Starting phenix.real_space_refine on Thu Aug 6 13:15:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9swr_55325/08_2026/9swr_55325.cif Found real_map, /net/cci-nas-00/data/ceres_data/9swr_55325/08_2026/9swr_55325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9swr_55325/08_2026/9swr_55325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9swr_55325/08_2026/9swr_55325.map" model { file = "/net/cci-nas-00/data/ceres_data/9swr_55325/08_2026/9swr_55325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9swr_55325/08_2026/9swr_55325.cif" } resolution = 2.86 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= 0.001 sd= 0.011 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 72 5.16 5 C 9590 2.51 5 N 2639 2.21 5 O 2672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14973 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2539 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 18, 'TRANS': 303} Chain breaks: 2 Chain: "B" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2509 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 18, 'TRANS': 299} Chain breaks: 2 Chain: "C" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2464 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain breaks: 3 Chain: "D" Number of atoms: 2525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2525 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 18, 'TRANS': 301} Chain breaks: 2 Chain: "E" Number of atoms: 2460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2460 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain breaks: 4 Chain: "F" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2476 Classifications: {'peptide': 314} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 294} Chain breaks: 3 Time building chain proxies: 3.52, per 1000 atoms: 0.24 Number of scatterers: 14973 At special positions: 0 Unit cell: (126.99, 99.6, 109.56, 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 72 16.00 O 2672 8.00 N 2639 7.00 C 9590 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: 1.07 Conformation dependent library (CDL) restraints added in 709.9 milliseconds 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3548 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 7 sheets defined 64.0% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 16 through 37 removed outlier: 3.598A pdb=" N LYS A 20 " --> pdb=" O HIS A 16 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 70 removed outlier: 3.794A pdb=" N THR A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 80 through 90 removed outlier: 3.708A pdb=" N THR A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 109 removed outlier: 3.655A pdb=" N LEU A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 134 removed outlier: 4.139A pdb=" N LYS A 120 " --> pdb=" O PRO A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 151 Processing helix chain 'A' and resid 154 through 167 removed outlier: 4.042A pdb=" N GLY A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.689A pdb=" N LEU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.790A pdb=" N ARG A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.816A pdb=" N MET A 214 " --> pdb=" O ASN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 removed outlier: 3.808A pdb=" N THR A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 300 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.606A pdb=" N SER A 305 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 306' Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.581A pdb=" N GLU A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 37 removed outlier: 3.886A pdb=" N LYS B 20 " --> pdb=" O HIS B 16 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 70 removed outlier: 3.812A pdb=" N THR B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.678A pdb=" N THR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 109 removed outlier: 3.502A pdb=" N LEU B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 134 Processing helix chain 'B' and resid 140 through 151 Processing helix chain 'B' and resid 154 through 167 removed outlier: 4.050A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.607A pdb=" N LEU B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.686A pdb=" N ARG B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 263 through 273 removed outlier: 3.848A pdb=" N THR B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 300 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.529A pdb=" N SER B 305 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN B 306 " --> pdb=" O PRO B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 306' Processing helix chain 'B' and resid 326 through 337 Processing helix chain 'C' and resid 16 through 37 removed outlier: 3.885A pdb=" N LYS C 20 " --> pdb=" O HIS C 16 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 70 removed outlier: 3.972A pdb=" N THR C 43 " --> pdb=" O PRO C 39 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C 68 " --> pdb=" O CYS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.762A pdb=" N LEU C 109 " --> pdb=" O PHE C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 134 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 154 through 167 removed outlier: 4.049A pdb=" N GLY C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 removed outlier: 3.640A pdb=" N LEU C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.598A pdb=" N ARG C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 272 removed outlier: 3.728A pdb=" N THR C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 302 Processing helix chain 'C' and resid 324 through 337 Processing helix chain 'D' and resid 16 through 37 removed outlier: 3.529A pdb=" N LYS D 20 " --> pdb=" O HIS D 16 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 70 removed outlier: 3.782A pdb=" N THR D 43 " --> pdb=" O PRO D 39 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU D 68 " --> pdb=" O CYS D 64 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 80 through 90 Processing helix chain 'D' and resid 91 through 109 removed outlier: 3.665A pdb=" N LEU D 109 " --> pdb=" O PHE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 134 removed outlier: 4.323A pdb=" N LYS D 120 " --> pdb=" O PRO D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'D' and resid 154 through 172 removed outlier: 4.066A pdb=" N GLY D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 186 removed outlier: 3.601A pdb=" N ARG D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR D 186 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 274 removed outlier: 3.788A pdb=" N THR D 267 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 300 Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.968A pdb=" N GLN D 306 " --> pdb=" O PRO D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 338 removed outlier: 4.190A pdb=" N LYS D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 37 removed outlier: 3.607A pdb=" N LYS E 20 " --> pdb=" O HIS E 16 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 70 removed outlier: 3.965A pdb=" N THR E 43 " --> pdb=" O PRO E 39 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA E 67 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU E 68 " --> pdb=" O CYS E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 80 through 90 removed outlier: 3.516A pdb=" N THR E 84 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 108 Processing helix chain 'E' and resid 117 through 134 Processing helix chain 'E' and resid 140 through 151 Processing helix chain 'E' and resid 154 through 167 removed outlier: 4.070A pdb=" N GLY E 158 " --> pdb=" O ASN E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 removed outlier: 3.552A pdb=" N LEU E 172 " --> pdb=" O LEU E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 186 removed outlier: 3.892A pdb=" N ARG E 178 " --> pdb=" O GLU E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 272 removed outlier: 3.936A pdb=" N GLN E 266 " --> pdb=" O ALA E 262 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 300 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.664A pdb=" N SER E 305 " --> pdb=" O ALA E 302 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN E 306 " --> pdb=" O PRO E 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 302 through 306' Processing helix chain 'E' and resid 324 through 337 Processing helix chain 'F' and resid 16 through 37 removed outlier: 3.585A pdb=" N GLY F 37 " --> pdb=" O LEU F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 70 removed outlier: 3.822A pdb=" N THR F 43 " --> pdb=" O PRO F 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 67 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU F 68 " --> pdb=" O CYS F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 73 No H-bonds generated for 'chain 'F' and resid 71 through 73' Processing helix chain 'F' and resid 80 through 90 removed outlier: 3.704A pdb=" N THR F 84 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 109 Processing helix chain 'F' and resid 117 through 134 Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 154 through 172 removed outlier: 4.375A pdb=" N GLY F 158 " --> pdb=" O ASN F 154 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG F 169 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU F 170 " --> pdb=" O GLY F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 186 removed outlier: 3.759A pdb=" N ARG F 178 " --> pdb=" O GLU F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 272 removed outlier: 4.035A pdb=" N GLN F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR F 267 " --> pdb=" O THR F 263 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER F 272 " --> pdb=" O LEU F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 300 Processing helix chain 'F' and resid 302 through 306 removed outlier: 4.007A pdb=" N GLN F 306 " --> pdb=" O PRO F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 338 removed outlier: 4.057A pdb=" N GLU F 328 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS F 338 " --> pdb=" O ARG F 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 224 removed outlier: 6.795A pdb=" N ILE A 244 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER A 243 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 259 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 255 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU A 198 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE A 312 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE A 200 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N TYR A 314 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 202 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 219 through 224 removed outlier: 6.793A pdb=" N ILE B 244 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER B 243 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL B 258 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR B 245 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N THR B 256 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU B 247 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU B 198 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 312 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE B 200 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N TYR B 314 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 202 " --> pdb=" O TYR B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 219 through 224 removed outlier: 6.989A pdb=" N ILE C 244 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER C 243 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 259 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR C 199 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 314 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 219 through 225 removed outlier: 6.028A pdb=" N ILE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU D 248 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE D 221 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU D 246 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP D 223 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN D 242 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N SER D 243 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL D 258 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR D 245 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR D 256 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU D 247 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N SER D 195 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR D 256 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ARG D 197 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL D 258 " --> pdb=" O ARG D 197 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG D 310 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU D 198 " --> pdb=" O ARG D 310 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE D 312 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE D 200 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N TYR D 314 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU D 202 " --> pdb=" O TYR D 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 220 through 225 removed outlier: 5.438A pdb=" N PHE E 221 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU E 246 " --> pdb=" O PHE E 221 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP E 223 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN E 242 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N SER E 243 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU E 259 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS E 257 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N THR E 256 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ARG E 197 " --> pdb=" O THR E 256 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL E 258 " --> pdb=" O ARG E 197 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR E 314 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.072A pdb=" N LEU F 198 " --> pdb=" O ARG F 310 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE F 312 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE F 200 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR F 314 " --> pdb=" O ILE F 200 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU F 202 " --> pdb=" O TYR F 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 219 through 224 removed outlier: 7.462A pdb=" N ILE F 244 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY F 255 " --> pdb=" O LEU F 247 " (cutoff:3.500A) 859 hydrogen bonds defined for protein. 2556 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: 2.33 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4824 1.34 - 1.46: 2372 1.46 - 1.57: 8014 1.57 - 1.69: 4 1.69 - 1.81: 84 Bond restraints: 15298 Sorted by residual: bond pdb=" C PRO D 115 " pdb=" N PRO D 116 " ideal model delta sigma weight residual 1.328 1.432 -0.104 1.25e-02 6.40e+03 6.97e+01 bond pdb=" CB PRO D 115 " pdb=" CG PRO D 115 " ideal model delta sigma weight residual 1.492 1.672 -0.180 5.00e-02 4.00e+02 1.29e+01 bond pdb=" C PRO B 115 " pdb=" N PRO B 116 " ideal model delta sigma weight residual 1.331 1.369 -0.038 1.21e-02 6.83e+03 9.72e+00 bond pdb=" C PRO C 115 " pdb=" N PRO C 116 " ideal model delta sigma weight residual 1.331 1.368 -0.037 1.21e-02 6.83e+03 9.22e+00 bond pdb=" CA ASP B 301 " pdb=" CB ASP B 301 " ideal model delta sigma weight residual 1.530 1.575 -0.044 1.69e-02 3.50e+03 6.90e+00 ... (remaining 15293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 20496 3.47 - 6.95: 222 6.95 - 10.42: 35 10.42 - 13.89: 9 13.89 - 17.36: 4 Bond angle restraints: 20766 Sorted by residual: angle pdb=" CA PRO D 115 " pdb=" N PRO D 115 " pdb=" CD PRO D 115 " ideal model delta sigma weight residual 112.00 99.77 12.23 1.40e+00 5.10e-01 7.64e+01 angle pdb=" C GLN F 252 " pdb=" N ARG F 253 " pdb=" CA ARG F 253 " ideal model delta sigma weight residual 121.70 136.91 -15.21 1.80e+00 3.09e-01 7.14e+01 angle pdb=" N VAL B 113 " pdb=" CA VAL B 113 " pdb=" C VAL B 113 " ideal model delta sigma weight residual 112.90 105.38 7.52 9.60e-01 1.09e+00 6.13e+01 angle pdb=" N PRO D 115 " pdb=" CA PRO D 115 " pdb=" C PRO D 115 " ideal model delta sigma weight residual 110.70 120.03 -9.33 1.22e+00 6.72e-01 5.84e+01 angle pdb=" CA PRO D 115 " pdb=" C PRO D 115 " pdb=" N PRO D 116 " ideal model delta sigma weight residual 117.93 126.34 -8.41 1.20e+00 6.94e-01 4.91e+01 ... (remaining 20761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7827 17.78 - 35.55: 1076 35.55 - 53.33: 254 53.33 - 71.11: 53 71.11 - 88.88: 20 Dihedral angle restraints: 9230 sinusoidal: 3704 harmonic: 5526 Sorted by residual: dihedral pdb=" CA PRO F 115 " pdb=" C PRO F 115 " pdb=" N PRO F 116 " pdb=" CA PRO F 116 " ideal model delta harmonic sigma weight residual 180.00 135.36 44.64 0 5.00e+00 4.00e-02 7.97e+01 dihedral pdb=" CA GLY F 114 " pdb=" C GLY F 114 " pdb=" N PRO F 115 " pdb=" CA PRO F 115 " ideal model delta harmonic sigma weight residual -180.00 -135.49 -44.51 0 5.00e+00 4.00e-02 7.93e+01 dihedral pdb=" CA PRO E 115 " pdb=" C PRO E 115 " pdb=" N PRO E 116 " pdb=" CA PRO E 116 " ideal model delta harmonic sigma weight residual -180.00 -140.05 -39.95 0 5.00e+00 4.00e-02 6.39e+01 ... (remaining 9227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2135 0.083 - 0.166: 192 0.166 - 0.250: 14 0.250 - 0.333: 1 0.333 - 0.416: 1 Chirality restraints: 2343 Sorted by residual: chirality pdb=" CA PRO D 115 " pdb=" N PRO D 115 " pdb=" C PRO D 115 " pdb=" CB PRO D 115 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CG LEU F 330 " pdb=" CB LEU F 330 " pdb=" CD1 LEU F 330 " pdb=" CD2 LEU F 330 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA PRO E 116 " pdb=" N PRO E 116 " pdb=" C PRO E 116 " pdb=" CB PRO E 116 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2340 not shown) Planarity restraints: 2662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 114 " -0.098 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO E 115 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO E 115 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO E 115 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 115 " -0.084 5.00e-02 4.00e+02 1.27e-01 2.60e+01 pdb=" N PRO A 116 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 114 " -0.088 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO D 115 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO D 115 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 115 " -0.064 5.00e-02 4.00e+02 ... (remaining 2659 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3577 2.80 - 3.33: 12463 3.33 - 3.85: 23460 3.85 - 4.38: 24848 4.38 - 4.90: 45588 Nonbonded interactions: 109936 Sorted by model distance: nonbonded pdb=" OG SER D 280 " pdb=" OD2 ASP D 283 " model vdw 2.278 3.040 nonbonded pdb=" O SER E 305 " pdb=" OG SER E 305 " model vdw 2.285 3.040 nonbonded pdb=" OG SER E 280 " pdb=" OD1 ASP E 283 " model vdw 2.319 3.040 nonbonded pdb=" OH TYR D 182 " pdb=" OD2 ASP D 223 " model vdw 2.331 3.040 nonbonded pdb=" OG SER C 280 " pdb=" OD1 ASP C 283 " model vdw 2.341 3.040 ... (remaining 109931 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 186 or resid 193 through 228 or resid 240 throug \ h 247 or resid 251 through 317 or resid 325 through 337)) selection = (chain 'B' and (resid 5 through 186 or resid 193 through 228 or resid 240 throug \ h 247 or resid 251 through 337)) selection = (chain 'C' and (resid 5 through 228 or resid 240 through 247 or resid 251 throug \ h 317 or resid 325 through 337)) selection = (chain 'D' and (resid 5 through 186 or resid 193 through 228 or resid 240 throug \ h 247 or resid 251 through 317 or resid 325 through 337)) selection = (chain 'E' and (resid 5 through 228 or resid 240 through 317 or resid 325 throug \ h 337)) selection = (chain 'F' and (resid 5 through 186 or resid 193 through 247 or resid 251 throug \ h 317 or resid 325 through 337)) } 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: 2.570 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.140 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:8.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 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 : 0.005 0.180 15298 Z= 0.230 Angle : 0.942 17.363 20766 Z= 0.514 Chirality : 0.048 0.416 2343 Planarity : 0.009 0.147 2662 Dihedral : 17.331 88.883 5682 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.13 % Favored : 96.71 % Rotamer: Outliers : 1.30 % Allowed : 25.19 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 3.70 % 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: -0.09 (0.18), residues: 1854 helix: 0.51 (0.14), residues: 1074 sheet: 1.18 (0.42), residues: 142 loop : -1.23 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 95 TYR 0.036 0.001 TYR D 186 PHE 0.057 0.002 PHE D 221 TRP 0.006 0.001 TRP E 161 HIS 0.005 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 (15298) covalent geometry : angle 0.94221 / 0.51 (20766) hydrogen bonds : bond 0.13772 / 9.07 ( 859) hydrogen bonds : angle 5.34816 / 3.78 ( 2556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 18 residues processed: 135 average time/residue: 0.5005 time to fit residues: 75.8660 Evaluate side-chains 130 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain F residue 279 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN C 266 GLN D 306 GLN F 307 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.081695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.053780 restraints weight = 36175.407| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 3.67 r_work: 0.2527 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 15298 Z= 0.173 Angle : 0.615 12.393 20766 Z= 0.309 Chirality : 0.040 0.157 2343 Planarity : 0.007 0.151 2662 Dihedral : 5.458 83.369 2136 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.56 % Favored : 96.33 % Rotamer: Outliers : 2.85 % Allowed : 21.65 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.85 % 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: 1.67 (0.20), residues: 1854 helix: 2.26 (0.16), residues: 1089 sheet: 1.28 (0.41), residues: 147 loop : -1.13 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.015 0.001 TYR D 186 PHE 0.022 0.001 PHE D 221 TRP 0.007 0.001 TRP C 161 HIS 0.006 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (15298) covalent geometry : angle 0.61535 / 0.31 (20766) hydrogen bonds : bond 0.05402 / 3.64 ( 859) hydrogen bonds : angle 3.78036 / 2.68 ( 2556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 ASP cc_start: 0.8846 (t0) cc_final: 0.8548 (t0) REVERT: B 301 ASP cc_start: 0.8697 (t0) cc_final: 0.8493 (t0) REVERT: F 224 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8136 (mmtt) outliers start: 46 outliers final: 18 residues processed: 150 average time/residue: 0.4506 time to fit residues: 75.9847 Evaluate side-chains 122 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 279 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 58 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 175 optimal weight: 0.0870 chunk 159 optimal weight: 0.7980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.083468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.055432 restraints weight = 36274.715| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.73 r_work: 0.2569 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 15298 Z= 0.114 Angle : 0.565 11.626 20766 Z= 0.281 Chirality : 0.039 0.160 2343 Planarity : 0.006 0.147 2662 Dihedral : 4.835 81.267 2118 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.86 % Favored : 97.03 % Rotamer: Outliers : 1.99 % Allowed : 22.46 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.85 % 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: 2.20 (0.20), residues: 1854 helix: 2.75 (0.16), residues: 1091 sheet: 1.48 (0.41), residues: 160 loop : -1.12 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 191 TYR 0.008 0.001 TYR E 199 PHE 0.013 0.001 PHE D 221 TRP 0.007 0.001 TRP E 161 HIS 0.003 0.000 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.11 (15298) covalent geometry : angle 0.56482 / 0.28 (20766) hydrogen bonds : bond 0.04403 / 2.97 ( 859) hydrogen bonds : angle 3.56031 / 2.52 ( 2556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 ASP cc_start: 0.8778 (t0) cc_final: 0.8250 (t0) REVERT: B 223 ASP cc_start: 0.8893 (t0) cc_final: 0.8686 (t0) REVERT: B 301 ASP cc_start: 0.8622 (t0) cc_final: 0.8284 (t0) REVERT: C 86 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8334 (tpt-90) REVERT: F 224 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8198 (mmtt) outliers start: 32 outliers final: 14 residues processed: 138 average time/residue: 0.5470 time to fit residues: 84.3203 Evaluate side-chains 125 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 101 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN C 227 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 ASN E 218 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.055087 restraints weight = 36205.522| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.72 r_work: 0.2554 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 15298 Z= 0.120 Angle : 0.561 12.349 20766 Z= 0.276 Chirality : 0.039 0.256 2343 Planarity : 0.006 0.143 2662 Dihedral : 4.600 81.673 2114 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.13 % Favored : 96.76 % Rotamer: Outliers : 2.11 % Allowed : 22.77 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.85 % 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: 2.44 (0.20), residues: 1854 helix: 2.94 (0.16), residues: 1093 sheet: 1.41 (0.41), residues: 164 loop : -0.99 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 191 TYR 0.012 0.001 TYR F 186 PHE 0.021 0.001 PHE E 221 TRP 0.007 0.001 TRP E 161 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (15298) covalent geometry : angle 0.56138 / 0.28 (20766) hydrogen bonds : bond 0.04354 / 2.94 ( 859) hydrogen bonds : angle 3.46179 / 2.45 ( 2556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 301 ASP cc_start: 0.8859 (t0) cc_final: 0.8395 (t0) REVERT: B 301 ASP cc_start: 0.8667 (t0) cc_final: 0.8291 (t0) REVERT: C 86 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8291 (tpt-90) REVERT: C 282 GLU cc_start: 0.9172 (mp0) cc_final: 0.8871 (pm20) REVERT: C 283 ASP cc_start: 0.9003 (m-30) cc_final: 0.8646 (m-30) REVERT: F 224 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8093 (mmtt) outliers start: 34 outliers final: 15 residues processed: 142 average time/residue: 0.5503 time to fit residues: 87.0042 Evaluate side-chains 121 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 185 HIS Chi-restraints excluded: chain E residue 279 PHE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 279 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 149 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 134 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 185 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 227 GLN C 335 GLN E 211 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.084327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.056647 restraints weight = 36183.043| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.69 r_work: 0.2594 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 15298 Z= 0.104 Angle : 0.556 12.073 20766 Z= 0.275 Chirality : 0.038 0.192 2343 Planarity : 0.005 0.140 2662 Dihedral : 4.089 55.689 2111 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.70 % Favored : 97.20 % Rotamer: Outliers : 1.99 % Allowed : 22.64 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.85 % 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: 2.60 (0.20), residues: 1854 helix: 3.09 (0.16), residues: 1093 sheet: 1.46 (0.40), residues: 164 loop : -0.95 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 334 TYR 0.006 0.001 TYR E 199 PHE 0.015 0.001 PHE E 221 TRP 0.008 0.001 TRP C 161 HIS 0.002 0.000 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.10 (15298) covalent geometry : angle 0.55554 / 0.27 (20766) hydrogen bonds : bond 0.03795 / 2.56 ( 859) hydrogen bonds : angle 3.32678 / 2.36 ( 2556) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 ASP cc_start: 0.8825 (t0) cc_final: 0.8331 (t0) REVERT: B 301 ASP cc_start: 0.8600 (t0) cc_final: 0.8215 (t0) REVERT: C 86 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8260 (tpt-90) REVERT: C 174 GLU cc_start: 0.8946 (mp0) cc_final: 0.8632 (mp0) REVERT: C 282 GLU cc_start: 0.9152 (mp0) cc_final: 0.8778 (pm20) REVERT: D 119 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7656 (ptmm) REVERT: F 224 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8360 (mmtt) outliers start: 32 outliers final: 16 residues processed: 135 average time/residue: 0.5522 time to fit residues: 82.9898 Evaluate side-chains 123 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 279 PHE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 96 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 227 GLN C 335 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.084348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.056733 restraints weight = 36009.422| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.69 r_work: 0.2595 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 15298 Z= 0.108 Angle : 0.564 12.867 20766 Z= 0.278 Chirality : 0.038 0.199 2343 Planarity : 0.005 0.137 2662 Dihedral : 4.022 53.514 2111 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.13 % Favored : 96.76 % Rotamer: Outliers : 1.99 % Allowed : 22.64 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.85 % 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: 2.72 (0.20), residues: 1854 helix: 3.20 (0.16), residues: 1093 sheet: 1.53 (0.40), residues: 160 loop : -0.92 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 253 TYR 0.012 0.001 TYR D 186 PHE 0.025 0.001 PHE C 221 TRP 0.006 0.001 TRP A 161 HIS 0.003 0.000 HIS C 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (15298) covalent geometry : angle 0.56438 / 0.28 (20766) hydrogen bonds : bond 0.03751 / 2.53 ( 859) hydrogen bonds : angle 3.27789 / 2.32 ( 2556) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8385 (mm) REVERT: A 301 ASP cc_start: 0.8850 (t0) cc_final: 0.8373 (t0) REVERT: B 301 ASP cc_start: 0.8611 (t0) cc_final: 0.8202 (t0) REVERT: C 174 GLU cc_start: 0.8908 (mp0) cc_final: 0.8603 (mp0) REVERT: C 282 GLU cc_start: 0.9142 (mp0) cc_final: 0.8715 (pm20) REVERT: C 283 ASP cc_start: 0.8915 (m-30) cc_final: 0.8548 (m-30) REVERT: D 119 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7643 (ptmm) REVERT: E 246 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8482 (tp30) REVERT: F 224 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8191 (mmtt) outliers start: 32 outliers final: 14 residues processed: 137 average time/residue: 0.5245 time to fit residues: 80.4907 Evaluate side-chains 122 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 279 PHE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 164 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 GLN C 227 GLN F 307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.082516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.054668 restraints weight = 36099.996| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 3.68 r_work: 0.2543 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 15298 Z= 0.146 Angle : 0.592 9.787 20766 Z= 0.290 Chirality : 0.040 0.267 2343 Planarity : 0.005 0.135 2662 Dihedral : 3.846 38.037 2109 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.13 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 22.95 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.85 % 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: 2.81 (0.20), residues: 1854 helix: 3.26 (0.16), residues: 1094 sheet: 1.77 (0.41), residues: 152 loop : -0.90 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.008 0.001 TYR E 106 PHE 0.020 0.001 PHE C 221 TRP 0.006 0.001 TRP C 161 HIS 0.005 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (15298) covalent geometry : angle 0.59180 / 0.29 (20766) hydrogen bonds : bond 0.04505 / 3.04 ( 859) hydrogen bonds : angle 3.38289 / 2.39 ( 2556) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.610 Fit side-chains REVERT: A 189 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8416 (mm) REVERT: A 301 ASP cc_start: 0.8969 (t0) cc_final: 0.8445 (t0) REVERT: B 301 ASP cc_start: 0.8734 (t0) cc_final: 0.8340 (t0) REVERT: C 86 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8259 (tpt-90) REVERT: C 174 GLU cc_start: 0.8889 (mp0) cc_final: 0.8571 (mp0) REVERT: E 246 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8502 (tp30) REVERT: F 224 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8284 (mmtt) outliers start: 30 outliers final: 16 residues processed: 135 average time/residue: 0.4803 time to fit residues: 72.8312 Evaluate side-chains 123 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 185 HIS Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 171 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 77 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 136 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 227 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.055399 restraints weight = 36150.970| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.69 r_work: 0.2566 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 15298 Z= 0.118 Angle : 0.581 9.524 20766 Z= 0.287 Chirality : 0.039 0.214 2343 Planarity : 0.005 0.133 2662 Dihedral : 3.850 38.166 2109 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 1.86 % Allowed : 23.26 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.85 % 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: 2.89 (0.20), residues: 1854 helix: 3.32 (0.16), residues: 1093 sheet: 1.87 (0.41), residues: 152 loop : -0.87 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.018 0.001 TYR F 186 PHE 0.019 0.001 PHE C 221 TRP 0.007 0.001 TRP C 161 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (15298) covalent geometry : angle 0.58060 / 0.29 (20766) hydrogen bonds : bond 0.04091 / 2.77 ( 859) hydrogen bonds : angle 3.29939 / 2.34 ( 2556) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.540 Fit side-chains REVERT: A 189 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8369 (mm) REVERT: A 223 ASP cc_start: 0.8858 (t0) cc_final: 0.8482 (t0) REVERT: A 259 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9007 (mm) REVERT: A 301 ASP cc_start: 0.8975 (t0) cc_final: 0.8463 (t0) REVERT: B 301 ASP cc_start: 0.8738 (t0) cc_final: 0.8355 (t0) REVERT: C 86 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8250 (tpt-90) REVERT: C 119 LYS cc_start: 0.8280 (ptpp) cc_final: 0.7890 (pmmt) REVERT: C 174 GLU cc_start: 0.8877 (mp0) cc_final: 0.8537 (mp0) REVERT: C 216 ASP cc_start: 0.8940 (t0) cc_final: 0.8460 (t0) REVERT: D 119 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7597 (ptmm) REVERT: E 246 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8495 (tp30) REVERT: F 224 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8161 (mmtt) outliers start: 30 outliers final: 12 residues processed: 136 average time/residue: 0.5231 time to fit residues: 79.5761 Evaluate side-chains 123 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 171 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 59 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 ASN C 227 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 ASN F 307 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.083680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.056172 restraints weight = 36227.642| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.70 r_work: 0.2584 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 15298 Z= 0.116 Angle : 0.600 10.119 20766 Z= 0.297 Chirality : 0.039 0.304 2343 Planarity : 0.005 0.131 2662 Dihedral : 3.799 37.558 2109 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.97 % Favored : 96.93 % Rotamer: Outliers : 1.36 % Allowed : 24.13 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.85 % 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: 2.92 (0.20), residues: 1854 helix: 3.35 (0.16), residues: 1094 sheet: 1.92 (0.41), residues: 152 loop : -0.88 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.016 0.001 TYR F 186 PHE 0.017 0.001 PHE C 221 TRP 0.006 0.001 TRP C 161 HIS 0.003 0.000 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (15298) covalent geometry : angle 0.59963 / 0.30 (20766) hydrogen bonds : bond 0.03862 / 2.61 ( 859) hydrogen bonds : angle 3.26512 / 2.31 ( 2556) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8408 (mm) REVERT: A 223 ASP cc_start: 0.8884 (t0) cc_final: 0.8452 (t0) REVERT: A 224 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8554 (ttmm) REVERT: A 301 ASP cc_start: 0.8988 (t0) cc_final: 0.8477 (t0) REVERT: B 301 ASP cc_start: 0.8777 (t0) cc_final: 0.8400 (t0) REVERT: C 86 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8232 (tpt-90) REVERT: C 174 GLU cc_start: 0.8869 (mp0) cc_final: 0.8520 (mp0) REVERT: C 216 ASP cc_start: 0.8929 (t0) cc_final: 0.8502 (t0) REVERT: D 119 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7552 (ptmm) REVERT: E 246 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8493 (tp30) REVERT: F 224 LYS cc_start: 0.8475 (mmmt) cc_final: 0.8113 (mmtt) outliers start: 22 outliers final: 10 residues processed: 127 average time/residue: 0.4565 time to fit residues: 64.9649 Evaluate side-chains 120 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 171 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 182 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 35 optimal weight: 0.1980 chunk 109 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 ASN C 227 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.056874 restraints weight = 36107.204| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.69 r_work: 0.2600 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 15298 Z= 0.111 Angle : 0.596 9.740 20766 Z= 0.295 Chirality : 0.038 0.296 2343 Planarity : 0.005 0.129 2662 Dihedral : 3.759 37.210 2109 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.18 % Favored : 96.71 % Rotamer: Outliers : 1.18 % Allowed : 24.32 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.85 % 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: 2.96 (0.20), residues: 1854 helix: 3.38 (0.16), residues: 1094 sheet: 1.89 (0.41), residues: 153 loop : -0.85 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 310 TYR 0.017 0.001 TYR D 186 PHE 0.017 0.001 PHE C 221 TRP 0.006 0.001 TRP A 161 HIS 0.002 0.000 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (15298) covalent geometry : angle 0.59623 / 0.30 (20766) hydrogen bonds : bond 0.03619 / 2.44 ( 859) hydrogen bonds : angle 3.23183 / 2.29 ( 2556) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8662 (m-80) cc_final: 0.8443 (m-80) REVERT: A 189 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8409 (mm) REVERT: A 223 ASP cc_start: 0.8946 (t0) cc_final: 0.8431 (t0) REVERT: A 224 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8533 (ttmm) REVERT: A 301 ASP cc_start: 0.8976 (t0) cc_final: 0.8490 (t0) REVERT: B 223 ASP cc_start: 0.8737 (t0) cc_final: 0.8329 (t0) REVERT: B 301 ASP cc_start: 0.8748 (t0) cc_final: 0.8386 (t0) REVERT: C 86 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8231 (tpt-90) REVERT: C 174 GLU cc_start: 0.8863 (mp0) cc_final: 0.8514 (mp0) REVERT: C 216 ASP cc_start: 0.8893 (t0) cc_final: 0.8416 (t0) REVERT: D 119 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7634 (ptmm) REVERT: D 296 GLU cc_start: 0.8918 (tp30) cc_final: 0.8665 (tm-30) REVERT: E 246 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8488 (tp30) outliers start: 19 outliers final: 11 residues processed: 125 average time/residue: 0.4845 time to fit residues: 67.3755 Evaluate side-chains 122 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 88 optimal weight: 0.2980 chunk 184 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN F 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.055446 restraints weight = 36095.525| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.69 r_work: 0.2560 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 15298 Z= 0.137 Angle : 0.624 12.305 20766 Z= 0.306 Chirality : 0.040 0.349 2343 Planarity : 0.005 0.128 2662 Dihedral : 3.787 36.865 2109 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.55 % Rotamer: Outliers : 1.24 % Allowed : 24.19 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.93 % 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: 2.99 (0.20), residues: 1854 helix: 3.41 (0.16), residues: 1094 sheet: 1.91 (0.41), residues: 154 loop : -0.86 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 191 TYR 0.015 0.001 TYR F 186 PHE 0.016 0.001 PHE C 221 TRP 0.006 0.001 TRP C 161 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (15298) covalent geometry : angle 0.62352 / 0.31 (20766) hydrogen bonds : bond 0.04211 / 2.84 ( 859) hydrogen bonds : angle 3.32786 / 2.35 ( 2556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3630.60 seconds wall clock time: 62 minutes 49.33 seconds (3769.33 seconds total)