003 0.028 6240 Dihedral : 16.614 87.261 12576 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.12), residues: 4368 helix: -0.83 (0.11), residues: 1656 sheet: 1.13 (0.14), residues: 1152 loop : -1.65 (0.16), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 648 time to evaluate : 4.417 Fit side-chains outliers start: 72 outliers final: 24 residues processed: 720 average time/residue: 1.5671 time to fit residues: 1338.6016 Evaluate side-chains 672 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 648 time to evaluate : 4.254 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.5916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 174 optimal weight: 0.0270 chunk 338 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 205 optimal weight: 7.9990 chunk 252 optimal weight: 20.0000 chunk 392 optimal weight: 10.0000 overall best weight: 7.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 97 ASN A 157 GLN A 201 GLN B 91 ASN B 97 ASN B 157 GLN B 201 GLN C 91 ASN C 97 ASN C 157 GLN C 201 GLN D 91 ASN D 97 ASN D 157 GLN D 201 GLN E 91 ASN E 97 ASN E 157 GLN E 201 GLN F 91 ASN F 97 ASN F 157 GLN F 201 GLN G 91 ASN G 97 ASN G 157 GLN G 201 GLN H 91 ASN H 97 ASN H 157 GLN H 201 GLN I 91 ASN I 97 ASN I 157 GLN I 201 GLN J 91 ASN J 97 ASN J 157 GLN J 201 GLN K 91 ASN K 97 ASN K 157 GLN K 201 GLN L 91 ASN L 97 ASN L 157 GLN L 201 GLN M 91 ASN M 97 ASN M 157 GLN M 201 GLN N 91 ASN N 97 ASN N 157 GLN N 201 GLN O 91 ASN O 97 ASN O 157 GLN O 201 GLN P 91 ASN P 97 ASN P 157 GLN P 201 GLN Q 91 ASN Q 97 ASN Q 157 GLN Q 201 GLN R 91 ASN R 97 ASN R 157 GLN R 201 GLN S 91 ASN S 97 ASN S 157 GLN S 201 GLN T 91 ASN T 97 ASN T 157 GLN T 201 GLN V 91 ASN V 97 ASN V 157 GLN V 201 GLN W 91 ASN W 97 ASN W 157 GLN W 201 GLN X 91 ASN X 97 ASN X 157 GLN X 201 GLN Y 91 ASN Y 97 ASN Y 157 GLN Y 201 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.042 34992 Z= 0.440 Angle : 0.930 8.329 47352 Z= 0.508 Chirality : 0.058 0.268 5400 Planarity : 0.006 0.036 6240 Dihedral : 5.442 19.066 4728 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.13), residues: 4368 helix: 1.33 (0.12), residues: 1656 sheet: 0.97 (0.14), residues: 1152 loop : -1.53 (0.18), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 624 time to evaluate : 4.296 Fit side-chains outliers start: 96 outliers final: 48 residues processed: 696 average time/residue: 1.8435 time to fit residues: 1480.5881 Evaluate side-chains 648 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 600 time to evaluate : 4.038 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 24 residues processed: 24 average time/residue: 0.2851 time to fit residues: 18.4294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 326 optimal weight: 20.0000 chunk 267 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 393 optimal weight: 9.9990 chunk 424 optimal weight: 10.0000 chunk 350 optimal weight: 4.9990 chunk 389 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 315 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 115 HIS A 157 GLN A 201 GLN B 91 ASN B 115 HIS B 157 GLN B 201 GLN C 91 ASN C 115 HIS C 157 GLN C 201 GLN D 91 ASN D 115 HIS D 157 GLN D 201 GLN E 91 ASN E 115 HIS E 157 GLN E 201 GLN F 91 ASN F 115 HIS F 157 GLN F 201 GLN G 91 ASN G 115 HIS G 157 GLN G 201 GLN H 91 ASN H 115 HIS H 157 GLN H 201 GLN I 91 ASN I 115 HIS I 157 GLN I 201 GLN J 91 ASN J 115 HIS J 157 GLN J 201 GLN K 91 ASN K 115 HIS K 157 GLN K 201 GLN L 91 ASN L 115 HIS L 157 GLN L 201 GLN M 91 ASN M 115 HIS M 157 GLN M 201 GLN N 91 ASN N 115 HIS N 157 GLN N 201 GLN O 91 ASN O 115 HIS O 157 GLN O 201 GLN P 91 ASN P 115 HIS P 157 GLN P 201 GLN Q 91 ASN Q 115 HIS Q 157 GLN Q 201 GLN R 91 ASN R 115 HIS R 157 GLN R 201 GLN S 91 ASN S 115 HIS S 157 GLN S 201 GLN T 91 ASN T 115 HIS T 157 GLN T 201 GLN V 91 ASN V 115 HIS V 157 GLN V 201 GLN W 91 ASN W 115 HIS W 157 GLN W 201 GLN X 91 ASN X 115 HIS X 157 GLN X 201 GLN Y 91 ASN Y 115 HIS Y 157 GLN Y 201 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 34992 Z= 0.259 Angle : 0.708 6.079 47352 Z= 0.390 Chirality : 0.049 0.148 5400 Planarity : 0.004 0.038 6240 Dihedral : 5.110 18.031 4728 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.13), residues: 4368 helix: 1.93 (0.11), residues: 1680 sheet: 0.95 (0.14), residues: 1152 loop : -1.57 (0.18), residues: 1536 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 696 time to evaluate : 4.475 Fit side-chains outliers start: 96 outliers final: 24 residues processed: 744 average time/residue: 1.6850 time to fit residues: 1467.9953 Evaluate side-chains 672 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 648 time to evaluate : 4.107 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2799 time to fit residues: 17.5876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 7.9990 chunk 295 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 394 optimal weight: 2.9990 chunk 417 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 373 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 170 ASN A 201 GLN B 91 ASN B 157 GLN B 170 ASN B 201 GLN C 91 ASN C 157 GLN C 170 ASN C 201 GLN D 91 ASN D 157 GLN D 170 ASN D 201 GLN E 91 ASN E 157 GLN E 170 ASN E 201 GLN F 91 ASN F 157 GLN F 170 ASN F 201 GLN G 91 ASN G 157 GLN G 170 ASN G 201 GLN H 91 ASN H 157 GLN H 170 ASN H 201 GLN I 91 ASN I 157 GLN I 170 ASN I 201 GLN J 91 ASN J 157 GLN J 170 ASN J 201 GLN K 91 ASN K 157 GLN K 170 ASN K 201 GLN L 91 ASN L 157 GLN L 170 ASN L 201 GLN M 91 ASN M 157 GLN M 170 ASN M 201 GLN N 91 ASN N 157 GLN N 170 ASN N 201 GLN O 91 ASN O 157 GLN O 170 ASN O 201 GLN P 91 ASN P 157 GLN P 170 ASN P 201 GLN Q 91 ASN Q 157 GLN Q 170 ASN Q 201 GLN R 91 ASN R 157 GLN R 170 ASN R 201 GLN S 91 ASN S 157 GLN S 170 ASN S 201 GLN T 91 ASN T 157 GLN T 170 ASN T 201 GLN V 91 ASN V 157 GLN V 170 ASN V 201 GLN W 91 ASN W 157 GLN W 170 ASN W 201 GLN X 91 ASN X 157 GLN X 170 ASN X 201 GLN Y 91 ASN Y 157 GLN Y 170 ASN Y 201 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 34992 Z= 0.432 Angle : 0.903 8.394 47352 Z= 0.493 Chirality : 0.059 0.273 5400 Planarity : 0.005 0.041 6240 Dihedral : 5.545 18.846 4728 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 4368 helix: 1.77 (0.11), residues: 1656 sheet: 0.78 (0.13), residues: 1152 loop : -1.70 (0.17), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 624 time to evaluate : 4.612 Fit side-chains outliers start: 72 outliers final: 24 residues processed: 672 average time/residue: 1.9111 time to fit residues: 1476.1580 Evaluate side-chains 648 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 624 time to evaluate : 4.436 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2995 time to fit residues: 19.6634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 20.0000 chunk 237 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 356 optimal weight: 1.9990 chunk 288 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 374 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 201 GLN B 91 ASN B 157 GLN B 201 GLN C 91 ASN C 157 GLN C 201 GLN D 91 ASN D 157 GLN D 201 GLN E 91 ASN E 157 GLN E 201 GLN F 91 ASN F 157 GLN F 201 GLN G 91 ASN G 157 GLN G 201 GLN H 91 ASN H 157 GLN H 201 GLN I 91 ASN I 157 GLN I 201 GLN J 91 ASN J 157 GLN J 201 GLN K 91 ASN K 157 GLN K 201 GLN L 91 ASN L 157 GLN L 201 GLN M 91 ASN M 157 GLN M 201 GLN N 91 ASN N 157 GLN N 201 GLN O 91 ASN O 157 GLN O 201 GLN P 91 ASN P 157 GLN P 201 GLN Q 91 ASN Q 157 GLN Q 201 GLN R 91 ASN R 157 GLN R 201 GLN S 91 ASN S 157 GLN S 201 GLN T 91 ASN T 157 GLN T 201 GLN V 91 ASN V 157 GLN V 201 GLN W 91 ASN W 157 GLN W 201 GLN X 91 ASN X 157 GLN X 201 GLN Y 91 ASN Y 157 GLN Y 201 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 34992 Z= 0.268 Angle : 0.719 6.144 47352 Z= 0.394 Chirality : 0.050 0.155 5400 Planarity : 0.004 0.041 6240 Dihedral : 5.182 18.002 4728 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.13), residues: 4368 helix: 2.11 (0.11), residues: 1656 sheet: 0.81 (0.13), residues: 1152 loop : -1.73 (0.17), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 648 time to evaluate : 4.326 Fit side-chains outliers start: 72 outliers final: 24 residues processed: 672 average time/residue: 1.6860 time to fit residues: 1328.8995 Evaluate side-chains 672 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 648 time to evaluate : 4.250 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3165 time to fit residues: 20.4680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 1.9990 chunk 376 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 245 optimal weight: 0.0670 chunk 103 optimal weight: 9.9990 chunk 417 optimal weight: 1.9990 chunk 346 optimal weight: 4.9990 chunk 193 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 219 optimal weight: 0.5980 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 170 ASN A 197 ASN A 201 GLN B 91 ASN B 157 GLN B 170 ASN B 197 ASN B 201 GLN C 91 ASN C 157 GLN C 170 ASN C 197 ASN C 201 GLN D 91 ASN D 157 GLN D 170 ASN D 197 ASN D 201 GLN E 91 ASN E 157 GLN E 170 ASN E 197 ASN E 201 GLN F 91 ASN F 157 GLN F 170 ASN F 197 ASN F 201 GLN G 91 ASN G 157 GLN G 170 ASN G 197 ASN G 201 GLN H 91 ASN H 157 GLN H 170 ASN H 197 ASN H 201 GLN I 91 ASN I 157 GLN I 170 ASN I 197 ASN I 201 GLN J 91 ASN J 157 GLN J 170 ASN J 197 ASN J 201 GLN K 91 ASN K 157 GLN K 170 ASN K 197 ASN K 201 GLN L 91 ASN L 157 GLN L 170 ASN L 197 ASN L 201 GLN M 91 ASN M 157 GLN M 170 ASN M 197 ASN M 201 GLN N 91 ASN N 157 GLN N 170 ASN N 197 ASN N 201 GLN O 91 ASN O 157 GLN O 170 ASN O 197 ASN O 201 GLN P 91 ASN P 157 GLN P 170 ASN P 197 ASN P 201 GLN Q 91 ASN Q 157 GLN Q 170 ASN Q 197 ASN Q 201 GLN R 91 ASN R 157 GLN R 170 ASN R 197 ASN R 201 GLN S 91 ASN S 157 GLN S 170 ASN S 197 ASN S 201 GLN T 91 ASN T 157 GLN T 170 ASN T 197 ASN T 201 GLN V 91 ASN V 157 GLN V 170 ASN V 197 ASN V 201 GLN W 91 ASN W 157 GLN W 170 ASN W 197 ASN W 201 GLN X 91 ASN X 157 GLN X 170 ASN X 197 ASN X 201 GLN Y 91 ASN Y 157 GLN Y 170 ASN Y 197 ASN Y 201 GLN Total number of N/Q/H flips: 120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 34992 Z= 0.185 Angle : 0.597 4.932 47352 Z= 0.329 Chirality : 0.046 0.143 5400 Planarity : 0.004 0.037 6240 Dihedral : 4.798 16.774 4728 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.13), residues: 4368 helix: 2.49 (0.11), residues: 1656 sheet: 0.90 (0.13), residues: 1152 loop : -1.77 (0.17), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 624 time to evaluate : 4.179 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 648 average time/residue: 1.6413 time to fit residues: 1257.6304 Evaluate side-chains 600 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 600 time to evaluate : 4.570 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 305 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 351 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 416 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 197 ASN A 201 GLN B 91 ASN B 157 GLN B 197 ASN B 201 GLN C 91 ASN C 157 GLN C 197 ASN C 201 GLN D 91 ASN D 157 GLN D 197 ASN D 201 GLN E 91 ASN E 157 GLN E 197 ASN E 201 GLN F 91 ASN F 157 GLN F 197 ASN F 201 GLN G 91 ASN G 157 GLN G 197 ASN G 201 GLN H 91 ASN H 157 GLN H 197 ASN H 201 GLN I 91 ASN I 157 GLN I 197 ASN I 201 GLN J 91 ASN J 157 GLN J 197 ASN J 201 GLN K 91 ASN K 157 GLN K 197 ASN K 201 GLN L 91 ASN L 157 GLN L 197 ASN L 201 GLN M 91 ASN M 157 GLN M 197 ASN M 201 GLN N 91 ASN N 157 GLN N 197 ASN N 201 GLN O 91 ASN O 157 GLN O 197 ASN O 201 GLN P 91 ASN P 157 GLN P 197 ASN P 201 GLN Q 91 ASN Q 157 GLN Q 197 ASN Q 201 GLN R 91 ASN R 157 GLN R 197 ASN R 201 GLN S 91 ASN S 157 GLN S 197 ASN S 201 GLN T 91 ASN T 157 GLN T 197 ASN T 201 GLN V 91 ASN V 157 GLN V 197 ASN V 201 GLN W 91 ASN W 157 GLN W 197 ASN W 201 GLN X 91 ASN X 157 GLN X 197 ASN X 201 GLN Y 91 ASN Y 157 GLN Y 197 ASN Y 201 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 34992 Z= 0.360 Angle : 0.819 7.664 47352 Z= 0.447 Chirality : 0.055 0.226 5400 Planarity : 0.005 0.041 6240 Dihedral : 5.337 18.604 4728 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.13), residues: 4368 helix: 2.07 (0.11), residues: 1656 sheet: 0.81 (0.13), residues: 1152 loop : -1.75 (0.17), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 624 time to evaluate : 4.408 Fit side-chains outliers start: 48 outliers final: 24 residues processed: 648 average time/residue: 1.7051 time to fit residues: 1288.5316 Evaluate side-chains 624 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 600 time to evaluate : 4.277 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2965 time to fit residues: 19.3459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 30.0000 chunk 166 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 264 optimal weight: 0.3980 chunk 283 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 overall best weight: 6.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 197 ASN A 201 GLN B 91 ASN B 157 GLN B 197 ASN B 201 GLN C 91 ASN C 157 GLN C 197 ASN C 201 GLN D 91 ASN D 157 GLN D 197 ASN D 201 GLN E 91 ASN E 157 GLN E 197 ASN E 201 GLN F 91 ASN F 157 GLN F 197 ASN F 201 GLN G 91 ASN G 157 GLN G 197 ASN G 201 GLN H 91 ASN H 157 GLN H 197 ASN H 201 GLN I 91 ASN I 157 GLN I 197 ASN I 201 GLN J 91 ASN J 157 GLN J 197 ASN J 201 GLN K 91 ASN K 157 GLN K 197 ASN K 201 GLN L 91 ASN L 157 GLN L 197 ASN L 201 GLN M 91 ASN M 157 GLN M 197 ASN M 201 GLN N 91 ASN N 157 GLN N 197 ASN N 201 GLN O 91 ASN O 157 GLN O 197 ASN O 201 GLN P 91 ASN P 157 GLN P 197 ASN P 201 GLN Q 91 ASN Q 157 GLN Q 197 ASN Q 201 GLN R 91 ASN R 157 GLN R 197 ASN R 201 GLN S 91 ASN S 157 GLN S 197 ASN S 201 GLN T 91 ASN T 157 GLN T 197 ASN T 201 GLN V 91 ASN V 157 GLN V 197 ASN V 201 GLN W 91 ASN W 157 GLN W 197 ASN W 201 GLN X 91 ASN X 157 GLN X 197 ASN X 201 GLN Y 91 ASN Y 157 GLN Y 197 ASN Y 201 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.035 34992 Z= 0.393 Angle : 0.866 7.798 47352 Z= 0.472 Chirality : 0.057 0.249 5400 Planarity : 0.005 0.040 6240 Dihedral : 5.452 18.775 4728 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.13), residues: 4368 helix: 1.86 (0.11), residues: 1656 sheet: 0.65 (0.13), residues: 1152 loop : -1.76 (0.17), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 624 time to evaluate : 4.338 Fit side-chains outliers start: 72 outliers final: 48 residues processed: 672 average time/residue: 1.7103 time to fit residues: 1348.8637 Evaluate side-chains 648 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 600 time to evaluate : 4.291 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 24 residues processed: 24 average time/residue: 0.3138 time to fit residues: 20.3909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 20.0000 chunk 398 optimal weight: 5.9990 chunk 363 optimal weight: 3.9990 chunk 388 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 304 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 350 optimal weight: 6.9990 chunk 366 optimal weight: 0.9990 chunk 386 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 197 ASN A 201 GLN B 91 ASN B 157 GLN B 197 ASN B 201 GLN C 91 ASN C 157 GLN C 197 ASN C 201 GLN D 91 ASN D 157 GLN D 197 ASN D 201 GLN E 91 ASN E 157 GLN E 197 ASN E 201 GLN F 91 ASN F 157 GLN F 197 ASN F 201 GLN G 91 ASN G 157 GLN G 197 ASN G 201 GLN H 91 ASN H 157 GLN H 197 ASN H 201 GLN I 91 ASN I 157 GLN I 197 ASN I 201 GLN J 91 ASN J 157 GLN J 197 ASN J 201 GLN K 91 ASN K 157 GLN K 197 ASN K 201 GLN L 91 ASN L 157 GLN L 197 ASN L 201 GLN M 91 ASN M 157 GLN M 197 ASN M 201 GLN N 91 ASN N 157 GLN N 197 ASN N 201 GLN O 91 ASN O 157 GLN O 197 ASN O 201 GLN P 91 ASN P 157 GLN P 197 ASN P 201 GLN Q 91 ASN Q 157 GLN Q 197 ASN Q 201 GLN R 91 ASN R 157 GLN R 197 ASN R 201 GLN S 91 ASN S 157 GLN S 197 ASN S 201 GLN T 91 ASN T 157 GLN T 197 ASN T 201 GLN V 91 ASN V 157 GLN V 197 ASN V 201 GLN W 91 ASN W 157 GLN W 197 ASN W 201 GLN X 91 ASN X 157 GLN X 197 ASN X 201 GLN Y 91 ASN Y 157 GLN Y 197 ASN Y 201 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 34992 Z= 0.276 Angle : 0.740 6.518 47352 Z= 0.403 Chirality : 0.051 0.166 5400 Planarity : 0.004 0.038 6240 Dihedral : 5.183 17.961 4728 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.13), residues: 4368 helix: 2.09 (0.11), residues: 1656 sheet: 0.75 (0.13), residues: 1152 loop : -1.81 (0.17), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 576 time to evaluate : 4.291 Fit side-chains outliers start: 48 outliers final: 24 residues processed: 624 average time/residue: 1.6619 time to fit residues: 1221.4122 Evaluate side-chains 600 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 576 time to evaluate : 4.215 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.5977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 4.9990 chunk 410 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 285 optimal weight: 7.9990 chunk 430 optimal weight: 7.9990 chunk 396 optimal weight: 20.0000 chunk 342 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 264 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 197 ASN A 201 GLN B 91 ASN B 157 GLN B 197 ASN B 201 GLN C 91 ASN C 157 GLN C 197 ASN C 201 GLN D 91 ASN D 157 GLN D 197 ASN D 201 GLN E 91 ASN E 157 GLN E 197 ASN E 201 GLN F 91 ASN F 157 GLN F 197 ASN F 201 GLN G 91 ASN G 157 GLN G 197 ASN G 201 GLN H 91 ASN H 157 GLN H 197 ASN H 201 GLN I 91 ASN I 157 GLN I 197 ASN I 201 GLN J 91 ASN J 157 GLN J 197 ASN J 201 GLN K 91 ASN K 157 GLN K 197 ASN K 201 GLN L 91 ASN L 157 GLN L 197 ASN L 201 GLN M 91 ASN M 157 GLN M 197 ASN M 201 GLN N 91 ASN N 157 GLN N 197 ASN N 201 GLN O 91 ASN O 157 GLN O 197 ASN O 201 GLN P 91 ASN P 157 GLN P 197 ASN P 201 GLN Q 91 ASN Q 157 GLN Q 197 ASN Q 201 GLN R 91 ASN R 157 GLN R 197 ASN R 201 GLN S 91 ASN S 157 GLN S 197 ASN S 201 GLN T 91 ASN T 157 GLN T 197 ASN T 201 GLN V 91 ASN V 157 GLN V 197 ASN V 201 GLN W 91 ASN W 157 GLN W 197 ASN W 201 GLN X 91 ASN X 157 GLN X 197 ASN X 201 GLN Y 91 ASN Y 157 GLN Y 197 ASN Y 201 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 34992 Z= 0.275 Angle : 0.737 6.556 47352 Z= 0.402 Chirality : 0.051 0.165 5400 Planarity : 0.004 0.039 6240 Dihedral : 5.186 17.997 4728 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.13), residues: 4368 helix: 2.08 (0.11), residues: 1656 sheet: 0.76 (0.13), residues: 1152 loop : -1.82 (0.17), residues: 1560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 576 time to evaluate : 4.557 Fit side-chains outliers start: 48 outliers final: 24 residues processed: 624 average time/residue: 1.6772 time to fit residues: 1229.4504 Evaluate side-chains 600 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 576 time to evaluate : 4.098 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.4540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 4.9990 chunk 365 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 316 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 chunk 343 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 352 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 197 ASN A 201 GLN B 91 ASN B 157 GLN B 197 ASN B 201 GLN C 91 ASN C 157 GLN C 197 ASN C 201 GLN D 91 ASN D 157 GLN D 197 ASN D 201 GLN E 91 ASN E 157 GLN E 197 ASN E 201 GLN F 91 ASN F 157 GLN F 197 ASN F 201 GLN G 91 ASN G 157 GLN G 197 ASN G 201 GLN H 91 ASN H 157 GLN H 197 ASN H 201 GLN I 91 ASN I 157 GLN I 197 ASN I 201 GLN J 91 ASN J 157 GLN J 197 ASN J 201 GLN K 91 ASN K 157 GLN K 197 ASN K 201 GLN L 91 ASN L 157 GLN L 197 ASN L 201 GLN M 91 ASN M 157 GLN M 197 ASN M 201 GLN N 91 ASN N 157 GLN N 197 ASN N 201 GLN O 91 ASN O 157 GLN O 197 ASN O 201 GLN P 91 ASN P 157 GLN P 197 ASN P 201 GLN Q 91 ASN Q 157 GLN Q 197 ASN Q 201 GLN R 91 ASN R 157 GLN R 197 ASN R 201 GLN S 91 ASN S 157 GLN S 197 ASN S 201 GLN T 91 ASN T 157 GLN T 197 ASN T 201 GLN V 91 ASN V 157 GLN V 197 ASN V 201 GLN W 91 ASN W 157 GLN W 197 ASN W 201 GLN X 91 ASN X 157 GLN X 197 ASN X 201 GLN Y 91 ASN Y 157 GLN Y 197 ASN Y 201 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.144536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.126470 restraints weight = 27424.582| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 0.79 r_work: 0.3148 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 34992 Z= 0.285 Angle : 0.751 6.728 47352 Z= 0.409 Chirality : 0.051 0.176 5400 Planarity : 0.004 0.038 6240 Dihedral : 5.199 17.940 4728 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.13), residues: 4368 helix: 2.08 (0.11), residues: 1656 sheet: 0.76 (0.13), residues: 1152 loop : -1.82 (0.17), residues: 1560 =============================================================================== Job complete usr+sys time: 17213.31 seconds wall clock time: 301 minutes 51.86 seconds (18111.86 seconds total)