Starting phenix.real_space_refine on Fri Feb 6 08:56:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x7m_66643/02_2026/9x7m_66643.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x7m_66643/02_2026/9x7m_66643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x7m_66643/02_2026/9x7m_66643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x7m_66643/02_2026/9x7m_66643.map" model { file = "/net/cci-nas-00/data/ceres_data/9x7m_66643/02_2026/9x7m_66643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x7m_66643/02_2026/9x7m_66643.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 sd= 0.055 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 143 5.16 5 C 14564 2.51 5 N 4455 2.21 5 O 4730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23892 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2172 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 2, 'TRANS': 277} Chain: "B" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2172 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 2, 'TRANS': 277} Chain: "C" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2172 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 2, 'TRANS': 277} Chain: "D" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2172 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 2, 'TRANS': 277} Chain: "E" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2172 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 2, 'TRANS': 277} Chain: "F" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2172 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 2, 'TRANS': 277} Chain: "G" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2172 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 2, 'TRANS': 277} Chain: "H" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2172 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 2, 'TRANS': 277} Chain: "I" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2172 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 2, 'TRANS': 277} Chain: "J" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2172 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 2, 'TRANS': 277} Chain: "K" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2172 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 2, 'TRANS': 277} Time building chain proxies: 5.32, per 1000 atoms: 0.22 Number of scatterers: 23892 At special positions: 0 Unit cell: (146.16, 145, 201.84, 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 143 16.00 O 4730 8.00 N 4455 7.00 C 14564 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 - 3.00 Amino acid : True - 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: 2.05 Conformation dependent library (CDL) restraints added in 997.9 milliseconds 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5786 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 13 sheets defined 72.8% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.596A pdb=" N PHE A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 98 Processing helix chain 'A' and resid 103 through 128 Processing helix chain 'A' and resid 187 through 242 removed outlier: 4.522A pdb=" N GLY A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 271 Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.535A pdb=" N GLY A 275 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 276 " --> pdb=" O PRO A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 33 removed outlier: 3.660A pdb=" N PHE B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 98 removed outlier: 3.878A pdb=" N GLN B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 128 removed outlier: 3.785A pdb=" N GLU B 113 " --> pdb=" O MET B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 242 removed outlier: 4.425A pdb=" N GLY B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 270 Processing helix chain 'B' and resid 271 through 280 Processing helix chain 'C' and resid 6 through 17 Processing helix chain 'C' and resid 18 through 33 Processing helix chain 'C' and resid 42 through 98 removed outlier: 3.767A pdb=" N GLN C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 128 Processing helix chain 'C' and resid 187 through 242 removed outlier: 3.767A pdb=" N ASP C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C 195 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 270 removed outlier: 3.837A pdb=" N GLN C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 280 Processing helix chain 'D' and resid 6 through 33 removed outlier: 3.701A pdb=" N GLN D 19 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU D 22 " --> pdb=" O PHE D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 98 removed outlier: 3.924A pdb=" N GLU D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER D 83 " --> pdb=" O PHE D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 128 removed outlier: 4.069A pdb=" N ARG D 107 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 193 removed outlier: 4.116A pdb=" N ASP D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 242 removed outlier: 3.781A pdb=" N ILE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 271 removed outlier: 3.860A pdb=" N ALA D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 280 removed outlier: 3.865A pdb=" N SER D 278 " --> pdb=" O GLY D 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 33 removed outlier: 4.069A pdb=" N GLU E 22 " --> pdb=" O PHE E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 98 removed outlier: 3.538A pdb=" N GLU E 82 " --> pdb=" O GLY E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 128 Processing helix chain 'E' and resid 187 through 193 removed outlier: 3.619A pdb=" N ASP E 193 " --> pdb=" O ASP E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 242 removed outlier: 4.198A pdb=" N THR E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN E 228 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 271 removed outlier: 3.668A pdb=" N VAL E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 280 removed outlier: 3.605A pdb=" N GLY E 275 " --> pdb=" O ARG E 272 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E 276 " --> pdb=" O PRO E 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 33 removed outlier: 3.802A pdb=" N GLU F 22 " --> pdb=" O PHE F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 98 removed outlier: 3.546A pdb=" N GLU F 82 " --> pdb=" O GLY F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 128 removed outlier: 3.518A pdb=" N GLU F 120 " --> pdb=" O GLN F 116 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 193 removed outlier: 3.883A pdb=" N ASP F 193 " --> pdb=" O ASP F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 242 removed outlier: 4.253A pdb=" N ALA F 200 " --> pdb=" O GLY F 196 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE F 240 " --> pdb=" O SER F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 271 removed outlier: 3.939A pdb=" N VAL F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 280 removed outlier: 3.740A pdb=" N GLY F 275 " --> pdb=" O ARG F 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 33 removed outlier: 3.602A pdb=" N PHE G 18 " --> pdb=" O ARG G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 79 Processing helix chain 'G' and resid 80 through 98 Processing helix chain 'G' and resid 103 through 128 removed outlier: 3.701A pdb=" N ARG G 107 " --> pdb=" O THR G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 193 removed outlier: 3.634A pdb=" N ASP G 193 " --> pdb=" O ASP G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 242 removed outlier: 3.691A pdb=" N THR G 197 " --> pdb=" O ASP G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 271 removed outlier: 4.473A pdb=" N VAL G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA G 251 " --> pdb=" O GLU G 247 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 280 removed outlier: 3.545A pdb=" N GLY G 275 " --> pdb=" O ARG G 272 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER G 278 " --> pdb=" O GLY G 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 33 Processing helix chain 'H' and resid 42 through 98 removed outlier: 3.997A pdb=" N GLU H 82 " --> pdb=" O GLY H 78 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER H 83 " --> pdb=" O PHE H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 128 removed outlier: 3.623A pdb=" N ILE H 110 " --> pdb=" O ASP H 106 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU H 113 " --> pdb=" O MET H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 242 removed outlier: 4.083A pdb=" N GLY H 196 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR H 197 " --> pdb=" O ASP H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 271 removed outlier: 4.007A pdb=" N VAL H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN H 260 " --> pdb=" O GLN H 256 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL H 271 " --> pdb=" O ALA H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 272 through 280 removed outlier: 3.508A pdb=" N GLY H 275 " --> pdb=" O ARG H 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 32 removed outlier: 3.566A pdb=" N GLU I 22 " --> pdb=" O PHE I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 98 removed outlier: 3.508A pdb=" N ARG I 64 " --> pdb=" O ARG I 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP I 85 " --> pdb=" O GLN I 81 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE I 86 " --> pdb=" O GLU I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 127 Processing helix chain 'I' and resid 187 through 242 removed outlier: 3.915A pdb=" N ASP I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE I 195 " --> pdb=" O SER I 191 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY I 196 " --> pdb=" O ASN I 192 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR I 197 " --> pdb=" O ASP I 193 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN I 208 " --> pdb=" O ARG I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 244 through 270 Processing helix chain 'I' and resid 271 through 280 removed outlier: 3.525A pdb=" N SER I 278 " --> pdb=" O GLY I 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 33 removed outlier: 3.596A pdb=" N LYS J 29 " --> pdb=" O LYS J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 98 removed outlier: 3.999A pdb=" N GLU J 82 " --> pdb=" O GLY J 78 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER J 83 " --> pdb=" O PHE J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 128 removed outlier: 3.576A pdb=" N GLU J 113 " --> pdb=" O MET J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 239 removed outlier: 3.648A pdb=" N ASP J 193 " --> pdb=" O ASP J 189 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE J 195 " --> pdb=" O SER J 191 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY J 196 " --> pdb=" O ASN J 192 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 271 removed outlier: 3.739A pdb=" N VAL J 250 " --> pdb=" O ALA J 246 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA J 251 " --> pdb=" O GLU J 247 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL J 271 " --> pdb=" O ALA J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 280 removed outlier: 3.565A pdb=" N GLY J 275 " --> pdb=" O ARG J 272 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER J 278 " --> pdb=" O GLY J 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 33 removed outlier: 3.606A pdb=" N PHE K 18 " --> pdb=" O ARG K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 98 removed outlier: 3.522A pdb=" N LEU K 72 " --> pdb=" O ASP K 68 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU K 82 " --> pdb=" O GLY K 78 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER K 83 " --> pdb=" O PHE K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 128 removed outlier: 4.075A pdb=" N GLU K 113 " --> pdb=" O MET K 109 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU K 120 " --> pdb=" O GLN K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 242 removed outlier: 4.326A pdb=" N ASP K 193 " --> pdb=" O ASP K 189 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA K 194 " --> pdb=" O LYS K 190 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE K 195 " --> pdb=" O SER K 191 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY K 196 " --> pdb=" O ASN K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 270 Processing helix chain 'K' and resid 271 through 280 Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 4.887A pdb=" N MET A 149 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 149 through 150 removed outlier: 4.759A pdb=" N MET B 149 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 163 " --> pdb=" O MET B 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 149 through 151 removed outlier: 4.224A pdb=" N MET C 149 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 149 through 151 removed outlier: 4.643A pdb=" N MET D 149 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 149 through 151 removed outlier: 4.366A pdb=" N MET E 149 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL E 163 " --> pdb=" O MET E 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 150 through 152 Processing sheet with id=AA8, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AA9, first strand: chain 'G' and resid 149 through 151 removed outlier: 4.691A pdb=" N MET G 149 " --> pdb=" O VAL G 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 149 through 152 removed outlier: 4.525A pdb=" N MET H 149 " --> pdb=" O VAL H 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 150 through 151 Processing sheet with id=AB3, first strand: chain 'J' and resid 150 through 152 Processing sheet with id=AB4, first strand: chain 'K' and resid 149 through 152 removed outlier: 4.542A pdb=" N MET K 149 " --> pdb=" O VAL K 163 " (cutoff:3.500A) 1897 hydrogen bonds defined for protein. 5493 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: 3.78 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5536 1.33 - 1.45: 4662 1.45 - 1.58: 13617 1.58 - 1.70: 0 1.70 - 1.82: 286 Bond restraints: 24101 Sorted by residual: bond pdb=" CA ALA D 43 " pdb=" CB ALA D 43 " ideal model delta sigma weight residual 1.532 1.488 0.044 1.58e-02 4.01e+03 7.90e+00 bond pdb=" CA SER D 44 " pdb=" CB SER D 44 " ideal model delta sigma weight residual 1.530 1.488 0.042 1.58e-02 4.01e+03 7.11e+00 bond pdb=" N ILE D 36 " pdb=" CA ILE D 36 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.86e+00 bond pdb=" CG HIS D 152 " pdb=" CD2 HIS D 152 " ideal model delta sigma weight residual 1.354 1.326 0.028 1.10e-02 8.26e+03 6.69e+00 bond pdb=" N ASP D 42 " pdb=" CA ASP D 42 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.52e+00 ... (remaining 24096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 32124 2.32 - 4.64: 213 4.64 - 6.96: 32 6.96 - 9.27: 11 9.27 - 11.59: 4 Bond angle restraints: 32384 Sorted by residual: angle pdb=" N GLY D 40 " pdb=" CA GLY D 40 " pdb=" C GLY D 40 " ideal model delta sigma weight residual 115.40 106.02 9.38 1.32e+00 5.74e-01 5.05e+01 angle pdb=" N ASP D 41 " pdb=" CA ASP D 41 " pdb=" C ASP D 41 " ideal model delta sigma weight residual 111.28 104.07 7.21 1.09e+00 8.42e-01 4.37e+01 angle pdb=" C PRO D 155 " pdb=" CA PRO D 155 " pdb=" CB PRO D 155 " ideal model delta sigma weight residual 111.56 103.37 8.19 1.65e+00 3.67e-01 2.46e+01 angle pdb=" CA ASN D 37 " pdb=" C ASN D 37 " pdb=" O ASN D 37 " ideal model delta sigma weight residual 121.89 116.39 5.50 1.17e+00 7.31e-01 2.21e+01 angle pdb=" C ARG D 38 " pdb=" CA ARG D 38 " pdb=" CB ARG D 38 " ideal model delta sigma weight residual 115.79 110.56 5.23 1.19e+00 7.06e-01 1.93e+01 ... (remaining 32379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 12620 17.95 - 35.89: 1701 35.89 - 53.84: 509 53.84 - 71.78: 109 71.78 - 89.73: 43 Dihedral angle restraints: 14982 sinusoidal: 6094 harmonic: 8888 Sorted by residual: dihedral pdb=" CA TYR D 102 " pdb=" C TYR D 102 " pdb=" N THR D 103 " pdb=" CA THR D 103 " ideal model delta harmonic sigma weight residual -180.00 -161.47 -18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" C PRO D 155 " pdb=" N PRO D 155 " pdb=" CA PRO D 155 " pdb=" CB PRO D 155 " ideal model delta harmonic sigma weight residual -120.70 -111.53 -9.17 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" CA ARG A 272 " pdb=" C ARG A 272 " pdb=" N PRO A 273 " pdb=" CA PRO A 273 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 14979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3445 0.069 - 0.138: 244 0.138 - 0.207: 4 0.207 - 0.276: 2 0.276 - 0.346: 1 Chirality restraints: 3696 Sorted by residual: chirality pdb=" CG LEU I 182 " pdb=" CB LEU I 182 " pdb=" CD1 LEU I 182 " pdb=" CD2 LEU I 182 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA ILE D 36 " pdb=" N ILE D 36 " pdb=" C ILE D 36 " pdb=" CB ILE D 36 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE D 153 " pdb=" N ILE D 153 " pdb=" C ILE D 153 " pdb=" CB ILE D 153 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3693 not shown) Planarity restraints: 4323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 18 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.83e+00 pdb=" C PHE C 18 " -0.051 2.00e-02 2.50e+03 pdb=" O PHE C 18 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN C 19 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 38 " -0.152 9.50e-02 1.11e+02 6.80e-02 2.84e+00 pdb=" NE ARG D 38 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG D 38 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG D 38 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 38 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 63 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" CD GLU B 63 " -0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU B 63 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU B 63 " 0.010 2.00e-02 2.50e+03 ... (remaining 4320 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2669 2.74 - 3.28: 24751 3.28 - 3.82: 41020 3.82 - 4.36: 43973 4.36 - 4.90: 78150 Nonbonded interactions: 190563 Sorted by model distance: nonbonded pdb=" OG SER G 144 " pdb=" O THR G 147 " model vdw 2.205 3.040 nonbonded pdb=" O ASN D 4 " pdb=" NZ LYS J 254 " model vdw 2.229 3.120 nonbonded pdb=" O ARG K 145 " pdb=" NE ARG K 145 " model vdw 2.234 3.120 nonbonded pdb=" O ALA C 62 " pdb=" OG1 THR C 66 " model vdw 2.240 3.040 nonbonded pdb=" O ILE I 205 " pdb=" NE2 GLN I 208 " model vdw 2.251 3.120 ... (remaining 190558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 3.570 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.460 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 0.049 24101 Z= 0.147 Angle : 0.533 11.593 32384 Z= 0.303 Chirality : 0.036 0.346 3696 Planarity : 0.003 0.068 4323 Dihedral : 18.519 89.729 9196 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Rotamer: Outliers : 3.92 % Allowed : 23.00 % Favored : 73.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.34 (0.16), residues: 3058 helix: 3.39 (0.11), residues: 2123 sheet: None (None), residues: 0 loop : -0.76 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 60 TYR 0.019 0.001 TYR D 215 PHE 0.008 0.001 PHE I 216 TRP 0.006 0.001 TRP K 150 HIS 0.004 0.000 HIS D 152 Details of bonding type rmsd covalent geometry : bond 0.00284 (24101) covalent geometry : angle 0.53272 (32384) hydrogen bonds : bond 0.11359 ( 1897) hydrogen bonds : angle 3.92743 ( 5493) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 416 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8997 (mmm) cc_final: 0.7980 (mmt) REVERT: A 67 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6358 (tt0) REVERT: A 85 ASP cc_start: 0.8704 (m-30) cc_final: 0.8240 (m-30) REVERT: A 120 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.4747 (tp30) REVERT: A 145 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.8015 (pmm150) REVERT: A 157 MET cc_start: 0.7455 (ttm) cc_final: 0.6832 (tpt) REVERT: A 171 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6478 (ttp-170) REVERT: B 26 ASN cc_start: 0.9080 (OUTLIER) cc_final: 0.8848 (t0) REVERT: B 109 MET cc_start: 0.8873 (mtm) cc_final: 0.8477 (mtt) REVERT: B 132 LYS cc_start: 0.8485 (mppt) cc_final: 0.7896 (pttm) REVERT: B 224 LYS cc_start: 0.7333 (mmtm) cc_final: 0.6507 (mttp) REVERT: B 254 LYS cc_start: 0.5572 (tttt) cc_final: 0.5157 (tttt) REVERT: C 14 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.7854 (ttm170) REVERT: C 120 GLU cc_start: 0.8946 (tp30) cc_final: 0.8128 (mm-30) REVERT: C 159 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7032 (mt0) REVERT: D 63 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7889 (tm-30) REVERT: D 88 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8551 (tp40) REVERT: D 160 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7580 (mtp85) REVERT: D 254 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8472 (tttt) REVERT: E 63 GLU cc_start: 0.8084 (pt0) cc_final: 0.7718 (pt0) REVERT: E 120 GLU cc_start: 0.4499 (OUTLIER) cc_final: 0.3720 (tp30) REVERT: E 176 LYS cc_start: 0.9091 (ptmm) cc_final: 0.8812 (ptmm) REVERT: E 242 ASP cc_start: 0.7947 (m-30) cc_final: 0.7626 (m-30) REVERT: E 254 LYS cc_start: 0.8974 (tmmt) cc_final: 0.8216 (tttp) REVERT: F 81 GLN cc_start: 0.8512 (tp40) cc_final: 0.8101 (tp-100) REVERT: F 160 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7395 (ptm-80) REVERT: F 254 LYS cc_start: 0.8859 (tttt) cc_final: 0.7971 (tttt) REVERT: F 265 MET cc_start: 0.8905 (tpp) cc_final: 0.8575 (tpp) REVERT: G 209 ARG cc_start: 0.5931 (ttt180) cc_final: 0.4868 (mmm-85) REVERT: H 38 ARG cc_start: 0.8537 (ttm170) cc_final: 0.8109 (ttt180) REVERT: H 52 MET cc_start: 0.9182 (mtp) cc_final: 0.8909 (mtp) REVERT: H 63 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8359 (tm-30) REVERT: H 160 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8356 (mtp180) REVERT: H 218 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.5956 (mtt-85) REVERT: H 220 GLU cc_start: 0.8424 (tt0) cc_final: 0.8030 (tm-30) REVERT: I 88 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8552 (mt0) REVERT: I 157 MET cc_start: 0.4788 (mtt) cc_final: 0.3364 (mmt) REVERT: J 51 LYS cc_start: 0.6508 (tttt) cc_final: 0.6154 (mtmm) REVERT: J 65 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7035 (m110) REVERT: J 157 MET cc_start: 0.5630 (tpt) cc_final: 0.5308 (tpt) REVERT: J 265 MET cc_start: 0.9144 (mmm) cc_final: 0.8877 (mmt) REVERT: K 77 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8040 (tm-30) REVERT: K 85 ASP cc_start: 0.8627 (m-30) cc_final: 0.8345 (m-30) outliers start: 101 outliers final: 71 residues processed: 487 average time/residue: 0.2070 time to fit residues: 146.1707 Evaluate side-chains 490 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 404 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 160 ARG Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 88 GLN Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 257 ILE Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 277 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0040 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN C 211 ASN ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 156 ASN H 4 ASN H 81 GLN ** I 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.094398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086683 restraints weight = 63961.251| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.61 r_work: 0.3315 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24101 Z= 0.116 Angle : 0.457 15.064 32384 Z= 0.249 Chirality : 0.035 0.172 3696 Planarity : 0.003 0.029 4323 Dihedral : 7.054 69.279 3531 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.04 % Allowed : 21.41 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.16), residues: 3058 helix: 3.22 (0.11), residues: 2200 sheet: None (None), residues: 0 loop : -1.22 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 60 TYR 0.017 0.001 TYR D 215 PHE 0.008 0.001 PHE H 18 TRP 0.011 0.001 TRP K 150 HIS 0.002 0.000 HIS H 152 Details of bonding type rmsd covalent geometry : bond 0.00235 (24101) covalent geometry : angle 0.45702 (32384) hydrogen bonds : bond 0.04900 ( 1897) hydrogen bonds : angle 3.41668 ( 5493) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 445 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8971 (mmm) cc_final: 0.7894 (mmt) REVERT: A 67 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6392 (tt0) REVERT: A 81 GLN cc_start: 0.8413 (tp40) cc_final: 0.8161 (tp40) REVERT: A 120 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.4639 (tp30) REVERT: A 157 MET cc_start: 0.7520 (ttm) cc_final: 0.6869 (tpt) REVERT: B 26 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8855 (t0) REVERT: B 120 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.4325 (mm-30) REVERT: B 132 LYS cc_start: 0.8511 (mppt) cc_final: 0.7895 (pttm) REVERT: B 171 ARG cc_start: 0.6518 (tmt170) cc_final: 0.5736 (tmm160) REVERT: B 224 LYS cc_start: 0.7259 (mmtm) cc_final: 0.6412 (mttp) REVERT: B 254 LYS cc_start: 0.5466 (tttt) cc_final: 0.5057 (tttt) REVERT: C 120 GLU cc_start: 0.9023 (tp30) cc_final: 0.8157 (mm-30) REVERT: D 63 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7816 (tm-30) REVERT: D 88 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8517 (tp40) REVERT: D 254 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8487 (tttt) REVERT: E 60 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.7739 (mmm-85) REVERT: E 63 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7969 (pt0) REVERT: E 120 GLU cc_start: 0.4055 (OUTLIER) cc_final: 0.3285 (tp30) REVERT: E 176 LYS cc_start: 0.9096 (ptmm) cc_final: 0.8778 (ptmm) REVERT: E 218 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8250 (ttm-80) REVERT: E 242 ASP cc_start: 0.8395 (m-30) cc_final: 0.8169 (m-30) REVERT: E 254 LYS cc_start: 0.9053 (tmmt) cc_final: 0.8332 (tttp) REVERT: F 53 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8637 (mtt180) REVERT: F 77 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: F 81 GLN cc_start: 0.8631 (tp40) cc_final: 0.8198 (tp-100) REVERT: F 254 LYS cc_start: 0.8894 (tttt) cc_final: 0.8045 (tttt) REVERT: G 171 ARG cc_start: 0.8707 (mtp-110) cc_final: 0.8366 (ppt170) REVERT: G 209 ARG cc_start: 0.5841 (ttt180) cc_final: 0.4625 (mmm-85) REVERT: G 248 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: H 4 ASN cc_start: 0.9003 (OUTLIER) cc_final: 0.8760 (t0) REVERT: H 38 ARG cc_start: 0.8489 (ttm170) cc_final: 0.8008 (ttt180) REVERT: H 63 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8259 (tm-30) REVERT: H 123 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.9064 (ttp80) REVERT: H 160 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8272 (mtp180) REVERT: H 218 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.5772 (mtt-85) REVERT: H 220 GLU cc_start: 0.8423 (tt0) cc_final: 0.8054 (tm-30) REVERT: I 88 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8539 (mt0) REVERT: I 157 MET cc_start: 0.4832 (mtt) cc_final: 0.3331 (mmt) REVERT: J 51 LYS cc_start: 0.6561 (tttt) cc_final: 0.6164 (mtmm) REVERT: J 65 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.6944 (m110) REVERT: J 157 MET cc_start: 0.5398 (tpt) cc_final: 0.5010 (tpt) REVERT: K 70 MET cc_start: 0.8481 (ptm) cc_final: 0.8236 (ptm) REVERT: K 85 ASP cc_start: 0.8665 (m-30) cc_final: 0.8368 (m-30) outliers start: 104 outliers final: 42 residues processed: 519 average time/residue: 0.1886 time to fit residues: 142.3314 Evaluate side-chains 462 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 402 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 145 ARG Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 29 LYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 123 ARG Chi-restraints excluded: chain H residue 160 ARG Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 88 GLN Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 167 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 98 optimal weight: 8.9990 chunk 232 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 248 optimal weight: 0.0020 chunk 161 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN H 4 ASN I 208 GLN J 255 ASN K 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.099707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091602 restraints weight = 65615.032| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.63 r_work: 0.3245 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24101 Z= 0.153 Angle : 0.491 15.036 32384 Z= 0.266 Chirality : 0.036 0.172 3696 Planarity : 0.003 0.038 4323 Dihedral : 5.826 70.092 3404 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.93 % Allowed : 21.45 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.15), residues: 3058 helix: 3.12 (0.11), residues: 2200 sheet: None (None), residues: 0 loop : -1.21 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 218 TYR 0.015 0.001 TYR D 215 PHE 0.013 0.001 PHE H 18 TRP 0.009 0.001 TRP K 150 HIS 0.003 0.001 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00340 (24101) covalent geometry : angle 0.49076 (32384) hydrogen bonds : bond 0.05255 ( 1897) hydrogen bonds : angle 3.47056 ( 5493) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 412 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6475 (tt0) REVERT: A 120 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.4753 (tp30) REVERT: A 157 MET cc_start: 0.7628 (ttm) cc_final: 0.6969 (tpt) REVERT: A 248 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7740 (tp30) REVERT: B 22 GLU cc_start: 0.8702 (tt0) cc_final: 0.8389 (tt0) REVERT: B 26 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8864 (t0) REVERT: B 63 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8613 (tm-30) REVERT: B 120 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.4447 (mm-30) REVERT: B 132 LYS cc_start: 0.8596 (mppt) cc_final: 0.7969 (pttm) REVERT: B 224 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6501 (mttp) REVERT: B 254 LYS cc_start: 0.5609 (tttt) cc_final: 0.5111 (tttt) REVERT: C 77 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8744 (tm-30) REVERT: C 99 ASN cc_start: 0.7493 (OUTLIER) cc_final: 0.7203 (t0) REVERT: C 120 GLU cc_start: 0.9013 (tp30) cc_final: 0.8202 (mm-30) REVERT: C 159 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7164 (mt0) REVERT: C 254 LYS cc_start: 0.4410 (tttt) cc_final: 0.3630 (tttp) REVERT: D 63 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7907 (tm-30) REVERT: D 88 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8497 (tp40) REVERT: D 199 ASP cc_start: 0.8200 (p0) cc_final: 0.7986 (p0) REVERT: D 254 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8506 (tttt) REVERT: E 60 ARG cc_start: 0.8421 (mmm-85) cc_final: 0.7817 (mmm-85) REVERT: E 63 GLU cc_start: 0.8312 (pt0) cc_final: 0.7859 (pt0) REVERT: E 120 GLU cc_start: 0.4373 (OUTLIER) cc_final: 0.3547 (tp30) REVERT: E 162 ARG cc_start: 0.9441 (OUTLIER) cc_final: 0.8377 (tpt90) REVERT: E 171 ARG cc_start: 0.6604 (ppt170) cc_final: 0.6268 (tmt170) REVERT: E 176 LYS cc_start: 0.9096 (ptmm) cc_final: 0.8789 (ptmm) REVERT: E 218 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8464 (ttm-80) REVERT: E 239 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7866 (ttm170) REVERT: E 254 LYS cc_start: 0.8957 (tmmt) cc_final: 0.8280 (tttp) REVERT: E 270 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8622 (t0) REVERT: F 53 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8864 (mtt180) REVERT: F 77 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: F 81 GLN cc_start: 0.8672 (tp40) cc_final: 0.8267 (tp-100) REVERT: F 254 LYS cc_start: 0.8941 (tttt) cc_final: 0.8106 (tttt) REVERT: F 265 MET cc_start: 0.8979 (tpp) cc_final: 0.8690 (tpp) REVERT: G 171 ARG cc_start: 0.8713 (mtp-110) cc_final: 0.8447 (ppt170) REVERT: G 209 ARG cc_start: 0.6149 (ttt180) cc_final: 0.4880 (mmm-85) REVERT: G 248 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: G 254 LYS cc_start: 0.9032 (tttp) cc_final: 0.8788 (tttp) REVERT: H 4 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8566 (t0) REVERT: H 38 ARG cc_start: 0.8477 (ttm170) cc_final: 0.7976 (tpt-90) REVERT: H 42 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.8037 (p0) REVERT: H 63 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8351 (tm-30) REVERT: H 123 ARG cc_start: 0.9385 (OUTLIER) cc_final: 0.9105 (ttp80) REVERT: H 160 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7952 (ptp90) REVERT: H 220 GLU cc_start: 0.8446 (tt0) cc_final: 0.8050 (tm-30) REVERT: I 88 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8749 (mt0) REVERT: I 157 MET cc_start: 0.5144 (mtt) cc_final: 0.3464 (mmt) REVERT: J 51 LYS cc_start: 0.6653 (tttt) cc_final: 0.6199 (mtmm) REVERT: J 157 MET cc_start: 0.5535 (tpt) cc_final: 0.5140 (tpt) REVERT: J 171 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.5877 (ptt90) REVERT: K 70 MET cc_start: 0.8465 (ptm) cc_final: 0.8232 (ptm) REVERT: K 85 ASP cc_start: 0.8602 (m-30) cc_final: 0.8347 (m-30) outliers start: 127 outliers final: 71 residues processed: 500 average time/residue: 0.1926 time to fit residues: 139.8828 Evaluate side-chains 491 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 396 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 145 ARG Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 29 LYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 123 ARG Chi-restraints excluded: chain H residue 160 ARG Chi-restraints excluded: chain H residue 224 LYS Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 88 GLN Chi-restraints excluded: chain I residue 153 ILE Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 171 ARG Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 167 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 6 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN E 19 GLN ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 GLN H 4 ASN ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.092527 restraints weight = 65268.545| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.61 r_work: 0.3243 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24101 Z= 0.143 Angle : 0.482 14.935 32384 Z= 0.261 Chirality : 0.036 0.169 3696 Planarity : 0.003 0.030 4323 Dihedral : 5.715 70.574 3397 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 5.13 % Allowed : 21.33 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.15), residues: 3058 helix: 3.17 (0.11), residues: 2244 sheet: None (None), residues: 0 loop : -1.33 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 38 TYR 0.017 0.001 TYR D 215 PHE 0.011 0.001 PHE H 18 TRP 0.009 0.001 TRP K 150 HIS 0.003 0.001 HIS E 152 Details of bonding type rmsd covalent geometry : bond 0.00314 (24101) covalent geometry : angle 0.48194 (32384) hydrogen bonds : bond 0.05182 ( 1897) hydrogen bonds : angle 3.43655 ( 5493) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 416 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8996 (mmm) cc_final: 0.8011 (mmt) REVERT: A 67 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6509 (tt0) REVERT: A 120 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.4773 (tp30) REVERT: A 157 MET cc_start: 0.7745 (ttm) cc_final: 0.7093 (tpt) REVERT: B 63 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8590 (tm-30) REVERT: B 120 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.4423 (mm-30) REVERT: B 132 LYS cc_start: 0.8580 (mppt) cc_final: 0.7977 (pttm) REVERT: B 224 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6480 (mttp) REVERT: C 77 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8769 (tm-30) REVERT: C 99 ASN cc_start: 0.7522 (OUTLIER) cc_final: 0.7229 (t0) REVERT: C 120 GLU cc_start: 0.9002 (tp30) cc_final: 0.8162 (mm-30) REVERT: C 159 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7154 (mt0) REVERT: C 254 LYS cc_start: 0.4492 (tttt) cc_final: 0.3690 (tttp) REVERT: D 63 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7870 (tm-30) REVERT: D 88 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8479 (tp40) REVERT: D 254 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8543 (tttt) REVERT: E 60 ARG cc_start: 0.8412 (mmm-85) cc_final: 0.7846 (mmm-85) REVERT: E 63 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7771 (pt0) REVERT: E 120 GLU cc_start: 0.4332 (OUTLIER) cc_final: 0.3510 (tp30) REVERT: E 162 ARG cc_start: 0.9447 (OUTLIER) cc_final: 0.8387 (tpt90) REVERT: E 171 ARG cc_start: 0.6574 (ppt170) cc_final: 0.6277 (tmt170) REVERT: E 176 LYS cc_start: 0.9112 (ptmm) cc_final: 0.8791 (ptmm) REVERT: E 218 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8434 (ttm-80) REVERT: E 239 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7734 (ttm-80) REVERT: E 254 LYS cc_start: 0.8967 (tmmt) cc_final: 0.8280 (tttp) REVERT: E 270 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8627 (t0) REVERT: F 53 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8808 (mtt180) REVERT: F 77 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8310 (tm-30) REVERT: F 81 GLN cc_start: 0.8649 (tp40) cc_final: 0.8231 (tp-100) REVERT: F 160 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7370 (ptm-80) REVERT: F 254 LYS cc_start: 0.8926 (tttt) cc_final: 0.8082 (tttt) REVERT: F 265 MET cc_start: 0.8989 (tpp) cc_final: 0.8620 (tpp) REVERT: G 171 ARG cc_start: 0.8716 (mtp-110) cc_final: 0.8473 (ppt170) REVERT: G 209 ARG cc_start: 0.6017 (ttt180) cc_final: 0.4766 (mmm-85) REVERT: G 248 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7610 (pm20) REVERT: H 4 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8525 (t0) REVERT: H 38 ARG cc_start: 0.8467 (ttm170) cc_final: 0.7964 (tpt-90) REVERT: H 63 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8338 (tm-30) REVERT: H 123 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.9116 (ttp80) REVERT: H 160 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7986 (ptp90) REVERT: H 220 GLU cc_start: 0.8445 (tt0) cc_final: 0.8019 (tm-30) REVERT: I 88 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8776 (mt0) REVERT: I 157 MET cc_start: 0.5123 (mtt) cc_final: 0.3440 (mmt) REVERT: J 6 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7927 (t0) REVERT: J 51 LYS cc_start: 0.6651 (tttt) cc_final: 0.6187 (mtmm) REVERT: J 157 MET cc_start: 0.5520 (tpt) cc_final: 0.5119 (tpt) REVERT: J 171 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.5863 (ptt90) REVERT: K 70 MET cc_start: 0.8456 (ptm) cc_final: 0.8227 (ptm) REVERT: K 85 ASP cc_start: 0.8653 (m-30) cc_final: 0.8387 (m-30) outliers start: 132 outliers final: 71 residues processed: 509 average time/residue: 0.2021 time to fit residues: 149.6838 Evaluate side-chains 487 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 391 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 145 ARG Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 29 LYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 123 ARG Chi-restraints excluded: chain H residue 160 ARG Chi-restraints excluded: chain H residue 224 LYS Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 88 GLN Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 153 ILE Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain J residue 171 ARG Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 167 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 257 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 241 optimal weight: 0.0870 chunk 196 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 223 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 284 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 ASN I 26 ASN ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN K 274 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.095323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.087683 restraints weight = 62181.809| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.52 r_work: 0.3279 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24101 Z= 0.114 Angle : 0.462 15.203 32384 Z= 0.249 Chirality : 0.035 0.168 3696 Planarity : 0.002 0.032 4323 Dihedral : 5.572 71.241 3395 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.93 % Allowed : 21.33 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.16), residues: 3058 helix: 3.20 (0.11), residues: 2211 sheet: None (None), residues: 0 loop : -1.20 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 38 TYR 0.018 0.001 TYR D 215 PHE 0.007 0.001 PHE H 18 TRP 0.010 0.001 TRP K 150 HIS 0.002 0.000 HIS H 5 Details of bonding type rmsd covalent geometry : bond 0.00230 (24101) covalent geometry : angle 0.46235 (32384) hydrogen bonds : bond 0.04777 ( 1897) hydrogen bonds : angle 3.32117 ( 5493) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 424 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6449 (tt0) REVERT: A 120 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.4791 (tp30) REVERT: A 157 MET cc_start: 0.7662 (ttm) cc_final: 0.7041 (tpt) REVERT: B 63 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8465 (tm-30) REVERT: B 120 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.4452 (mm-30) REVERT: B 132 LYS cc_start: 0.8548 (mppt) cc_final: 0.7961 (pttm) REVERT: B 224 LYS cc_start: 0.7295 (mmtm) cc_final: 0.6484 (mttp) REVERT: C 99 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.7193 (t0) REVERT: C 120 GLU cc_start: 0.8945 (tp30) cc_final: 0.8148 (mm-30) REVERT: C 254 LYS cc_start: 0.4587 (tttt) cc_final: 0.3736 (tttp) REVERT: D 63 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7823 (tm-30) REVERT: D 88 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8471 (tp40) REVERT: D 254 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8484 (tttt) REVERT: E 60 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.7774 (mmm-85) REVERT: E 63 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7646 (pt0) REVERT: E 120 GLU cc_start: 0.4708 (OUTLIER) cc_final: 0.3771 (tp30) REVERT: E 171 ARG cc_start: 0.6293 (ppt170) cc_final: 0.5936 (tmt170) REVERT: E 176 LYS cc_start: 0.9111 (ptmm) cc_final: 0.8775 (ptmm) REVERT: E 218 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8444 (ttm-80) REVERT: E 239 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7775 (ttm-80) REVERT: E 254 LYS cc_start: 0.9013 (tmmt) cc_final: 0.8314 (tttp) REVERT: E 270 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8621 (t0) REVERT: F 77 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: F 81 GLN cc_start: 0.8634 (tp40) cc_final: 0.8385 (tm-30) REVERT: F 160 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7339 (ptm-80) REVERT: F 254 LYS cc_start: 0.8951 (tttt) cc_final: 0.8082 (tttt) REVERT: G 171 ARG cc_start: 0.8732 (mtp-110) cc_final: 0.8404 (ppt170) REVERT: G 209 ARG cc_start: 0.5965 (ttt180) cc_final: 0.4752 (mmm-85) REVERT: G 248 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: G 254 LYS cc_start: 0.8967 (tttp) cc_final: 0.8707 (tttp) REVERT: H 4 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8442 (t0) REVERT: H 35 ARG cc_start: 0.8385 (ttt-90) cc_final: 0.8155 (ptt90) REVERT: H 38 ARG cc_start: 0.8454 (ttm170) cc_final: 0.8033 (ttt90) REVERT: H 63 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8252 (tm-30) REVERT: H 160 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7995 (ptp90) REVERT: H 220 GLU cc_start: 0.8441 (tt0) cc_final: 0.8022 (tm-30) REVERT: I 42 ASP cc_start: 0.6892 (p0) cc_final: 0.6455 (p0) REVERT: I 88 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8863 (mt0) REVERT: I 118 ILE cc_start: 0.9419 (pt) cc_final: 0.9098 (mt) REVERT: I 157 MET cc_start: 0.5153 (mtt) cc_final: 0.3556 (mmt) REVERT: I 168 MET cc_start: 0.9149 (mmm) cc_final: 0.8944 (mmm) REVERT: J 30 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8363 (tt) REVERT: J 51 LYS cc_start: 0.6545 (tttt) cc_final: 0.6199 (mtmm) REVERT: J 157 MET cc_start: 0.5610 (tpt) cc_final: 0.5269 (tpt) REVERT: J 171 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.5774 (ptt90) REVERT: K 34 MET cc_start: 0.8996 (mtp) cc_final: 0.8566 (mtm) REVERT: K 70 MET cc_start: 0.8437 (ptm) cc_final: 0.8209 (ptm) REVERT: K 85 ASP cc_start: 0.8659 (m-30) cc_final: 0.8361 (m-30) outliers start: 127 outliers final: 73 residues processed: 517 average time/residue: 0.1949 time to fit residues: 146.5645 Evaluate side-chains 490 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 398 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 145 ARG Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 160 ARG Chi-restraints excluded: chain H residue 224 LYS Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 88 GLN Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain J residue 171 ARG Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 186 SER Chi-restraints excluded: chain K residue 277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 169 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 305 optimal weight: 0.8980 chunk 294 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 209 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN E 19 GLN ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN G 37 ASN H 4 ASN ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.102201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.094057 restraints weight = 64810.217| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.60 r_work: 0.3255 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24101 Z= 0.137 Angle : 0.483 14.947 32384 Z= 0.261 Chirality : 0.036 0.166 3696 Planarity : 0.003 0.029 4323 Dihedral : 5.571 70.811 3391 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 5.21 % Allowed : 21.41 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.16), residues: 3058 helix: 3.16 (0.11), residues: 2255 sheet: None (None), residues: 0 loop : -1.32 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.017 0.001 TYR D 215 PHE 0.012 0.001 PHE F 252 TRP 0.008 0.001 TRP K 150 HIS 0.002 0.000 HIS E 152 Details of bonding type rmsd covalent geometry : bond 0.00299 (24101) covalent geometry : angle 0.48330 (32384) hydrogen bonds : bond 0.04976 ( 1897) hydrogen bonds : angle 3.39135 ( 5493) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 409 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6521 (tt0) REVERT: A 120 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.4818 (tp30) REVERT: A 157 MET cc_start: 0.7677 (ttm) cc_final: 0.7032 (tpt) REVERT: B 120 GLU cc_start: 0.5833 (OUTLIER) cc_final: 0.4429 (mm-30) REVERT: B 132 LYS cc_start: 0.8585 (mppt) cc_final: 0.7988 (pttm) REVERT: B 224 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6486 (mttp) REVERT: C 99 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.7212 (t0) REVERT: C 120 GLU cc_start: 0.8954 (tp30) cc_final: 0.8131 (mm-30) REVERT: C 159 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7089 (mt0) REVERT: C 254 LYS cc_start: 0.4292 (tttt) cc_final: 0.3432 (tttp) REVERT: D 63 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7851 (tm-30) REVERT: D 88 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8472 (tp40) REVERT: D 254 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8533 (tttt) REVERT: E 63 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7905 (pt0) REVERT: E 88 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8627 (tp40) REVERT: E 120 GLU cc_start: 0.4277 (OUTLIER) cc_final: 0.3443 (tp30) REVERT: E 162 ARG cc_start: 0.9461 (OUTLIER) cc_final: 0.8455 (tpt90) REVERT: E 168 MET cc_start: 0.9354 (tpp) cc_final: 0.9144 (mmm) REVERT: E 171 ARG cc_start: 0.6284 (ppt170) cc_final: 0.5929 (tmt170) REVERT: E 176 LYS cc_start: 0.9123 (ptmm) cc_final: 0.8803 (ptmm) REVERT: E 218 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8445 (ttm-80) REVERT: E 239 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7726 (ttm-80) REVERT: E 254 LYS cc_start: 0.8952 (tmmt) cc_final: 0.8261 (tttp) REVERT: E 270 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8582 (t0) REVERT: F 77 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: F 81 GLN cc_start: 0.8655 (tp40) cc_final: 0.8404 (tm-30) REVERT: F 160 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7362 (ptm-80) REVERT: F 254 LYS cc_start: 0.8983 (tttt) cc_final: 0.8093 (tttt) REVERT: G 171 ARG cc_start: 0.8744 (mtp-110) cc_final: 0.8429 (ppt170) REVERT: G 209 ARG cc_start: 0.6072 (ttt180) cc_final: 0.4823 (mmm-85) REVERT: G 248 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7529 (pm20) REVERT: G 254 LYS cc_start: 0.8967 (tttp) cc_final: 0.8753 (tttp) REVERT: H 4 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8473 (t0) REVERT: H 38 ARG cc_start: 0.8469 (ttm170) cc_final: 0.8037 (ttt90) REVERT: H 63 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8304 (tm-30) REVERT: H 160 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8513 (ptm-80) REVERT: H 220 GLU cc_start: 0.8445 (tt0) cc_final: 0.8025 (tm-30) REVERT: I 42 ASP cc_start: 0.6929 (p0) cc_final: 0.6324 (p0) REVERT: I 88 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8910 (mt0) REVERT: I 157 MET cc_start: 0.5213 (mtt) cc_final: 0.3587 (mmt) REVERT: J 51 LYS cc_start: 0.6870 (tttt) cc_final: 0.6390 (mtmm) REVERT: J 65 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7045 (m110) REVERT: J 157 MET cc_start: 0.5525 (tpt) cc_final: 0.5126 (tpt) REVERT: J 171 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.5836 (ptt90) REVERT: K 34 MET cc_start: 0.8995 (mtp) cc_final: 0.8587 (mtm) REVERT: K 70 MET cc_start: 0.8491 (ptm) cc_final: 0.8265 (ptm) REVERT: K 85 ASP cc_start: 0.8634 (m-30) cc_final: 0.8352 (m-30) outliers start: 134 outliers final: 87 residues processed: 509 average time/residue: 0.2000 time to fit residues: 148.2852 Evaluate side-chains 505 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 395 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 145 ARG Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 29 LYS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 160 ARG Chi-restraints excluded: chain H residue 224 LYS Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 88 GLN Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 74 GLN Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain J residue 171 ARG Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 244 optimal weight: 0.5980 chunk 199 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 247 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN H 4 ASN ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.093624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.086195 restraints weight = 63416.870| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.44 r_work: 0.3269 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24101 Z= 0.125 Angle : 0.481 14.973 32384 Z= 0.258 Chirality : 0.035 0.164 3696 Planarity : 0.002 0.030 4323 Dihedral : 5.522 71.013 3391 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 5.05 % Allowed : 22.11 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.16), residues: 3058 helix: 3.12 (0.11), residues: 2211 sheet: None (None), residues: 0 loop : -1.20 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.023 0.001 TYR D 215 PHE 0.011 0.001 PHE F 252 TRP 0.009 0.001 TRP K 150 HIS 0.003 0.000 HIS H 5 Details of bonding type rmsd covalent geometry : bond 0.00267 (24101) covalent geometry : angle 0.48143 (32384) hydrogen bonds : bond 0.04882 ( 1897) hydrogen bonds : angle 3.37226 ( 5493) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 415 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6481 (tt0) REVERT: A 120 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.4847 (tp30) REVERT: A 157 MET cc_start: 0.7634 (ttm) cc_final: 0.7017 (tpt) REVERT: B 120 GLU cc_start: 0.5779 (OUTLIER) cc_final: 0.3796 (tp30) REVERT: B 132 LYS cc_start: 0.8382 (mppt) cc_final: 0.7862 (pttm) REVERT: B 224 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6506 (mttp) REVERT: C 120 GLU cc_start: 0.8932 (tp30) cc_final: 0.8122 (mm-30) REVERT: C 159 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7049 (mt0) REVERT: C 254 LYS cc_start: 0.4582 (tttt) cc_final: 0.3720 (tttp) REVERT: D 63 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7810 (tm-30) REVERT: D 88 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8472 (tp40) REVERT: D 160 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.7851 (mtp85) REVERT: D 248 GLU cc_start: 0.8081 (tp30) cc_final: 0.7709 (tp30) REVERT: D 254 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8478 (tttt) REVERT: E 88 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8618 (tp40) REVERT: E 120 GLU cc_start: 0.4687 (OUTLIER) cc_final: 0.3768 (tp30) REVERT: E 162 ARG cc_start: 0.9453 (OUTLIER) cc_final: 0.8453 (tpt90) REVERT: E 176 LYS cc_start: 0.9143 (ptmm) cc_final: 0.8821 (ptmm) REVERT: E 218 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8443 (ttm-80) REVERT: E 239 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7768 (ttm-80) REVERT: E 254 LYS cc_start: 0.9048 (tmmt) cc_final: 0.8433 (mttt) REVERT: E 270 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8572 (t0) REVERT: F 77 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8234 (tm-30) REVERT: F 81 GLN cc_start: 0.8632 (tp40) cc_final: 0.8375 (tm-30) REVERT: F 160 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7333 (ptm-80) REVERT: F 254 LYS cc_start: 0.8921 (tttt) cc_final: 0.8063 (tttt) REVERT: G 171 ARG cc_start: 0.8700 (mtp-110) cc_final: 0.8422 (ppt170) REVERT: G 209 ARG cc_start: 0.6025 (ttt180) cc_final: 0.4811 (mmm-85) REVERT: G 248 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: G 254 LYS cc_start: 0.8927 (tttp) cc_final: 0.8710 (tttp) REVERT: H 4 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8493 (t0) REVERT: H 38 ARG cc_start: 0.8408 (ttm170) cc_final: 0.7959 (ttt90) REVERT: H 63 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8261 (tm-30) REVERT: H 160 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8509 (ptm-80) REVERT: H 220 GLU cc_start: 0.8411 (tt0) cc_final: 0.8006 (tm-30) REVERT: I 42 ASP cc_start: 0.7001 (p0) cc_final: 0.6379 (p0) REVERT: I 52 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.8244 (mpp) REVERT: I 118 ILE cc_start: 0.9436 (pt) cc_final: 0.9137 (mt) REVERT: I 157 MET cc_start: 0.5176 (mtt) cc_final: 0.3569 (mmt) REVERT: J 51 LYS cc_start: 0.6576 (tttt) cc_final: 0.6210 (mtmm) REVERT: J 157 MET cc_start: 0.5613 (tpt) cc_final: 0.5274 (tpt) REVERT: J 171 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.5805 (ptt90) REVERT: J 265 MET cc_start: 0.9039 (mmm) cc_final: 0.8778 (mmt) REVERT: K 70 MET cc_start: 0.8490 (ptm) cc_final: 0.8270 (ptm) REVERT: K 85 ASP cc_start: 0.8625 (m-30) cc_final: 0.8341 (m-30) REVERT: K 265 MET cc_start: 0.8920 (mmm) cc_final: 0.8232 (ptp) outliers start: 130 outliers final: 85 residues processed: 509 average time/residue: 0.1994 time to fit residues: 148.0999 Evaluate side-chains 501 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 395 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 268 GLN Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 145 ARG Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 29 LYS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 160 ARG Chi-restraints excluded: chain H residue 224 LYS Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 74 GLN Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain J residue 171 ARG Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 186 SER Chi-restraints excluded: chain K residue 277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 40 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 294 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 237 optimal weight: 0.1980 chunk 182 optimal weight: 5.9990 chunk 251 optimal weight: 0.1980 chunk 152 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN D 81 GLN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN H 4 ASN I 127 GLN ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN J 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.102887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094760 restraints weight = 64635.649| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.61 r_work: 0.3280 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24101 Z= 0.114 Angle : 0.474 15.071 32384 Z= 0.254 Chirality : 0.035 0.163 3696 Planarity : 0.002 0.033 4323 Dihedral : 5.321 71.198 3388 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.43 % Allowed : 22.92 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.16), residues: 3058 helix: 3.17 (0.11), residues: 2211 sheet: None (None), residues: 0 loop : -1.20 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 38 TYR 0.023 0.001 TYR D 215 PHE 0.012 0.001 PHE F 252 TRP 0.009 0.001 TRP K 150 HIS 0.002 0.000 HIS H 5 Details of bonding type rmsd covalent geometry : bond 0.00234 (24101) covalent geometry : angle 0.47423 (32384) hydrogen bonds : bond 0.04674 ( 1897) hydrogen bonds : angle 3.31928 ( 5493) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 417 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6436 (tt0) REVERT: A 120 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.4818 (tp30) REVERT: A 157 MET cc_start: 0.7620 (ttm) cc_final: 0.6993 (tpt) REVERT: B 120 GLU cc_start: 0.5862 (OUTLIER) cc_final: 0.3893 (tp30) REVERT: B 132 LYS cc_start: 0.8371 (mppt) cc_final: 0.7819 (pttm) REVERT: B 224 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6428 (mttp) REVERT: C 120 GLU cc_start: 0.8935 (tp30) cc_final: 0.7989 (mm-30) REVERT: C 159 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.6997 (mt0) REVERT: C 254 LYS cc_start: 0.4678 (tttt) cc_final: 0.3802 (tttp) REVERT: D 63 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7835 (tm-30) REVERT: D 88 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8519 (tp40) REVERT: D 248 GLU cc_start: 0.8048 (tp30) cc_final: 0.7614 (tp30) REVERT: D 254 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8439 (tttt) REVERT: E 60 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.8017 (mmm-85) REVERT: E 63 GLU cc_start: 0.8218 (pt0) cc_final: 0.7856 (pt0) REVERT: E 88 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8626 (tp40) REVERT: E 120 GLU cc_start: 0.4639 (OUTLIER) cc_final: 0.3677 (tp30) REVERT: E 145 ARG cc_start: 0.4568 (tpm170) cc_final: 0.4247 (tpm170) REVERT: E 162 ARG cc_start: 0.9443 (OUTLIER) cc_final: 0.8438 (tpt90) REVERT: E 176 LYS cc_start: 0.9133 (ptmm) cc_final: 0.8790 (ptmm) REVERT: E 218 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8432 (ttm-80) REVERT: E 239 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7741 (ttm-80) REVERT: E 242 ASP cc_start: 0.8334 (m-30) cc_final: 0.8112 (m-30) REVERT: E 254 LYS cc_start: 0.9044 (tmmt) cc_final: 0.8403 (mttt) REVERT: F 77 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: F 81 GLN cc_start: 0.8651 (tp40) cc_final: 0.8349 (tm-30) REVERT: F 160 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7316 (ptm-80) REVERT: F 254 LYS cc_start: 0.8920 (tttt) cc_final: 0.8059 (tttt) REVERT: G 171 ARG cc_start: 0.8733 (mtp-110) cc_final: 0.8369 (ppt170) REVERT: G 209 ARG cc_start: 0.5940 (ttt180) cc_final: 0.4822 (mmm-85) REVERT: G 248 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: H 4 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8486 (t0) REVERT: H 35 ARG cc_start: 0.8331 (ttt-90) cc_final: 0.8033 (ptt90) REVERT: H 38 ARG cc_start: 0.8386 (ttm170) cc_final: 0.8044 (ttt90) REVERT: H 44 SER cc_start: 0.7556 (m) cc_final: 0.7137 (p) REVERT: H 63 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8248 (tm-30) REVERT: H 81 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8437 (tp-100) REVERT: H 160 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8492 (ptm-80) REVERT: H 220 GLU cc_start: 0.8445 (tt0) cc_final: 0.8012 (tm-30) REVERT: I 42 ASP cc_start: 0.7183 (p0) cc_final: 0.6551 (p0) REVERT: I 52 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8214 (mpp) REVERT: I 118 ILE cc_start: 0.9431 (pt) cc_final: 0.9134 (mt) REVERT: I 157 MET cc_start: 0.5125 (mtt) cc_final: 0.3537 (mmt) REVERT: I 244 ASP cc_start: 0.8330 (t0) cc_final: 0.7911 (t70) REVERT: J 51 LYS cc_start: 0.6557 (tttt) cc_final: 0.6199 (mtmm) REVERT: J 157 MET cc_start: 0.5664 (tpt) cc_final: 0.5329 (tpt) REVERT: J 171 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.5773 (ptt90) REVERT: K 85 ASP cc_start: 0.8647 (m-30) cc_final: 0.8361 (m-30) outliers start: 114 outliers final: 71 residues processed: 500 average time/residue: 0.1907 time to fit residues: 139.2938 Evaluate side-chains 489 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 399 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 268 GLN Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 145 ARG Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 160 ARG Chi-restraints excluded: chain H residue 224 LYS Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 257 ILE Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 74 GLN Chi-restraints excluded: chain J residue 171 ARG Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 186 SER Chi-restraints excluded: chain K residue 277 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 232 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 253 optimal weight: 0.9990 chunk 195 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN E 37 ASN H 4 ASN ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN J 211 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.094576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086940 restraints weight = 62932.786| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.54 r_work: 0.3266 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24101 Z= 0.130 Angle : 0.502 14.867 32384 Z= 0.266 Chirality : 0.036 0.176 3696 Planarity : 0.002 0.031 4323 Dihedral : 5.334 70.978 3385 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.31 % Allowed : 22.84 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.15), residues: 3058 helix: 3.09 (0.11), residues: 2211 sheet: None (None), residues: 0 loop : -1.23 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 241 TYR 0.026 0.001 TYR D 215 PHE 0.023 0.001 PHE D 252 TRP 0.008 0.001 TRP D 150 HIS 0.002 0.000 HIS E 152 Details of bonding type rmsd covalent geometry : bond 0.00283 (24101) covalent geometry : angle 0.50194 (32384) hydrogen bonds : bond 0.04823 ( 1897) hydrogen bonds : angle 3.37549 ( 5493) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 401 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6505 (tt0) REVERT: A 120 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.4862 (tp30) REVERT: A 157 MET cc_start: 0.7646 (ttm) cc_final: 0.7020 (tpt) REVERT: B 120 GLU cc_start: 0.5885 (OUTLIER) cc_final: 0.3911 (tp30) REVERT: B 132 LYS cc_start: 0.8385 (mppt) cc_final: 0.7831 (pttm) REVERT: B 224 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6459 (mttp) REVERT: C 120 GLU cc_start: 0.9009 (tp30) cc_final: 0.8175 (mm-30) REVERT: C 159 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7049 (mt0) REVERT: C 254 LYS cc_start: 0.4720 (tttt) cc_final: 0.3859 (tttp) REVERT: D 63 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7823 (tm-30) REVERT: D 88 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8532 (tp40) REVERT: D 160 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7830 (mtp85) REVERT: D 248 GLU cc_start: 0.8021 (tp30) cc_final: 0.7664 (tp30) REVERT: D 254 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8454 (tttt) REVERT: E 60 ARG cc_start: 0.8241 (mmm-85) cc_final: 0.7956 (mmm-85) REVERT: E 63 GLU cc_start: 0.8208 (pt0) cc_final: 0.7829 (pt0) REVERT: E 88 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8632 (tp40) REVERT: E 120 GLU cc_start: 0.4321 (OUTLIER) cc_final: 0.3472 (tp30) REVERT: E 162 ARG cc_start: 0.9450 (OUTLIER) cc_final: 0.8458 (tpt90) REVERT: E 176 LYS cc_start: 0.9137 (ptmm) cc_final: 0.8811 (ptmm) REVERT: E 218 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8448 (ttm-80) REVERT: E 239 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7783 (ttm-80) REVERT: E 254 LYS cc_start: 0.9025 (tmmt) cc_final: 0.8386 (mttt) REVERT: F 77 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: F 81 GLN cc_start: 0.8638 (tp40) cc_final: 0.8363 (tm-30) REVERT: F 160 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7344 (ptm-80) REVERT: F 254 LYS cc_start: 0.8944 (tttt) cc_final: 0.8063 (tttt) REVERT: G 171 ARG cc_start: 0.8704 (mtp-110) cc_final: 0.8410 (ppt170) REVERT: G 209 ARG cc_start: 0.6029 (ttt180) cc_final: 0.4818 (mmm-85) REVERT: G 248 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: H 4 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8502 (t0) REVERT: H 35 ARG cc_start: 0.8312 (ttt-90) cc_final: 0.8030 (ptt90) REVERT: H 38 ARG cc_start: 0.8381 (ttm170) cc_final: 0.8049 (ttt90) REVERT: H 63 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8263 (tm-30) REVERT: H 81 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8457 (tp-100) REVERT: H 220 GLU cc_start: 0.8467 (tt0) cc_final: 0.8039 (tm-30) REVERT: I 42 ASP cc_start: 0.7078 (p0) cc_final: 0.6433 (p0) REVERT: I 52 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8343 (mpp) REVERT: I 88 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8843 (mt0) REVERT: I 118 ILE cc_start: 0.9428 (pt) cc_final: 0.9149 (mt) REVERT: I 157 MET cc_start: 0.5055 (mtt) cc_final: 0.3423 (mmt) REVERT: I 244 ASP cc_start: 0.8371 (t0) cc_final: 0.8003 (t70) REVERT: J 51 LYS cc_start: 0.6608 (tttt) cc_final: 0.6221 (mtmm) REVERT: J 149 MET cc_start: 0.7460 (ppp) cc_final: 0.7165 (ppp) REVERT: J 157 MET cc_start: 0.5711 (tpt) cc_final: 0.5373 (tpt) REVERT: J 171 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.5826 (ptt90) REVERT: J 265 MET cc_start: 0.9059 (mmm) cc_final: 0.8751 (mmt) REVERT: K 85 ASP cc_start: 0.8641 (m-30) cc_final: 0.8368 (m-30) REVERT: K 265 MET cc_start: 0.8969 (mmm) cc_final: 0.8270 (ptp) outliers start: 111 outliers final: 77 residues processed: 484 average time/residue: 0.1787 time to fit residues: 126.9394 Evaluate side-chains 490 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 393 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 145 ARG Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 224 LYS Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 88 GLN Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 74 GLN Chi-restraints excluded: chain J residue 171 ARG Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 186 SER Chi-restraints excluded: chain K residue 192 ASN Chi-restraints excluded: chain K residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 248 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 chunk 301 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 219 optimal weight: 0.7980 chunk 263 optimal weight: 0.9980 chunk 304 optimal weight: 4.9990 chunk 293 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 229 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN G 37 ASN H 4 ASN ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.091778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.084299 restraints weight = 65055.823| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.54 r_work: 0.3269 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24101 Z= 0.129 Angle : 0.513 14.768 32384 Z= 0.272 Chirality : 0.036 0.175 3696 Planarity : 0.002 0.033 4323 Dihedral : 5.263 71.029 3381 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.08 % Allowed : 23.12 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.97 (0.15), residues: 3058 helix: 3.06 (0.11), residues: 2211 sheet: None (None), residues: 0 loop : -1.21 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 241 TYR 0.025 0.001 TYR D 215 PHE 0.012 0.001 PHE I 216 TRP 0.008 0.001 TRP D 150 HIS 0.002 0.000 HIS E 152 Details of bonding type rmsd covalent geometry : bond 0.00281 (24101) covalent geometry : angle 0.51291 (32384) hydrogen bonds : bond 0.04837 ( 1897) hydrogen bonds : angle 3.39843 ( 5493) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 402 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6487 (tt0) REVERT: A 120 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.4970 (tp30) REVERT: A 157 MET cc_start: 0.7649 (ttm) cc_final: 0.7015 (tpt) REVERT: B 120 GLU cc_start: 0.5855 (OUTLIER) cc_final: 0.3900 (tp30) REVERT: B 132 LYS cc_start: 0.8390 (mppt) cc_final: 0.7843 (pttm) REVERT: B 224 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6439 (mttp) REVERT: C 120 GLU cc_start: 0.9029 (tp30) cc_final: 0.8178 (mm-30) REVERT: C 159 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7014 (mt0) REVERT: C 254 LYS cc_start: 0.4782 (tttt) cc_final: 0.3933 (tttp) REVERT: D 63 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7824 (tm-30) REVERT: D 160 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7836 (mtp85) REVERT: D 248 GLU cc_start: 0.8033 (tp30) cc_final: 0.7661 (tp30) REVERT: D 254 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8471 (tttt) REVERT: E 60 ARG cc_start: 0.8235 (mmm-85) cc_final: 0.7932 (mmm-85) REVERT: E 63 GLU cc_start: 0.8232 (pt0) cc_final: 0.7846 (pt0) REVERT: E 88 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8622 (tp40) REVERT: E 120 GLU cc_start: 0.4286 (OUTLIER) cc_final: 0.3443 (tp30) REVERT: E 162 ARG cc_start: 0.9450 (OUTLIER) cc_final: 0.8452 (tpt90) REVERT: E 176 LYS cc_start: 0.9136 (ptmm) cc_final: 0.8806 (ptmm) REVERT: E 218 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8445 (ttm-80) REVERT: E 239 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7828 (ttm-80) REVERT: E 254 LYS cc_start: 0.9023 (tmmt) cc_final: 0.8381 (mttt) REVERT: F 77 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8248 (tm-30) REVERT: F 81 GLN cc_start: 0.8647 (tp40) cc_final: 0.8364 (tm-30) REVERT: F 160 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7321 (ptm-80) REVERT: F 254 LYS cc_start: 0.8922 (tttt) cc_final: 0.8050 (tttt) REVERT: F 265 MET cc_start: 0.8683 (tpp) cc_final: 0.8358 (tpp) REVERT: G 171 ARG cc_start: 0.8702 (mtp-110) cc_final: 0.8409 (ppt170) REVERT: G 209 ARG cc_start: 0.6013 (ttt180) cc_final: 0.4785 (mmm-85) REVERT: G 248 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7613 (pm20) REVERT: H 4 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8483 (t0) REVERT: H 35 ARG cc_start: 0.8324 (ttt-90) cc_final: 0.8033 (ptt90) REVERT: H 38 ARG cc_start: 0.8385 (ttm170) cc_final: 0.8062 (ttt90) REVERT: H 63 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8257 (tm-30) REVERT: H 81 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8443 (tp-100) REVERT: H 220 GLU cc_start: 0.8441 (tt0) cc_final: 0.8017 (tm-30) REVERT: I 34 MET cc_start: 0.8392 (mtp) cc_final: 0.8192 (ttp) REVERT: I 42 ASP cc_start: 0.7085 (p0) cc_final: 0.6434 (p0) REVERT: I 52 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.8345 (mpp) REVERT: I 88 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8845 (mt0) REVERT: I 118 ILE cc_start: 0.9434 (pt) cc_final: 0.9154 (mt) REVERT: I 157 MET cc_start: 0.5035 (mtt) cc_final: 0.3403 (mmt) REVERT: I 244 ASP cc_start: 0.8332 (t0) cc_final: 0.7979 (t70) REVERT: J 51 LYS cc_start: 0.6610 (tttt) cc_final: 0.6199 (mtmm) REVERT: J 157 MET cc_start: 0.5699 (tpt) cc_final: 0.5363 (tpt) REVERT: J 171 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5819 (ptt90) REVERT: J 265 MET cc_start: 0.9095 (mmm) cc_final: 0.8793 (mmt) REVERT: K 85 ASP cc_start: 0.8663 (m-30) cc_final: 0.8377 (m-30) REVERT: K 265 MET cc_start: 0.8870 (mmm) cc_final: 0.8241 (ptp) outliers start: 105 outliers final: 82 residues processed: 482 average time/residue: 0.1981 time to fit residues: 138.7218 Evaluate side-chains 498 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 397 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 145 ARG Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 224 LYS Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 88 GLN Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 257 ILE Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 74 GLN Chi-restraints excluded: chain J residue 171 ARG Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 186 SER Chi-restraints excluded: chain K residue 192 ASN Chi-restraints excluded: chain K residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 282 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 202 optimal weight: 0.5980 chunk 195 optimal weight: 0.7980 chunk 238 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN G 19 GLN ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 ASN ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN J 211 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.091644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.084161 restraints weight = 65096.101| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.53 r_work: 0.3275 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24101 Z= 0.126 Angle : 0.506 14.754 32384 Z= 0.268 Chirality : 0.035 0.159 3696 Planarity : 0.002 0.033 4323 Dihedral : 5.156 71.049 3378 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.08 % Allowed : 23.15 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.15), residues: 3058 helix: 3.07 (0.11), residues: 2211 sheet: None (None), residues: 0 loop : -1.19 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 241 TYR 0.021 0.001 TYR D 215 PHE 0.021 0.001 PHE D 252 TRP 0.009 0.001 TRP A 150 HIS 0.002 0.000 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00271 (24101) covalent geometry : angle 0.50565 (32384) hydrogen bonds : bond 0.04786 ( 1897) hydrogen bonds : angle 3.39563 ( 5493) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5099.54 seconds wall clock time: 88 minutes 15.38 seconds (5295.38 seconds total)