Starting phenix.real_space_refine on Sat Mar 16 14:32:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddj_27337/03_2024/8ddj_27337.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddj_27337/03_2024/8ddj_27337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddj_27337/03_2024/8ddj_27337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddj_27337/03_2024/8ddj_27337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddj_27337/03_2024/8ddj_27337.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddj_27337/03_2024/8ddj_27337.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 9548 2.51 5 N 2590 2.21 5 O 2716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D ASP 274": "OD1" <-> "OD2" Residue "D PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 62": "OD1" <-> "OD2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G GLU 255": "OE1" <-> "OE2" Residue "G PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14903 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "C" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "D" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "G" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Time building chain proxies: 7.56, per 1000 atoms: 0.51 Number of scatterers: 14903 At special positions: 0 Unit cell: (103.111, 103.111, 130.749, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 2716 8.00 N 2590 7.00 C 9548 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: 5.46 Conformation dependent library (CDL) restraints added in 2.9 seconds 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 9 sheets defined 57.0% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 10 through 14 removed outlier: 3.650A pdb=" N GLY A 14 " --> pdb=" O ASN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 20 through 59 removed outlier: 3.538A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 90 Processing helix chain 'A' and resid 93 through 112 removed outlier: 3.877A pdb=" N ILE A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 128 removed outlier: 3.618A pdb=" N MET A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.665A pdb=" N GLY B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 20 through 59 Processing helix chain 'B' and resid 62 through 90 Processing helix chain 'B' and resid 93 through 112 removed outlier: 3.834A pdb=" N ILE B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 128 Processing helix chain 'B' and resid 167 through 173 removed outlier: 3.509A pdb=" N ILE B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'C' and resid 10 through 14 removed outlier: 3.708A pdb=" N GLY C 14 " --> pdb=" O ASN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 20 through 59 removed outlier: 3.508A pdb=" N SER C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 90 Processing helix chain 'C' and resid 94 through 112 Processing helix chain 'C' and resid 112 through 128 removed outlier: 3.626A pdb=" N MET C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.669A pdb=" N GLY D 14 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 20 through 59 removed outlier: 3.609A pdb=" N ARG D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 90 Processing helix chain 'D' and resid 94 through 112 Processing helix chain 'D' and resid 112 through 128 Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 245 through 265 Processing helix chain 'E' and resid 10 through 14 removed outlier: 3.741A pdb=" N GLY E 14 " --> pdb=" O ASN E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 20 through 59 removed outlier: 3.558A pdb=" N ARG E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 90 Processing helix chain 'E' and resid 93 through 112 Processing helix chain 'E' and resid 112 through 128 Processing helix chain 'E' and resid 167 through 173 Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 245 through 265 Processing helix chain 'F' and resid 10 through 14 removed outlier: 3.731A pdb=" N GLY F 14 " --> pdb=" O ASN F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 20 through 59 Processing helix chain 'F' and resid 62 through 90 Processing helix chain 'F' and resid 93 through 112 Processing helix chain 'F' and resid 112 through 128 Processing helix chain 'F' and resid 167 through 173 Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 245 through 265 Processing helix chain 'G' and resid 10 through 14 removed outlier: 3.656A pdb=" N GLY G 14 " --> pdb=" O ASN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 20 Processing helix chain 'G' and resid 20 through 59 Processing helix chain 'G' and resid 62 through 90 Processing helix chain 'G' and resid 93 through 112 removed outlier: 3.833A pdb=" N ILE G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 128 Processing helix chain 'G' and resid 167 through 173 Processing helix chain 'G' and resid 197 through 211 Processing helix chain 'G' and resid 245 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 137 removed outlier: 6.849A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE E 162 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 7.251A pdb=" N ASN A 234 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 279 removed outlier: 8.359A pdb=" N MET B 273 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ASP A 274 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE B 277 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LYS A 278 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N ARG B 279 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N MET C 273 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASP B 274 " --> pdb=" O MET C 273 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL C 275 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASN B 276 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N PHE C 277 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LYS B 278 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N ARG C 279 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N MET D 273 " --> pdb=" O GLN C 272 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASP C 274 " --> pdb=" O MET D 273 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL D 275 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ASN C 276 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE D 277 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LYS C 278 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ARG D 279 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N MET E 273 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP D 274 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL E 275 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN D 276 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE E 277 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LYS D 278 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N ARG E 279 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N MET F 273 " --> pdb=" O GLN E 272 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASP E 274 " --> pdb=" O MET F 273 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL F 275 " --> pdb=" O ASP E 274 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN E 276 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE F 277 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LYS E 278 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ARG F 279 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N MET G 273 " --> pdb=" O GLN F 272 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASP F 274 " --> pdb=" O MET G 273 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL G 275 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASN F 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N PHE G 277 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LYS F 278 " --> pdb=" O PHE G 277 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ARG G 279 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 7.310A pdb=" N ASN B 234 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 7.327A pdb=" N ASN C 234 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 7.286A pdb=" N ASN D 234 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 7.237A pdb=" N ASN E 234 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 7.218A pdb=" N ASN F 234 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 7.159A pdb=" N ASN G 234 " --> pdb=" O ASN G 226 " (cutoff:3.500A) 1069 hydrogen bonds defined for protein. 3105 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: 4.81 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4990 1.34 - 1.46: 3023 1.46 - 1.58: 6981 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 15092 Sorted by residual: bond pdb=" CA ARG D 128 " pdb=" CB ARG D 128 " ideal model delta sigma weight residual 1.525 1.538 -0.013 8.30e-03 1.45e+04 2.41e+00 bond pdb=" CA VAL B 91 " pdb=" C VAL B 91 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.27e-02 6.20e+03 1.23e+00 bond pdb=" CA VAL A 91 " pdb=" C VAL A 91 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.27e-02 6.20e+03 1.16e+00 bond pdb=" CA VAL E 91 " pdb=" C VAL E 91 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.31e-02 5.83e+03 1.15e+00 bond pdb=" CA VAL D 91 " pdb=" C VAL D 91 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.27e-02 6.20e+03 1.13e+00 ... (remaining 15087 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.22: 186 106.22 - 113.16: 8519 113.16 - 120.10: 5033 120.10 - 127.04: 6657 127.04 - 133.98: 87 Bond angle restraints: 20482 Sorted by residual: angle pdb=" CB MET B 273 " pdb=" CG MET B 273 " pdb=" SD MET B 273 " ideal model delta sigma weight residual 112.70 101.47 11.23 3.00e+00 1.11e-01 1.40e+01 angle pdb=" C VAL C 91 " pdb=" N GLN C 92 " pdb=" CA GLN C 92 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C VAL D 91 " pdb=" N GLN D 92 " pdb=" CA GLN D 92 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C VAL G 91 " pdb=" N GLN G 92 " pdb=" CA GLN G 92 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C GLN D 112 " pdb=" N GLY D 113 " pdb=" CA GLY D 113 " ideal model delta sigma weight residual 119.98 123.49 -3.51 1.11e+00 8.12e-01 1.00e+01 ... (remaining 20477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 8231 16.92 - 33.84: 663 33.84 - 50.75: 123 50.75 - 67.67: 19 67.67 - 84.59: 15 Dihedral angle restraints: 9051 sinusoidal: 3444 harmonic: 5607 Sorted by residual: dihedral pdb=" CA LEU D 111 " pdb=" C LEU D 111 " pdb=" N GLN D 112 " pdb=" CA GLN D 112 " ideal model delta harmonic sigma weight residual -180.00 -157.57 -22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PHE F 277 " pdb=" C PHE F 277 " pdb=" N LYS F 278 " pdb=" CA LYS F 278 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CG ARG B 279 " pdb=" CD ARG B 279 " pdb=" NE ARG B 279 " pdb=" CZ ARG B 279 " ideal model delta sinusoidal sigma weight residual 180.00 135.44 44.56 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 9048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1772 0.039 - 0.078: 522 0.078 - 0.117: 182 0.117 - 0.156: 30 0.156 - 0.195: 7 Chirality restraints: 2513 Sorted by residual: chirality pdb=" CB VAL C 6 " pdb=" CA VAL C 6 " pdb=" CG1 VAL C 6 " pdb=" CG2 VAL C 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA ILE B 176 " pdb=" N ILE B 176 " pdb=" C ILE B 176 " pdb=" CB ILE B 176 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA GLU B 260 " pdb=" N GLU B 260 " pdb=" C GLU B 260 " pdb=" CB GLU B 260 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 2510 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 80 " -0.013 2.00e-02 2.50e+03 1.75e-02 5.35e+00 pdb=" CG PHE F 80 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE F 80 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE F 80 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE F 80 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 80 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 80 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 80 " -0.011 2.00e-02 2.50e+03 1.44e-02 3.62e+00 pdb=" CG PHE G 80 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE G 80 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE G 80 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE G 80 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE G 80 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE G 80 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 256 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ARG B 256 " 0.033 2.00e-02 2.50e+03 pdb=" O ARG B 256 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE B 257 " -0.011 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2583 2.77 - 3.30: 15346 3.30 - 3.83: 24928 3.83 - 4.37: 27298 4.37 - 4.90: 48610 Nonbonded interactions: 118765 Sorted by model distance: nonbonded pdb=" NZ LYS A 169 " pdb=" OD1 ASN G 174 " model vdw 2.236 2.520 nonbonded pdb=" OD1 ASN B 174 " pdb=" NZ LYS C 169 " model vdw 2.236 2.520 nonbonded pdb=" OE2 GLU C 255 " pdb=" NE ARG C 259 " model vdw 2.242 2.520 nonbonded pdb=" OE2 GLU D 220 " pdb=" NE1 TRP D 240 " model vdw 2.246 2.520 nonbonded pdb=" OE2 GLU C 220 " pdb=" NE1 TRP C 240 " model vdw 2.254 2.520 ... (remaining 118760 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.010 Extract box with map and model: 4.390 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 40.500 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.003 0.029 15092 Z= 0.192 Angle : 0.625 11.228 20482 Z= 0.341 Chirality : 0.044 0.195 2513 Planarity : 0.002 0.026 2604 Dihedral : 13.091 84.591 5439 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.52 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.19), residues: 1946 helix: 2.80 (0.16), residues: 1022 sheet: 1.35 (0.32), residues: 245 loop : -0.98 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 251 PHE 0.040 0.002 PHE F 80 TYR 0.014 0.001 TYR F 135 ARG 0.002 0.000 ARG G 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8068 (tt0) cc_final: 0.7725 (tt0) REVERT: A 203 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8631 (tm-30) REVERT: A 227 GLU cc_start: 0.8369 (pp20) cc_final: 0.8061 (pp20) REVERT: B 47 MET cc_start: 0.8977 (mmp) cc_final: 0.8711 (mmm) REVERT: B 112 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8874 (tm-30) REVERT: B 134 GLU cc_start: 0.8372 (tt0) cc_final: 0.7604 (tt0) REVERT: B 176 ILE cc_start: 0.8843 (mm) cc_final: 0.8616 (mm) REVERT: B 203 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8598 (tm-30) REVERT: B 260 GLU cc_start: 0.8762 (mp0) cc_final: 0.8194 (mp0) REVERT: B 278 LYS cc_start: 0.9020 (mtmm) cc_final: 0.8729 (mtmm) REVERT: C 56 MET cc_start: 0.8937 (ttm) cc_final: 0.8711 (ttm) REVERT: C 112 GLN cc_start: 0.9285 (tp40) cc_final: 0.9069 (tp40) REVERT: C 134 GLU cc_start: 0.8193 (tt0) cc_final: 0.7892 (tt0) REVERT: C 149 GLN cc_start: 0.9056 (mm110) cc_final: 0.8783 (mm110) REVERT: C 181 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8955 (mm-30) REVERT: C 203 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8585 (tm-30) REVERT: C 227 GLU cc_start: 0.8327 (pp20) cc_final: 0.8025 (pp20) REVERT: C 260 GLU cc_start: 0.8675 (mp0) cc_final: 0.8069 (mp0) REVERT: C 274 ASP cc_start: 0.7741 (t0) cc_final: 0.7419 (t0) REVERT: D 112 GLN cc_start: 0.8393 (mp10) cc_final: 0.8191 (mp10) REVERT: D 203 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8688 (tm-30) REVERT: D 260 GLU cc_start: 0.8692 (mp0) cc_final: 0.8035 (mp0) REVERT: E 131 ARG cc_start: 0.8850 (ptt-90) cc_final: 0.8604 (ptp90) REVERT: E 134 GLU cc_start: 0.7880 (pt0) cc_final: 0.7384 (pt0) REVERT: E 149 GLN cc_start: 0.9189 (mm110) cc_final: 0.8847 (mm110) REVERT: E 203 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8616 (tm-30) REVERT: E 227 GLU cc_start: 0.8363 (pp20) cc_final: 0.8098 (pp20) REVERT: F 134 GLU cc_start: 0.7961 (tt0) cc_final: 0.7412 (tt0) REVERT: F 203 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8652 (tm-30) REVERT: F 227 GLU cc_start: 0.8399 (pp20) cc_final: 0.8064 (pp20) REVERT: G 134 GLU cc_start: 0.8008 (tt0) cc_final: 0.7678 (tt0) REVERT: G 203 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8608 (tm-30) REVERT: G 227 GLU cc_start: 0.8497 (pp20) cc_final: 0.8126 (pp20) REVERT: G 255 GLU cc_start: 0.9226 (tt0) cc_final: 0.8983 (tt0) REVERT: G 260 GLU cc_start: 0.8733 (mp0) cc_final: 0.7998 (mp0) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2469 time to fit residues: 122.1284 Evaluate side-chains 273 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 177 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN D 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15092 Z= 0.279 Angle : 0.563 8.002 20482 Z= 0.294 Chirality : 0.043 0.177 2513 Planarity : 0.003 0.021 2604 Dihedral : 4.135 16.490 2121 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.93 % Favored : 94.71 % Rotamer: Outliers : 0.88 % Allowed : 10.13 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.20), residues: 1946 helix: 2.78 (0.16), residues: 1043 sheet: 1.17 (0.31), residues: 259 loop : -0.84 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 16 PHE 0.028 0.002 PHE F 80 TYR 0.007 0.001 TYR E 135 ARG 0.002 0.000 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 286 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8833 (mmm) cc_final: 0.8632 (mmm) REVERT: A 149 GLN cc_start: 0.8580 (mm110) cc_final: 0.8344 (mm110) REVERT: A 203 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8666 (tm-30) REVERT: A 227 GLU cc_start: 0.8401 (pp20) cc_final: 0.8106 (pp20) REVERT: B 47 MET cc_start: 0.8911 (mmp) cc_final: 0.8609 (mmm) REVERT: B 112 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8900 (tm-30) REVERT: B 134 GLU cc_start: 0.8266 (tt0) cc_final: 0.7489 (tt0) REVERT: B 203 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8594 (tm-30) REVERT: B 260 GLU cc_start: 0.8846 (mp0) cc_final: 0.8272 (mp0) REVERT: B 278 LYS cc_start: 0.9123 (mtmm) cc_final: 0.8604 (mttm) REVERT: C 56 MET cc_start: 0.8945 (ttm) cc_final: 0.8724 (ttm) REVERT: C 112 GLN cc_start: 0.9298 (tp40) cc_final: 0.9076 (tp40) REVERT: C 134 GLU cc_start: 0.7993 (tt0) cc_final: 0.7740 (tt0) REVERT: C 149 GLN cc_start: 0.9146 (mm110) cc_final: 0.8820 (mm110) REVERT: C 181 GLU cc_start: 0.9311 (mm-30) cc_final: 0.8825 (mm-30) REVERT: C 203 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8669 (tm-30) REVERT: C 227 GLU cc_start: 0.8363 (pp20) cc_final: 0.8061 (pp20) REVERT: D 112 GLN cc_start: 0.8499 (mp10) cc_final: 0.8289 (mp10) REVERT: D 203 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8727 (tm-30) REVERT: E 55 LEU cc_start: 0.9234 (tt) cc_final: 0.8923 (mm) REVERT: E 134 GLU cc_start: 0.7887 (pt0) cc_final: 0.7670 (pt0) REVERT: E 149 GLN cc_start: 0.9218 (mm110) cc_final: 0.8861 (mm110) REVERT: E 203 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8683 (tm-30) REVERT: E 227 GLU cc_start: 0.8360 (pp20) cc_final: 0.8122 (pp20) REVERT: F 126 MET cc_start: 0.9240 (ppp) cc_final: 0.9018 (tmm) REVERT: F 134 GLU cc_start: 0.7851 (tt0) cc_final: 0.7611 (tt0) REVERT: F 149 GLN cc_start: 0.8725 (mm110) cc_final: 0.8502 (mm110) REVERT: F 203 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8655 (tm-30) REVERT: F 227 GLU cc_start: 0.8401 (pp20) cc_final: 0.8099 (pp20) REVERT: G 47 MET cc_start: 0.8740 (mmm) cc_final: 0.8358 (mmm) REVERT: G 134 GLU cc_start: 0.7944 (tt0) cc_final: 0.7614 (tt0) REVERT: G 149 GLN cc_start: 0.8745 (mm110) cc_final: 0.8534 (mm110) REVERT: G 150 ILE cc_start: 0.9472 (pt) cc_final: 0.9253 (pt) REVERT: G 227 GLU cc_start: 0.8499 (pp20) cc_final: 0.8134 (pp20) REVERT: G 255 GLU cc_start: 0.9207 (tt0) cc_final: 0.9004 (tt0) outliers start: 14 outliers final: 10 residues processed: 288 average time/residue: 0.2557 time to fit residues: 111.0318 Evaluate side-chains 278 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 268 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 153 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 192 optimal weight: 0.5980 chunk 158 optimal weight: 0.4980 chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15092 Z= 0.160 Angle : 0.538 8.656 20482 Z= 0.275 Chirality : 0.043 0.191 2513 Planarity : 0.002 0.021 2604 Dihedral : 4.032 15.457 2121 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.57 % Favored : 95.07 % Rotamer: Outliers : 1.01 % Allowed : 13.28 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.19), residues: 1946 helix: 2.69 (0.16), residues: 1064 sheet: 1.00 (0.29), residues: 273 loop : -0.99 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 16 PHE 0.022 0.001 PHE F 80 TYR 0.004 0.001 TYR D 135 ARG 0.001 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 275 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8723 (mmm) cc_final: 0.8497 (mmm) REVERT: A 149 GLN cc_start: 0.8722 (mm110) cc_final: 0.8455 (mm110) REVERT: A 203 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8607 (tm-30) REVERT: A 227 GLU cc_start: 0.8352 (pp20) cc_final: 0.8042 (pp20) REVERT: B 47 MET cc_start: 0.8869 (mmp) cc_final: 0.8544 (mmm) REVERT: B 112 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8859 (tm-30) REVERT: B 134 GLU cc_start: 0.8346 (tt0) cc_final: 0.7482 (tt0) REVERT: B 203 GLN cc_start: 0.9015 (tm-30) cc_final: 0.8608 (tm-30) REVERT: B 278 LYS cc_start: 0.9097 (mtmm) cc_final: 0.8398 (mttp) REVERT: C 134 GLU cc_start: 0.8016 (tt0) cc_final: 0.7641 (tt0) REVERT: C 149 GLN cc_start: 0.9152 (mm110) cc_final: 0.8829 (mm110) REVERT: C 176 ILE cc_start: 0.9329 (mm) cc_final: 0.9086 (mm) REVERT: C 181 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8809 (mm-30) REVERT: C 203 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8641 (tm-30) REVERT: C 227 GLU cc_start: 0.8361 (pp20) cc_final: 0.8026 (pp20) REVERT: C 260 GLU cc_start: 0.8781 (mp0) cc_final: 0.8161 (mp0) REVERT: D 112 GLN cc_start: 0.8524 (mp10) cc_final: 0.8284 (mp10) REVERT: D 203 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8710 (tm-30) REVERT: D 260 GLU cc_start: 0.8829 (mp0) cc_final: 0.8516 (mp0) REVERT: E 55 LEU cc_start: 0.9234 (tt) cc_final: 0.8926 (mm) REVERT: E 149 GLN cc_start: 0.9246 (mm110) cc_final: 0.8885 (mm110) REVERT: E 181 GLU cc_start: 0.9398 (mm-30) cc_final: 0.8498 (tp30) REVERT: E 203 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8730 (tm-30) REVERT: E 227 GLU cc_start: 0.8329 (pp20) cc_final: 0.8043 (pp20) REVERT: F 134 GLU cc_start: 0.7785 (tt0) cc_final: 0.7512 (tt0) REVERT: F 149 GLN cc_start: 0.8761 (mm110) cc_final: 0.8531 (mm110) REVERT: F 203 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8616 (tm-30) REVERT: F 227 GLU cc_start: 0.8397 (pp20) cc_final: 0.8092 (pp20) REVERT: F 260 GLU cc_start: 0.8874 (mp0) cc_final: 0.8140 (mp0) REVERT: G 47 MET cc_start: 0.8712 (mmm) cc_final: 0.8334 (mmm) REVERT: G 134 GLU cc_start: 0.7921 (tt0) cc_final: 0.7471 (tt0) REVERT: G 149 GLN cc_start: 0.8769 (mm110) cc_final: 0.8526 (mm110) REVERT: G 150 ILE cc_start: 0.9459 (pt) cc_final: 0.9258 (pt) REVERT: G 227 GLU cc_start: 0.8498 (pp20) cc_final: 0.8132 (pp20) REVERT: G 255 GLU cc_start: 0.9197 (tt0) cc_final: 0.8987 (tt0) outliers start: 16 outliers final: 10 residues processed: 280 average time/residue: 0.2482 time to fit residues: 104.8825 Evaluate side-chains 273 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 263 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 153 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 85 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15092 Z= 0.251 Angle : 0.533 9.087 20482 Z= 0.275 Chirality : 0.043 0.179 2513 Planarity : 0.002 0.024 2604 Dihedral : 4.016 15.405 2121 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.83 % Favored : 94.81 % Rotamer: Outliers : 2.20 % Allowed : 13.97 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.20), residues: 1946 helix: 2.75 (0.16), residues: 1064 sheet: 0.77 (0.28), residues: 308 loop : -0.89 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 16 PHE 0.023 0.001 PHE F 80 TYR 0.005 0.001 TYR D 270 ARG 0.002 0.000 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 264 time to evaluate : 1.810 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.8731 (mmm) cc_final: 0.8502 (mmm) REVERT: A 149 GLN cc_start: 0.8803 (mm110) cc_final: 0.8514 (mm110) REVERT: A 203 GLN cc_start: 0.9134 (tm-30) cc_final: 0.8649 (tm-30) REVERT: A 227 GLU cc_start: 0.8414 (pp20) cc_final: 0.8102 (pp20) REVERT: B 47 MET cc_start: 0.8874 (mmp) cc_final: 0.8544 (mmm) REVERT: B 112 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8904 (tm-30) REVERT: B 203 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8620 (tm-30) REVERT: C 149 GLN cc_start: 0.9170 (mm110) cc_final: 0.8838 (mm110) REVERT: C 181 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8735 (mm-30) REVERT: C 203 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8655 (tm-30) REVERT: C 227 GLU cc_start: 0.8433 (pp20) cc_final: 0.8144 (pp20) REVERT: C 273 MET cc_start: 0.8430 (ttt) cc_final: 0.8158 (ttt) REVERT: D 203 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8717 (tm-30) REVERT: E 47 MET cc_start: 0.8836 (mmm) cc_final: 0.8452 (mmm) REVERT: E 55 LEU cc_start: 0.9229 (tt) cc_final: 0.8908 (mm) REVERT: E 149 GLN cc_start: 0.9219 (mm110) cc_final: 0.8806 (mm110) REVERT: E 203 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8733 (tm-30) REVERT: E 227 GLU cc_start: 0.8389 (pp20) cc_final: 0.8128 (pp20) REVERT: F 134 GLU cc_start: 0.7874 (tt0) cc_final: 0.7632 (tp30) REVERT: F 149 GLN cc_start: 0.8821 (mm110) cc_final: 0.8592 (mm110) REVERT: F 203 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8667 (tm-30) REVERT: F 227 GLU cc_start: 0.8428 (pp20) cc_final: 0.8129 (pp20) REVERT: F 260 GLU cc_start: 0.8888 (mp0) cc_final: 0.8137 (mp0) REVERT: G 47 MET cc_start: 0.8739 (mmm) cc_final: 0.8334 (mmm) REVERT: G 134 GLU cc_start: 0.7833 (tt0) cc_final: 0.7223 (tt0) REVERT: G 149 GLN cc_start: 0.8798 (mm110) cc_final: 0.8565 (mm110) REVERT: G 227 GLU cc_start: 0.8514 (pp20) cc_final: 0.8157 (pp20) REVERT: G 255 GLU cc_start: 0.9221 (tt0) cc_final: 0.9003 (tt0) outliers start: 35 outliers final: 16 residues processed: 278 average time/residue: 0.2720 time to fit residues: 113.2674 Evaluate side-chains 270 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 254 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 273 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 96 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15092 Z= 0.203 Angle : 0.532 8.877 20482 Z= 0.274 Chirality : 0.043 0.192 2513 Planarity : 0.002 0.022 2604 Dihedral : 4.096 23.345 2121 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.52 % Favored : 95.12 % Rotamer: Outliers : 1.64 % Allowed : 15.10 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.20), residues: 1946 helix: 2.70 (0.16), residues: 1071 sheet: 0.81 (0.29), residues: 308 loop : -0.82 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 16 PHE 0.027 0.001 PHE F 80 TYR 0.005 0.000 TYR D 270 ARG 0.001 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 276 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8738 (mmm) cc_final: 0.8504 (mmm) REVERT: A 112 GLN cc_start: 0.9249 (tm-30) cc_final: 0.8943 (tm-30) REVERT: A 149 GLN cc_start: 0.8837 (mm110) cc_final: 0.8530 (mm110) REVERT: A 203 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8628 (tm-30) REVERT: A 210 GLN cc_start: 0.9384 (mm110) cc_final: 0.9183 (mm-40) REVERT: A 227 GLU cc_start: 0.8394 (pp20) cc_final: 0.8085 (pp20) REVERT: B 47 MET cc_start: 0.8847 (mmp) cc_final: 0.8498 (mmm) REVERT: B 112 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8915 (tm-30) REVERT: B 203 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8601 (tm-30) REVERT: B 210 GLN cc_start: 0.9473 (mm110) cc_final: 0.9240 (mm-40) REVERT: B 212 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8713 (tp30) REVERT: B 278 LYS cc_start: 0.9088 (mtmm) cc_final: 0.8255 (mttm) REVERT: C 149 GLN cc_start: 0.9202 (mm110) cc_final: 0.8811 (mm110) REVERT: C 181 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8736 (mm-30) REVERT: C 203 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8640 (tm-30) REVERT: C 227 GLU cc_start: 0.8435 (pp20) cc_final: 0.8186 (pp20) REVERT: D 203 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8714 (tm-30) REVERT: E 47 MET cc_start: 0.8829 (mmm) cc_final: 0.8417 (mmm) REVERT: E 55 LEU cc_start: 0.9224 (tt) cc_final: 0.8932 (mm) REVERT: E 149 GLN cc_start: 0.9241 (mm110) cc_final: 0.8805 (mm110) REVERT: E 203 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8755 (tm-30) REVERT: E 227 GLU cc_start: 0.8362 (pp20) cc_final: 0.8084 (pp20) REVERT: F 134 GLU cc_start: 0.7901 (tt0) cc_final: 0.7603 (tp30) REVERT: F 149 GLN cc_start: 0.8859 (mm110) cc_final: 0.8624 (mm110) REVERT: F 203 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8662 (tm-30) REVERT: F 227 GLU cc_start: 0.8415 (pp20) cc_final: 0.8114 (pp20) REVERT: G 47 MET cc_start: 0.8667 (mmm) cc_final: 0.8250 (mmm) REVERT: G 134 GLU cc_start: 0.7853 (tt0) cc_final: 0.7117 (tt0) REVERT: G 149 GLN cc_start: 0.8803 (mm110) cc_final: 0.8550 (mm110) REVERT: G 150 ILE cc_start: 0.9482 (pt) cc_final: 0.9273 (pt) REVERT: G 203 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8623 (tm-30) REVERT: G 227 GLU cc_start: 0.8508 (pp20) cc_final: 0.8145 (pp20) REVERT: G 255 GLU cc_start: 0.9216 (tt0) cc_final: 0.8989 (tt0) outliers start: 26 outliers final: 16 residues processed: 284 average time/residue: 0.2346 time to fit residues: 100.0904 Evaluate side-chains 274 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 258 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 153 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15092 Z= 0.392 Angle : 0.591 9.773 20482 Z= 0.306 Chirality : 0.044 0.293 2513 Planarity : 0.003 0.023 2604 Dihedral : 4.255 24.000 2121 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.88 % Favored : 94.76 % Rotamer: Outliers : 1.89 % Allowed : 15.48 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.20), residues: 1946 helix: 2.72 (0.16), residues: 1071 sheet: 1.01 (0.30), residues: 294 loop : -0.75 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 16 PHE 0.029 0.002 PHE D 80 TYR 0.005 0.001 TYR D 270 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 257 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8740 (mmm) cc_final: 0.8504 (mmm) REVERT: A 126 MET cc_start: 0.9202 (ptm) cc_final: 0.8999 (ppp) REVERT: A 149 GLN cc_start: 0.8892 (mm110) cc_final: 0.8596 (mm110) REVERT: A 203 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8676 (tm-30) REVERT: A 227 GLU cc_start: 0.8468 (pp20) cc_final: 0.8143 (pp20) REVERT: B 47 MET cc_start: 0.8835 (mmp) cc_final: 0.8503 (mmm) REVERT: B 112 GLN cc_start: 0.9286 (tm-30) cc_final: 0.8969 (tm-30) REVERT: B 203 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8623 (tm-30) REVERT: C 91 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8446 (p) REVERT: C 134 GLU cc_start: 0.7992 (tt0) cc_final: 0.7703 (tt0) REVERT: C 149 GLN cc_start: 0.9175 (mm110) cc_final: 0.8735 (mm110) REVERT: C 181 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8727 (mm-30) REVERT: C 203 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8640 (tm-30) REVERT: C 227 GLU cc_start: 0.8474 (pp20) cc_final: 0.8150 (pp20) REVERT: D 181 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8699 (mm-30) REVERT: D 203 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8727 (tm-30) REVERT: E 47 MET cc_start: 0.8815 (mmm) cc_final: 0.8382 (mmm) REVERT: E 149 GLN cc_start: 0.9224 (mm110) cc_final: 0.8722 (mm110) REVERT: E 203 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8712 (tm-30) REVERT: E 227 GLU cc_start: 0.8404 (pp20) cc_final: 0.8144 (pp20) REVERT: F 149 GLN cc_start: 0.8882 (mm110) cc_final: 0.8660 (mm110) REVERT: F 203 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8713 (tm-30) REVERT: F 227 GLU cc_start: 0.8456 (pp20) cc_final: 0.8133 (pp20) REVERT: F 270 TYR cc_start: 0.9322 (m-80) cc_final: 0.9041 (m-10) REVERT: G 47 MET cc_start: 0.8604 (mmm) cc_final: 0.8176 (mmm) REVERT: G 134 GLU cc_start: 0.7859 (tt0) cc_final: 0.7117 (tt0) REVERT: G 149 GLN cc_start: 0.8808 (mm110) cc_final: 0.8563 (mm110) REVERT: G 150 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9210 (pt) REVERT: G 227 GLU cc_start: 0.8609 (pp20) cc_final: 0.8270 (pp20) outliers start: 30 outliers final: 23 residues processed: 268 average time/residue: 0.2375 time to fit residues: 94.7101 Evaluate side-chains 272 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 247 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 273 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 0.0060 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 105 optimal weight: 0.0060 chunk 188 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.0018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15092 Z= 0.182 Angle : 0.568 10.652 20482 Z= 0.282 Chirality : 0.044 0.252 2513 Planarity : 0.002 0.023 2604 Dihedral : 4.123 20.462 2121 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.73 % Favored : 94.91 % Rotamer: Outliers : 1.26 % Allowed : 16.93 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.20), residues: 1946 helix: 2.76 (0.16), residues: 1071 sheet: 1.02 (0.30), residues: 294 loop : -0.71 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 16 PHE 0.033 0.002 PHE D 80 TYR 0.005 0.000 TYR D 270 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 262 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8747 (mmm) cc_final: 0.8502 (mmm) REVERT: A 112 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8923 (tm-30) REVERT: A 149 GLN cc_start: 0.8883 (mm110) cc_final: 0.8571 (mm110) REVERT: A 203 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8632 (tm-30) REVERT: A 210 GLN cc_start: 0.9366 (mm110) cc_final: 0.9160 (mm-40) REVERT: A 227 GLU cc_start: 0.8412 (pp20) cc_final: 0.8125 (pp20) REVERT: B 47 MET cc_start: 0.8840 (mmp) cc_final: 0.8487 (mmm) REVERT: B 56 MET cc_start: 0.9105 (mtp) cc_final: 0.8771 (mtm) REVERT: B 69 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9146 (pp) REVERT: B 112 GLN cc_start: 0.9265 (tm-30) cc_final: 0.8933 (tm-30) REVERT: B 134 GLU cc_start: 0.8115 (tt0) cc_final: 0.7139 (tt0) REVERT: B 161 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.9070 (mmmm) REVERT: B 203 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8623 (tm-30) REVERT: B 212 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8714 (tp30) REVERT: C 91 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8482 (p) REVERT: C 149 GLN cc_start: 0.9204 (mm110) cc_final: 0.8957 (mm-40) REVERT: C 157 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.8866 (p) REVERT: C 181 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8726 (mm-30) REVERT: C 203 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8627 (tm-30) REVERT: C 227 GLU cc_start: 0.8390 (pp20) cc_final: 0.8076 (pp20) REVERT: D 149 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8780 (mm110) REVERT: D 181 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8762 (mm-30) REVERT: D 203 GLN cc_start: 0.9170 (tm-30) cc_final: 0.8700 (tm-30) REVERT: E 47 MET cc_start: 0.8766 (mmm) cc_final: 0.8311 (mmm) REVERT: E 149 GLN cc_start: 0.9235 (mm110) cc_final: 0.8836 (mm-40) REVERT: E 181 GLU cc_start: 0.9364 (mm-30) cc_final: 0.8832 (mm-30) REVERT: E 203 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8677 (tm-30) REVERT: E 227 GLU cc_start: 0.8423 (pp20) cc_final: 0.8107 (pp20) REVERT: F 134 GLU cc_start: 0.7824 (tt0) cc_final: 0.7540 (tt0) REVERT: F 149 GLN cc_start: 0.8903 (mm110) cc_final: 0.8666 (mm110) REVERT: F 181 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9157 (mm-30) REVERT: F 203 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8666 (tm-30) REVERT: F 227 GLU cc_start: 0.8384 (pp20) cc_final: 0.8082 (pp20) REVERT: F 270 TYR cc_start: 0.9311 (m-80) cc_final: 0.9019 (m-10) REVERT: F 274 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.7889 (t0) REVERT: G 47 MET cc_start: 0.8621 (mmm) cc_final: 0.8182 (mmm) REVERT: G 134 GLU cc_start: 0.7904 (tt0) cc_final: 0.7095 (tt0) REVERT: G 150 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9261 (pt) REVERT: G 203 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8650 (tm-30) REVERT: G 222 THR cc_start: 0.9508 (m) cc_final: 0.9157 (p) REVERT: G 227 GLU cc_start: 0.8522 (pp20) cc_final: 0.8183 (pp20) REVERT: G 255 GLU cc_start: 0.9202 (tt0) cc_final: 0.8996 (tt0) outliers start: 20 outliers final: 12 residues processed: 268 average time/residue: 0.2557 time to fit residues: 102.0014 Evaluate side-chains 271 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 253 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 273 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 50.0000 chunk 56 optimal weight: 50.0000 chunk 37 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15092 Z= 0.344 Angle : 0.594 9.103 20482 Z= 0.302 Chirality : 0.044 0.244 2513 Planarity : 0.003 0.024 2604 Dihedral : 4.247 32.450 2121 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.78 % Favored : 94.91 % Rotamer: Outliers : 1.89 % Allowed : 16.87 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.20), residues: 1946 helix: 2.75 (0.16), residues: 1071 sheet: 1.07 (0.31), residues: 294 loop : -0.68 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 16 PHE 0.037 0.002 PHE D 80 TYR 0.005 0.001 TYR B 194 ARG 0.002 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 251 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8703 (mmm) cc_final: 0.8459 (mmm) REVERT: A 112 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8947 (tm-30) REVERT: A 149 GLN cc_start: 0.8903 (mm110) cc_final: 0.8598 (mm110) REVERT: A 203 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8715 (tm-30) REVERT: A 227 GLU cc_start: 0.8478 (pp20) cc_final: 0.8202 (pp20) REVERT: B 47 MET cc_start: 0.8844 (mmp) cc_final: 0.8491 (mmm) REVERT: B 112 GLN cc_start: 0.9298 (tm-30) cc_final: 0.8961 (tm-30) REVERT: B 161 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9060 (mmmm) REVERT: B 203 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8633 (tm-30) REVERT: B 212 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8708 (tp30) REVERT: C 91 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8396 (p) REVERT: C 134 GLU cc_start: 0.8130 (tt0) cc_final: 0.7848 (tt0) REVERT: C 149 GLN cc_start: 0.9207 (mm110) cc_final: 0.8889 (mm-40) REVERT: C 157 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.8872 (p) REVERT: C 181 GLU cc_start: 0.9391 (mm-30) cc_final: 0.8718 (mm-30) REVERT: C 203 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8615 (tm-30) REVERT: C 227 GLU cc_start: 0.8476 (pp20) cc_final: 0.8132 (pp20) REVERT: D 149 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8831 (mm110) REVERT: D 181 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8726 (mm-30) REVERT: D 203 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8711 (tm-30) REVERT: E 47 MET cc_start: 0.8690 (mmm) cc_final: 0.8246 (mmm) REVERT: E 149 GLN cc_start: 0.9232 (mm110) cc_final: 0.8813 (mm-40) REVERT: E 181 GLU cc_start: 0.9380 (mm-30) cc_final: 0.8837 (mm-30) REVERT: E 203 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8688 (tm-30) REVERT: E 227 GLU cc_start: 0.8497 (pp20) cc_final: 0.8192 (pp20) REVERT: F 134 GLU cc_start: 0.7785 (tt0) cc_final: 0.7548 (tt0) REVERT: F 149 GLN cc_start: 0.8904 (mm110) cc_final: 0.8684 (mm110) REVERT: F 181 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9140 (mm-30) REVERT: F 203 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8698 (tm-30) REVERT: F 227 GLU cc_start: 0.8452 (pp20) cc_final: 0.8124 (pp20) REVERT: F 270 TYR cc_start: 0.9315 (m-80) cc_final: 0.9039 (m-10) REVERT: F 274 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.7928 (t0) REVERT: G 47 MET cc_start: 0.8624 (mmm) cc_final: 0.8185 (mmm) REVERT: G 134 GLU cc_start: 0.7792 (tt0) cc_final: 0.6935 (tt0) REVERT: G 150 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9151 (pt) REVERT: G 203 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8649 (tm-30) REVERT: G 227 GLU cc_start: 0.8593 (pp20) cc_final: 0.8268 (pp20) outliers start: 30 outliers final: 20 residues processed: 262 average time/residue: 0.2531 time to fit residues: 99.4592 Evaluate side-chains 271 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 246 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 273 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 176 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 272 GLN D 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15092 Z= 0.172 Angle : 0.581 10.229 20482 Z= 0.285 Chirality : 0.044 0.235 2513 Planarity : 0.002 0.023 2604 Dihedral : 4.097 28.831 2121 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.83 % Favored : 94.86 % Rotamer: Outliers : 1.57 % Allowed : 17.87 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.20), residues: 1946 helix: 2.79 (0.16), residues: 1071 sheet: 1.01 (0.31), residues: 294 loop : -0.68 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 16 PHE 0.024 0.002 PHE B 80 TYR 0.004 0.000 TYR D 270 ARG 0.002 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 258 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8702 (mmm) cc_final: 0.8456 (mmm) REVERT: A 112 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8917 (tm-30) REVERT: A 134 GLU cc_start: 0.8089 (tt0) cc_final: 0.7482 (tt0) REVERT: A 149 GLN cc_start: 0.8892 (mm110) cc_final: 0.8579 (mm110) REVERT: A 203 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8633 (tm-30) REVERT: A 210 GLN cc_start: 0.9352 (mm110) cc_final: 0.9139 (mm-40) REVERT: A 212 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8767 (tp30) REVERT: A 227 GLU cc_start: 0.8449 (pp20) cc_final: 0.8149 (pp20) REVERT: B 47 MET cc_start: 0.8839 (mmp) cc_final: 0.8485 (mmm) REVERT: B 112 GLN cc_start: 0.9273 (tm-30) cc_final: 0.8926 (tm-30) REVERT: B 134 GLU cc_start: 0.8170 (tt0) cc_final: 0.7832 (tt0) REVERT: B 161 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8985 (mmmm) REVERT: B 203 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8597 (tm-30) REVERT: B 212 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8693 (tp30) REVERT: C 91 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8386 (p) REVERT: C 134 GLU cc_start: 0.8113 (tt0) cc_final: 0.7803 (tt0) REVERT: C 149 GLN cc_start: 0.9225 (mm110) cc_final: 0.8943 (mm-40) REVERT: C 157 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.8854 (p) REVERT: C 181 GLU cc_start: 0.9361 (mm-30) cc_final: 0.8769 (mm-30) REVERT: C 203 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8590 (tm-30) REVERT: C 227 GLU cc_start: 0.8386 (pp20) cc_final: 0.8098 (pp20) REVERT: D 149 GLN cc_start: 0.9027 (mm110) cc_final: 0.8816 (mm110) REVERT: D 181 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8253 (tp30) REVERT: D 203 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8685 (tm-30) REVERT: D 260 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8830 (mp0) REVERT: E 47 MET cc_start: 0.8721 (mmm) cc_final: 0.8241 (mmm) REVERT: E 149 GLN cc_start: 0.9266 (mm110) cc_final: 0.8845 (mm-40) REVERT: E 181 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8857 (mm-30) REVERT: E 203 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8660 (tm-30) REVERT: E 227 GLU cc_start: 0.8468 (pp20) cc_final: 0.8135 (pp20) REVERT: F 134 GLU cc_start: 0.7941 (tt0) cc_final: 0.7642 (tt0) REVERT: F 149 GLN cc_start: 0.8846 (mm110) cc_final: 0.8632 (mm110) REVERT: F 181 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9152 (mm-30) REVERT: F 203 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8663 (tm-30) REVERT: F 227 GLU cc_start: 0.8387 (pp20) cc_final: 0.8077 (pp20) REVERT: F 270 TYR cc_start: 0.9298 (m-80) cc_final: 0.9008 (m-10) REVERT: F 274 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.7928 (t0) REVERT: G 47 MET cc_start: 0.8622 (mmm) cc_final: 0.8178 (mmm) REVERT: G 134 GLU cc_start: 0.7921 (tt0) cc_final: 0.7024 (tt0) REVERT: G 150 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9166 (pt) REVERT: G 222 THR cc_start: 0.9511 (m) cc_final: 0.9170 (p) REVERT: G 227 GLU cc_start: 0.8527 (pp20) cc_final: 0.8190 (pp20) REVERT: G 255 GLU cc_start: 0.9197 (tt0) cc_final: 0.8993 (tt0) outliers start: 25 outliers final: 14 residues processed: 264 average time/residue: 0.2593 time to fit residues: 102.4294 Evaluate side-chains 271 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 252 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 150 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15092 Z= 0.197 Angle : 0.603 12.266 20482 Z= 0.292 Chirality : 0.044 0.215 2513 Planarity : 0.002 0.023 2604 Dihedral : 4.076 24.638 2121 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.57 % Favored : 95.12 % Rotamer: Outliers : 1.38 % Allowed : 18.31 % Favored : 80.30 % 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: 2.26 (0.20), residues: 1946 helix: 2.76 (0.16), residues: 1071 sheet: 0.85 (0.30), residues: 308 loop : -0.68 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 16 PHE 0.023 0.002 PHE D 80 TYR 0.004 0.000 TYR D 270 ARG 0.001 0.000 ARG D 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 253 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8715 (mmm) cc_final: 0.8472 (mmm) REVERT: A 112 GLN cc_start: 0.9221 (tm-30) cc_final: 0.8899 (tm-30) REVERT: A 134 GLU cc_start: 0.8041 (tt0) cc_final: 0.7636 (tt0) REVERT: A 149 GLN cc_start: 0.8880 (mm110) cc_final: 0.8557 (mm110) REVERT: A 203 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8629 (tm-30) REVERT: A 210 GLN cc_start: 0.9339 (mm110) cc_final: 0.9129 (mm-40) REVERT: A 212 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8775 (tp30) REVERT: A 227 GLU cc_start: 0.8477 (pp20) cc_final: 0.8157 (pp20) REVERT: B 47 MET cc_start: 0.8834 (mmp) cc_final: 0.8486 (mmm) REVERT: B 56 MET cc_start: 0.9116 (mtp) cc_final: 0.8800 (mtm) REVERT: B 69 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9147 (pp) REVERT: B 112 GLN cc_start: 0.9262 (tm-30) cc_final: 0.8916 (tm-30) REVERT: B 134 GLU cc_start: 0.8081 (tt0) cc_final: 0.7068 (tt0) REVERT: B 161 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8992 (mmmm) REVERT: B 203 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8623 (tm-30) REVERT: B 212 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8703 (tp30) REVERT: C 149 GLN cc_start: 0.9222 (mm110) cc_final: 0.8944 (mm-40) REVERT: C 157 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8785 (p) REVERT: C 181 GLU cc_start: 0.9352 (mm-30) cc_final: 0.8763 (mm-30) REVERT: C 203 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8625 (tm-30) REVERT: C 227 GLU cc_start: 0.8439 (pp20) cc_final: 0.8149 (pp20) REVERT: D 181 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8875 (mm-30) REVERT: D 203 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8692 (tm-30) REVERT: D 260 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8829 (mp0) REVERT: E 47 MET cc_start: 0.8711 (mmm) cc_final: 0.8230 (mmm) REVERT: E 149 GLN cc_start: 0.9247 (mm110) cc_final: 0.8823 (mm-40) REVERT: E 181 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8847 (mm-30) REVERT: E 203 GLN cc_start: 0.9135 (tm-30) cc_final: 0.8678 (tm-30) REVERT: E 227 GLU cc_start: 0.8503 (pp20) cc_final: 0.8164 (pp20) REVERT: F 134 GLU cc_start: 0.7939 (tt0) cc_final: 0.7628 (tt0) REVERT: F 149 GLN cc_start: 0.8856 (mm110) cc_final: 0.8654 (mm110) REVERT: F 181 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9150 (mm-30) REVERT: F 203 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8665 (tm-30) REVERT: F 227 GLU cc_start: 0.8433 (pp20) cc_final: 0.8110 (pp20) REVERT: F 270 TYR cc_start: 0.9296 (m-80) cc_final: 0.9006 (m-10) REVERT: F 274 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.7659 (t0) REVERT: G 47 MET cc_start: 0.8618 (mmm) cc_final: 0.8177 (mmm) REVERT: G 134 GLU cc_start: 0.7885 (tt0) cc_final: 0.7018 (tt0) REVERT: G 150 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9097 (pt) REVERT: G 203 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8665 (tm-30) REVERT: G 222 THR cc_start: 0.9508 (m) cc_final: 0.9184 (p) REVERT: G 227 GLU cc_start: 0.8561 (pp20) cc_final: 0.8206 (pp20) outliers start: 22 outliers final: 13 residues processed: 263 average time/residue: 0.2423 time to fit residues: 96.1307 Evaluate side-chains 270 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 252 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 150 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 50.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.110028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.071239 restraints weight = 35244.756| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.46 r_work: 0.2671 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15092 Z= 0.229 Angle : 0.602 11.640 20482 Z= 0.294 Chirality : 0.044 0.218 2513 Planarity : 0.002 0.024 2604 Dihedral : 4.105 23.673 2121 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.83 % Favored : 94.86 % Rotamer: Outliers : 1.32 % Allowed : 18.31 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.20), residues: 1946 helix: 2.76 (0.16), residues: 1071 sheet: 1.02 (0.31), residues: 294 loop : -0.64 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 16 PHE 0.024 0.001 PHE G 80 TYR 0.005 0.001 TYR D 270 ARG 0.001 0.000 ARG C 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3011.44 seconds wall clock time: 55 minutes 44.75 seconds (3344.75 seconds total)