Starting phenix.real_space_refine on Wed Jan 14 21:01:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y3t_33598/01_2026/7y3t_33598.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y3t_33598/01_2026/7y3t_33598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y3t_33598/01_2026/7y3t_33598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y3t_33598/01_2026/7y3t_33598.map" model { file = "/net/cci-nas-00/data/ceres_data/7y3t_33598/01_2026/7y3t_33598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y3t_33598/01_2026/7y3t_33598.cif" } resolution = 3.9 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 12176 2.51 5 N 3343 2.21 5 O 3810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19378 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2704 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain breaks: 1 Chain: "A" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2779 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 15, 'TRANS': 345} Chain: "B" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2779 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 15, 'TRANS': 345} Chain: "C" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2779 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 15, 'TRANS': 345} Chain: "D" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2779 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 15, 'TRANS': 345} Chain: "E" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2779 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 15, 'TRANS': 345} Chain: "F" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2779 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 15, 'TRANS': 345} Time building chain proxies: 4.51, per 1000 atoms: 0.23 Number of scatterers: 19378 At special positions: 0 Unit cell: (175.5, 234, 136.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 3810 8.00 N 3343 7.00 C 12176 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: 1.45 Conformation dependent library (CDL) restraints added in 749.0 milliseconds 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4740 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 27 sheets defined 25.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'G' and resid 39 through 44 Processing helix chain 'G' and resid 99 through 105 Processing helix chain 'G' and resid 110 through 141 removed outlier: 3.646A pdb=" N LYS G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 148 removed outlier: 3.694A pdb=" N ARG G 147 " --> pdb=" O THR G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 188 removed outlier: 3.639A pdb=" N LEU G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 211 removed outlier: 3.611A pdb=" N ALA G 207 " --> pdb=" O LYS G 203 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP G 210 " --> pdb=" O ASN G 206 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N MET G 211 " --> pdb=" O ALA G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 353 removed outlier: 3.797A pdb=" N LYS G 350 " --> pdb=" O THR G 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 removed outlier: 3.682A pdb=" N HIS A 43 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 142 removed outlier: 3.545A pdb=" N LYS A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 171 through 189 removed outlier: 4.033A pdb=" N LEU A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 210 removed outlier: 3.508A pdb=" N ALA A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 320 through 323 Processing helix chain 'B' and resid 39 through 43 removed outlier: 3.650A pdb=" N HIS B 43 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 141 removed outlier: 3.673A pdb=" N LYS B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'B' and resid 171 through 189 removed outlier: 3.527A pdb=" N LEU B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 210 removed outlier: 3.660A pdb=" N ALA B 207 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 344 through 355 removed outlier: 3.512A pdb=" N VAL B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 43 removed outlier: 3.577A pdb=" N HIS C 43 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 142 removed outlier: 3.510A pdb=" N LYS C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN C 142 " --> pdb=" O GLY C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 189 removed outlier: 3.946A pdb=" N LEU C 175 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 210 removed outlier: 3.685A pdb=" N ALA C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 320 through 323 Processing helix chain 'C' and resid 344 through 353 Processing helix chain 'D' and resid 39 through 43 removed outlier: 3.858A pdb=" N SER D 42 " --> pdb=" O ASN D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 111 through 142 removed outlier: 3.548A pdb=" N ASN D 142 " --> pdb=" O GLY D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 189 removed outlier: 3.799A pdb=" N LEU D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 210 removed outlier: 3.633A pdb=" N ASP D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 216 Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.733A pdb=" N MET D 272 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 355 removed outlier: 3.640A pdb=" N VAL D 348 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 105 removed outlier: 3.767A pdb=" N GLN E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 141 removed outlier: 3.736A pdb=" N LYS E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 148 Processing helix chain 'E' and resid 171 through 188 removed outlier: 3.782A pdb=" N LEU E 175 " --> pdb=" O SER E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 210 Processing helix chain 'E' and resid 211 through 216 Processing helix chain 'E' and resid 225 through 229 Processing helix chain 'E' and resid 269 through 273 removed outlier: 3.772A pdb=" N MET E 272 " --> pdb=" O THR E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 346 removed outlier: 3.699A pdb=" N ASP E 345 " --> pdb=" O GLY E 342 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR E 346 " --> pdb=" O ALA E 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 342 through 346' Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.508A pdb=" N SER F 42 " --> pdb=" O ASN F 39 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS F 43 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 142 removed outlier: 4.299A pdb=" N ASN F 142 " --> pdb=" O GLY F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 171 removed outlier: 4.118A pdb=" N GLU F 169 " --> pdb=" O ALA F 165 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER F 171 " --> pdb=" O THR F 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 165 through 171' Processing helix chain 'F' and resid 171 through 189 removed outlier: 4.002A pdb=" N LEU F 175 " --> pdb=" O SER F 171 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 210 removed outlier: 3.501A pdb=" N ALA F 207 " --> pdb=" O LYS F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 216 Processing helix chain 'F' and resid 269 through 273 removed outlier: 3.651A pdb=" N MET F 272 " --> pdb=" O THR F 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 54 through 56 Processing sheet with id=AA2, first strand: chain 'G' and resid 93 through 94 removed outlier: 3.779A pdb=" N TYR G 311 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR G 294 " --> pdb=" O TYR G 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 159 through 160 removed outlier: 6.891A pdb=" N ILE G 159 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE G 198 " --> pdb=" O VAL G 240 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE G 230 " --> pdb=" O VAL G 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 285 through 289 Processing sheet with id=AA5, first strand: chain 'A' and resid 25 through 31 removed outlier: 6.752A pdb=" N THR B 54 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASN A 27 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N SER B 56 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LYS A 29 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS B 58 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP B 82 " --> pdb=" O TYR B 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 87 Processing sheet with id=AA7, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.682A pdb=" N THR F 305 " --> pdb=" O GLU F 300 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR F 311 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR F 294 " --> pdb=" O TYR F 311 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA F 313 " --> pdb=" O GLU F 292 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU F 292 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N GLY F 315 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N THR F 290 " --> pdb=" O GLY F 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 288 through 296 removed outlier: 7.626A pdb=" N THR A 290 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N GLY A 315 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU A 292 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ALA A 313 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 294 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 288 through 296 removed outlier: 7.626A pdb=" N THR A 290 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N GLY A 315 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU A 292 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ALA A 313 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 294 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 159 through 163 removed outlier: 6.393A pdb=" N ILE A 159 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR A 328 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL A 161 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR A 329 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ALA A 275 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE A 198 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 357 through 359 removed outlier: 4.018A pdb=" N ILE A 357 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 30 through 31 Processing sheet with id=AB4, first strand: chain 'B' and resid 47 through 48 removed outlier: 7.987A pdb=" N GLY B 288 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ILE B 317 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR B 290 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N GLY B 315 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLU B 292 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ALA B 313 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR B 305 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR B 91 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 159 through 163 removed outlier: 3.737A pdb=" N ILE B 159 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE B 198 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 237 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.599A pdb=" N LEU D 60 " --> pdb=" O ARG C 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.795A pdb=" N ARG C 289 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY C 288 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE C 317 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR C 290 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N GLY C 315 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU C 292 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ALA C 313 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR C 91 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 159 through 160 removed outlier: 6.484A pdb=" N ILE C 159 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE C 198 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 25 through 31 removed outlier: 3.611A pdb=" N LYS D 25 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 56 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN D 27 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N LYS E 58 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS D 29 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU E 60 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG D 31 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 55 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP E 82 " --> pdb=" O TYR E 59 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 47 through 48 removed outlier: 5.950A pdb=" N GLU D 47 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ILE D 291 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR D 290 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA D 313 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU D 292 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR D 311 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 161 through 162 removed outlier: 5.843A pdb=" N VAL D 161 " --> pdb=" O THR D 328 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 230 through 232 removed outlier: 6.277A pdb=" N ILE D 198 " --> pdb=" O VAL D 240 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 46 through 48 removed outlier: 6.580A pdb=" N GLU E 47 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ILE E 291 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA E 313 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLU E 292 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR E 311 " --> pdb=" O GLU E 292 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR E 294 " --> pdb=" O ASP E 309 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP E 309 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP E 296 " --> pdb=" O TYR E 307 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR E 307 " --> pdb=" O ASP E 296 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 161 through 163 removed outlier: 6.004A pdb=" N VAL E 161 " --> pdb=" O THR E 328 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 231 through 232 removed outlier: 3.604A pdb=" N MET E 200 " --> pdb=" O VAL E 240 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 358 through 359 Processing sheet with id=AC8, first strand: chain 'F' and resid 54 through 57 Processing sheet with id=AC9, first strand: chain 'F' and resid 159 through 163 removed outlier: 4.086A pdb=" N VAL F 327 " --> pdb=" O ALA F 277 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA F 277 " --> pdb=" O VAL F 327 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE F 198 " --> pdb=" O VAL F 240 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 1.96 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: 6536 1.34 - 1.46: 2929 1.46 - 1.57: 10142 1.57 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 19705 Sorted by residual: bond pdb=" N THR A 346 " pdb=" CA THR A 346 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.60e+00 bond pdb=" CA ARG D 320 " pdb=" C ARG D 320 " ideal model delta sigma weight residual 1.523 1.503 0.020 1.23e-02 6.61e+03 2.55e+00 bond pdb=" CA GLU D 62 " pdb=" C GLU D 62 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.82e+00 bond pdb=" C GLU A 300 " pdb=" N LYS A 301 " ideal model delta sigma weight residual 1.335 1.318 0.017 1.36e-02 5.41e+03 1.61e+00 bond pdb=" C THR D 77 " pdb=" N PRO D 78 " ideal model delta sigma weight residual 1.328 1.344 -0.015 1.26e-02 6.30e+03 1.51e+00 ... (remaining 19700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 26257 2.35 - 4.70: 475 4.70 - 7.04: 47 7.04 - 9.39: 13 9.39 - 11.74: 8 Bond angle restraints: 26800 Sorted by residual: angle pdb=" N VAL A 347 " pdb=" CA VAL A 347 " pdb=" C VAL A 347 " ideal model delta sigma weight residual 110.72 98.98 11.74 1.01e+00 9.80e-01 1.35e+02 angle pdb=" C SER D 73 " pdb=" N PRO D 74 " pdb=" CA PRO D 74 " ideal model delta sigma weight residual 119.76 127.62 -7.86 1.03e+00 9.43e-01 5.82e+01 angle pdb=" C ASP F 337 " pdb=" N PRO F 338 " pdb=" CA PRO F 338 " ideal model delta sigma weight residual 119.76 126.56 -6.80 1.00e+00 1.00e+00 4.62e+01 angle pdb=" N GLU D 62 " pdb=" CA GLU D 62 " pdb=" C GLU D 62 " ideal model delta sigma weight residual 110.91 118.73 -7.82 1.17e+00 7.31e-01 4.47e+01 angle pdb=" C ASP A 345 " pdb=" N THR A 346 " pdb=" CA THR A 346 " ideal model delta sigma weight residual 121.54 133.07 -11.53 1.91e+00 2.74e-01 3.64e+01 ... (remaining 26795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10821 17.97 - 35.93: 906 35.93 - 53.90: 169 53.90 - 71.86: 44 71.86 - 89.83: 19 Dihedral angle restraints: 11959 sinusoidal: 4655 harmonic: 7304 Sorted by residual: dihedral pdb=" CA GLU D 62 " pdb=" C GLU D 62 " pdb=" N THR D 63 " pdb=" CA THR D 63 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ILE G 308 " pdb=" C ILE G 308 " pdb=" N ASP G 309 " pdb=" CA ASP G 309 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU F 22 " pdb=" C LEU F 22 " pdb=" N ILE F 23 " pdb=" CA ILE F 23 " ideal model delta harmonic sigma weight residual 180.00 -158.68 -21.32 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 11956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2599 0.059 - 0.118: 493 0.118 - 0.178: 78 0.178 - 0.237: 5 0.237 - 0.296: 3 Chirality restraints: 3178 Sorted by residual: chirality pdb=" CA VAL A 347 " pdb=" N VAL A 347 " pdb=" C VAL A 347 " pdb=" CB VAL A 347 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA GLU D 62 " pdb=" N GLU D 62 " pdb=" C GLU D 62 " pdb=" CB GLU D 62 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA LYS A 301 " pdb=" N LYS A 301 " pdb=" C LYS A 301 " pdb=" CB LYS A 301 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 3175 not shown) Planarity restraints: 3493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 354 " -0.250 9.50e-02 1.11e+02 1.12e-01 8.29e+00 pdb=" NE ARG B 354 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 354 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 354 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 354 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 319 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C ASP D 319 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP D 319 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG D 320 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 342 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C GLY A 342 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY A 342 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA A 343 " 0.013 2.00e-02 2.50e+03 ... (remaining 3490 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 254 2.62 - 3.19: 18036 3.19 - 3.76: 27117 3.76 - 4.33: 36653 4.33 - 4.90: 61761 Nonbonded interactions: 143821 Sorted by model distance: nonbonded pdb=" OE1 GLU G 62 " pdb=" O THR G 63 " model vdw 2.052 3.040 nonbonded pdb=" N GLN A 173 " pdb=" OE1 GLN A 173 " model vdw 2.078 3.120 nonbonded pdb=" N GLU C 24 " pdb=" OE1 GLU C 24 " model vdw 2.148 3.120 nonbonded pdb=" OD1 ASP A 82 " pdb=" N LYS A 83 " model vdw 2.202 3.120 nonbonded pdb=" O TRP D 321 " pdb=" CB GLU D 322 " model vdw 2.206 3.440 ... (remaining 143816 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 2 through 217 or resid 228 through 362)) selection = (chain 'B' and (resid 2 through 217 or resid 228 through 362)) selection = (chain 'C' and (resid 2 through 217 or resid 228 through 362)) selection = (chain 'D' and (resid 2 through 217 or resid 228 through 362)) selection = (chain 'E' and (resid 2 through 217 or resid 228 through 362)) selection = (chain 'F' and (resid 2 through 217 or resid 228 through 362)) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 88.110 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.500 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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 : 0.004 0.036 19705 Z= 0.190 Angle : 0.790 11.740 26800 Z= 0.459 Chirality : 0.048 0.296 3178 Planarity : 0.005 0.112 3493 Dihedral : 14.407 89.826 7219 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.44 % Favored : 91.36 % Rotamer: Outliers : 0.14 % Allowed : 0.61 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.16), residues: 2501 helix: 1.23 (0.22), residues: 556 sheet: -0.67 (0.21), residues: 600 loop : -2.12 (0.14), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 354 TYR 0.036 0.002 TYR D 174 PHE 0.021 0.002 PHE C 26 TRP 0.026 0.002 TRP A 299 HIS 0.009 0.001 HIS G 255 Details of bonding type rmsd covalent geometry : bond 0.00382 (19705) covalent geometry : angle 0.79015 (26800) hydrogen bonds : bond 0.17320 ( 597) hydrogen bonds : angle 6.09795 ( 1626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 419 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 29 LYS cc_start: 0.6580 (OUTLIER) cc_final: 0.5899 (pttp) REVERT: G 217 ARG cc_start: 0.7449 (ptm-80) cc_final: 0.7221 (ppt170) REVERT: A 52 THR cc_start: 0.8982 (m) cc_final: 0.8601 (p) REVERT: A 301 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8163 (tttm) REVERT: A 311 TYR cc_start: 0.9507 (p90) cc_final: 0.9217 (p90) REVERT: B 17 GLU cc_start: 0.5505 (pt0) cc_final: 0.4317 (mm-30) REVERT: B 82 ASP cc_start: 0.8485 (t70) cc_final: 0.8065 (t0) REVERT: B 127 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7107 (mt-10) REVERT: B 319 ASP cc_start: 0.8471 (t70) cc_final: 0.8251 (t0) REVERT: C 19 ASP cc_start: 0.7839 (m-30) cc_final: 0.7619 (m-30) REVERT: C 80 LYS cc_start: 0.8687 (mmtp) cc_final: 0.7767 (mmmt) REVERT: C 181 TYR cc_start: 0.8931 (t80) cc_final: 0.8227 (t80) REVERT: C 272 MET cc_start: 0.8832 (ptp) cc_final: 0.8612 (ptt) REVERT: C 282 MET cc_start: 0.8794 (tmm) cc_final: 0.8294 (tmm) REVERT: D 136 MET cc_start: 0.9028 (tpp) cc_final: 0.8693 (mmm) REVERT: D 159 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8507 (tp) REVERT: D 185 GLN cc_start: 0.8546 (tt0) cc_final: 0.7755 (tt0) REVERT: E 89 ASP cc_start: 0.6785 (t0) cc_final: 0.6454 (t0) REVERT: E 200 MET cc_start: 0.8850 (mtp) cc_final: 0.8478 (mtp) REVERT: E 247 LYS cc_start: 0.8484 (ttmm) cc_final: 0.8233 (ttmm) outliers start: 3 outliers final: 0 residues processed: 420 average time/residue: 0.1265 time to fit residues: 85.2470 Evaluate side-chains 294 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain D residue 159 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN G 255 HIS A 118 ASN B 250 GLN C 33 GLN D 259 ASN E 149 ASN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 332 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.107137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.097676 restraints weight = 32775.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.099590 restraints weight = 19968.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.100888 restraints weight = 13646.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.101879 restraints weight = 10084.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.102592 restraints weight = 7795.428| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19705 Z= 0.138 Angle : 0.643 11.350 26800 Z= 0.338 Chirality : 0.046 0.177 3178 Planarity : 0.004 0.051 3493 Dihedral : 5.192 33.783 2675 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.56 % Favored : 92.32 % Rotamer: Outliers : 1.18 % Allowed : 10.35 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.16), residues: 2501 helix: 1.55 (0.22), residues: 578 sheet: -0.63 (0.21), residues: 620 loop : -2.11 (0.15), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 354 TYR 0.023 0.001 TYR D 174 PHE 0.017 0.001 PHE D 204 TRP 0.015 0.001 TRP A 299 HIS 0.007 0.001 HIS G 255 Details of bonding type rmsd covalent geometry : bond 0.00299 (19705) covalent geometry : angle 0.64277 (26800) hydrogen bonds : bond 0.04779 ( 597) hydrogen bonds : angle 5.00185 ( 1626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 349 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: G 41 LEU cc_start: 0.8422 (tp) cc_final: 0.8159 (tt) REVERT: G 124 LYS cc_start: 0.8997 (tppt) cc_final: 0.8266 (mttt) REVERT: G 190 GLU cc_start: 0.8113 (mp0) cc_final: 0.7364 (tt0) REVERT: A 52 THR cc_start: 0.8929 (m) cc_final: 0.8534 (p) REVERT: A 192 ASP cc_start: 0.8497 (t0) cc_final: 0.8165 (t0) REVERT: A 240 VAL cc_start: 0.9425 (t) cc_final: 0.9080 (m) REVERT: A 301 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8039 (tttt) REVERT: A 311 TYR cc_start: 0.9310 (p90) cc_final: 0.8923 (p90) REVERT: B 17 GLU cc_start: 0.5314 (pt0) cc_final: 0.4442 (mm-30) REVERT: C 80 LYS cc_start: 0.8642 (mmtp) cc_final: 0.7764 (mmmt) REVERT: C 181 TYR cc_start: 0.8992 (t80) cc_final: 0.8350 (t80) REVERT: C 282 MET cc_start: 0.8654 (tmm) cc_final: 0.8161 (tmm) REVERT: D 301 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8070 (pttt) REVERT: E 89 ASP cc_start: 0.6682 (t0) cc_final: 0.6328 (t0) REVERT: E 130 MET cc_start: 0.8803 (tmm) cc_final: 0.8503 (tmm) REVERT: E 247 LYS cc_start: 0.8355 (ttmm) cc_final: 0.8084 (ttmm) REVERT: F 283 ASP cc_start: 0.8285 (p0) cc_final: 0.7974 (p0) outliers start: 25 outliers final: 18 residues processed: 362 average time/residue: 0.1230 time to fit residues: 72.0830 Evaluate side-chains 314 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 296 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain F residue 257 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 113 optimal weight: 20.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN A 118 ASN B 84 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.105513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.096049 restraints weight = 33109.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.097976 restraints weight = 20279.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.099321 restraints weight = 13776.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.100279 restraints weight = 10066.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.100972 restraints weight = 7789.672| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19705 Z= 0.146 Angle : 0.617 11.800 26800 Z= 0.325 Chirality : 0.045 0.178 3178 Planarity : 0.004 0.047 3493 Dihedral : 4.982 22.550 2669 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.72 % Favored : 92.16 % Rotamer: Outliers : 2.73 % Allowed : 13.55 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.16), residues: 2501 helix: 1.61 (0.22), residues: 577 sheet: -0.64 (0.21), residues: 621 loop : -2.13 (0.15), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.015 0.001 TYR D 174 PHE 0.016 0.001 PHE D 204 TRP 0.016 0.001 TRP A 299 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00329 (19705) covalent geometry : angle 0.61743 (26800) hydrogen bonds : bond 0.04689 ( 597) hydrogen bonds : angle 4.79409 ( 1626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 316 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: G 38 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7413 (mm-30) REVERT: G 41 LEU cc_start: 0.8488 (tp) cc_final: 0.8132 (tt) REVERT: G 124 LYS cc_start: 0.9023 (tppt) cc_final: 0.8294 (mttt) REVERT: G 190 GLU cc_start: 0.8140 (mp0) cc_final: 0.7415 (tt0) REVERT: A 52 THR cc_start: 0.9011 (m) cc_final: 0.8651 (p) REVERT: A 100 MET cc_start: 0.7711 (ttp) cc_final: 0.7490 (ttp) REVERT: A 195 ASP cc_start: 0.8407 (p0) cc_final: 0.8135 (p0) REVERT: A 240 VAL cc_start: 0.9389 (t) cc_final: 0.9077 (m) REVERT: A 311 TYR cc_start: 0.9323 (p90) cc_final: 0.8887 (p90) REVERT: B 17 GLU cc_start: 0.5290 (pt0) cc_final: 0.4402 (mm-30) REVERT: B 65 ILE cc_start: 0.9496 (mt) cc_final: 0.9272 (mm) REVERT: B 84 ASN cc_start: 0.8984 (OUTLIER) cc_final: 0.8783 (t0) REVERT: B 301 LYS cc_start: 0.6732 (tmtt) cc_final: 0.6513 (tmtt) REVERT: C 80 LYS cc_start: 0.8685 (mmtp) cc_final: 0.7643 (mtpt) REVERT: C 181 TYR cc_start: 0.8992 (t80) cc_final: 0.8343 (t80) REVERT: C 210 ASP cc_start: 0.8036 (t0) cc_final: 0.7792 (m-30) REVERT: C 221 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9192 (pp) REVERT: C 282 MET cc_start: 0.8656 (tmm) cc_final: 0.8164 (tmm) REVERT: C 311 TYR cc_start: 0.8990 (p90) cc_final: 0.8629 (p90) REVERT: C 358 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8734 (tt) REVERT: D 223 ASP cc_start: 0.7706 (t0) cc_final: 0.7295 (t0) REVERT: D 242 SER cc_start: 0.9496 (t) cc_final: 0.9255 (t) REVERT: E 89 ASP cc_start: 0.6827 (t0) cc_final: 0.6457 (t0) REVERT: E 130 MET cc_start: 0.8788 (tmm) cc_final: 0.8411 (tmm) REVERT: E 200 MET cc_start: 0.8835 (mtp) cc_final: 0.8583 (mtp) REVERT: E 221 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8753 (pp) REVERT: E 247 LYS cc_start: 0.8407 (ttmm) cc_final: 0.8117 (ttmm) REVERT: E 302 LYS cc_start: 0.5690 (mmtt) cc_final: 0.5193 (mmtm) REVERT: F 136 MET cc_start: 0.9341 (tpp) cc_final: 0.9088 (mmm) REVERT: F 283 ASP cc_start: 0.8230 (p0) cc_final: 0.8018 (p0) outliers start: 58 outliers final: 31 residues processed: 357 average time/residue: 0.1201 time to fit residues: 70.6112 Evaluate side-chains 325 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 290 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain G residue 321 TRP Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 321 TRP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 71 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 218 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 39 optimal weight: 0.0970 chunk 153 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN A 186 GLN A 250 GLN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN D 259 ASN F 119 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.102511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.092765 restraints weight = 33374.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.094712 restraints weight = 20442.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.096063 restraints weight = 13963.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.097035 restraints weight = 10278.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.097735 restraints weight = 7992.531| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19705 Z= 0.169 Angle : 0.633 11.900 26800 Z= 0.332 Chirality : 0.046 0.181 3178 Planarity : 0.004 0.050 3493 Dihedral : 5.042 27.036 2669 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.12 % Favored : 91.76 % Rotamer: Outliers : 3.06 % Allowed : 15.57 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.29 (0.16), residues: 2501 helix: 1.57 (0.22), residues: 577 sheet: -0.72 (0.21), residues: 623 loop : -2.16 (0.15), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 265 TYR 0.016 0.001 TYR D 174 PHE 0.015 0.002 PHE D 204 TRP 0.016 0.002 TRP A 299 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00396 (19705) covalent geometry : angle 0.63255 (26800) hydrogen bonds : bond 0.04935 ( 597) hydrogen bonds : angle 4.79641 ( 1626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 305 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 124 LYS cc_start: 0.9037 (tppt) cc_final: 0.8361 (mttt) REVERT: G 130 MET cc_start: 0.8578 (tmm) cc_final: 0.8249 (tmm) REVERT: G 190 GLU cc_start: 0.8160 (mp0) cc_final: 0.7455 (tt0) REVERT: A 52 THR cc_start: 0.9132 (m) cc_final: 0.8791 (p) REVERT: A 195 ASP cc_start: 0.8418 (p0) cc_final: 0.8120 (p0) REVERT: A 240 VAL cc_start: 0.9389 (t) cc_final: 0.9080 (m) REVERT: A 261 ASP cc_start: 0.6661 (t0) cc_final: 0.6433 (m-30) REVERT: B 17 GLU cc_start: 0.5451 (pt0) cc_final: 0.4393 (mm-30) REVERT: B 195 ASP cc_start: 0.8042 (p0) cc_final: 0.7823 (p0) REVERT: B 301 LYS cc_start: 0.5890 (tttt) cc_final: 0.5469 (tmtt) REVERT: C 80 LYS cc_start: 0.8741 (mmtp) cc_final: 0.7880 (mmmt) REVERT: C 181 TYR cc_start: 0.9023 (t80) cc_final: 0.8317 (t80) REVERT: C 210 ASP cc_start: 0.8124 (t0) cc_final: 0.7902 (m-30) REVERT: C 221 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9197 (pp) REVERT: C 282 MET cc_start: 0.8663 (tmm) cc_final: 0.8159 (tmm) REVERT: C 358 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8859 (tt) REVERT: D 223 ASP cc_start: 0.7856 (t0) cc_final: 0.7601 (t0) REVERT: D 224 GLU cc_start: 0.7506 (tt0) cc_final: 0.7132 (tt0) REVERT: D 242 SER cc_start: 0.9566 (t) cc_final: 0.9346 (t) REVERT: E 6 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7735 (m) REVERT: E 39 ASN cc_start: 0.8693 (t0) cc_final: 0.8480 (t0) REVERT: E 89 ASP cc_start: 0.6755 (t0) cc_final: 0.6428 (t0) REVERT: E 130 MET cc_start: 0.8762 (tmm) cc_final: 0.8457 (tmm) REVERT: E 221 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8833 (pp) REVERT: E 247 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8181 (ttmm) REVERT: E 302 LYS cc_start: 0.5307 (mmtt) cc_final: 0.4793 (mmtm) REVERT: F 283 ASP cc_start: 0.8330 (p0) cc_final: 0.8015 (p0) outliers start: 65 outliers final: 43 residues processed: 350 average time/residue: 0.1136 time to fit residues: 66.4042 Evaluate side-chains 333 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 286 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain G residue 321 TRP Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 321 TRP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 341 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 120 optimal weight: 0.7980 chunk 218 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 182 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN D 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.102957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.093284 restraints weight = 33191.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.095225 restraints weight = 20264.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.096573 restraints weight = 13801.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.097537 restraints weight = 10155.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.098213 restraints weight = 7904.555| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19705 Z= 0.149 Angle : 0.614 11.790 26800 Z= 0.321 Chirality : 0.046 0.194 3178 Planarity : 0.004 0.053 3493 Dihedral : 4.952 22.779 2669 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.20 % Favored : 91.68 % Rotamer: Outliers : 3.72 % Allowed : 16.37 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.16), residues: 2501 helix: 1.63 (0.22), residues: 576 sheet: -0.73 (0.21), residues: 627 loop : -2.14 (0.15), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 354 TYR 0.014 0.001 TYR D 174 PHE 0.013 0.001 PHE D 204 TRP 0.013 0.001 TRP C 299 HIS 0.003 0.001 HIS G 155 Details of bonding type rmsd covalent geometry : bond 0.00341 (19705) covalent geometry : angle 0.61361 (26800) hydrogen bonds : bond 0.04678 ( 597) hydrogen bonds : angle 4.69445 ( 1626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 305 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 82 ASP cc_start: 0.8536 (t70) cc_final: 0.8235 (t0) REVERT: G 124 LYS cc_start: 0.9019 (tppt) cc_final: 0.8375 (mttt) REVERT: G 190 GLU cc_start: 0.8114 (mp0) cc_final: 0.7491 (tt0) REVERT: G 325 SER cc_start: 0.9186 (t) cc_final: 0.8962 (p) REVERT: A 52 THR cc_start: 0.9108 (m) cc_final: 0.8778 (p) REVERT: A 195 ASP cc_start: 0.8430 (p0) cc_final: 0.8133 (p0) REVERT: A 240 VAL cc_start: 0.9384 (t) cc_final: 0.9113 (m) REVERT: A 261 ASP cc_start: 0.6591 (t0) cc_final: 0.6382 (m-30) REVERT: B 17 GLU cc_start: 0.5493 (pt0) cc_final: 0.4473 (mm-30) REVERT: B 195 ASP cc_start: 0.8056 (p0) cc_final: 0.7752 (p0) REVERT: B 301 LYS cc_start: 0.5447 (tttt) cc_final: 0.4948 (tmtt) REVERT: C 62 GLU cc_start: 0.7875 (tp30) cc_final: 0.7403 (tp30) REVERT: C 181 TYR cc_start: 0.9027 (t80) cc_final: 0.8336 (t80) REVERT: C 210 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7874 (m-30) REVERT: C 221 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9256 (pp) REVERT: C 282 MET cc_start: 0.8600 (tmm) cc_final: 0.8105 (tmm) REVERT: C 311 TYR cc_start: 0.9017 (p90) cc_final: 0.8649 (p90) REVERT: C 358 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8888 (tt) REVERT: D 223 ASP cc_start: 0.7834 (t0) cc_final: 0.7599 (t0) REVERT: D 224 GLU cc_start: 0.7509 (tt0) cc_final: 0.7155 (tt0) REVERT: D 242 SER cc_start: 0.9544 (t) cc_final: 0.9330 (t) REVERT: E 6 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7718 (m) REVERT: E 89 ASP cc_start: 0.6751 (t0) cc_final: 0.6448 (t0) REVERT: E 130 MET cc_start: 0.8854 (tmm) cc_final: 0.8487 (tmm) REVERT: E 221 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8815 (pp) REVERT: E 302 LYS cc_start: 0.5516 (mmtt) cc_final: 0.5027 (tttt) REVERT: F 283 ASP cc_start: 0.8218 (p0) cc_final: 0.7945 (p0) outliers start: 79 outliers final: 52 residues processed: 357 average time/residue: 0.1158 time to fit residues: 68.7010 Evaluate side-chains 343 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 286 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 321 TRP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 341 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 68 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 243 optimal weight: 0.0370 chunk 141 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 0.0370 chunk 122 optimal weight: 1.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN C 142 ASN D 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.107013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.097456 restraints weight = 32739.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.099426 restraints weight = 19855.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.100772 restraints weight = 13464.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.101744 restraints weight = 9888.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.102449 restraints weight = 7649.130| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19705 Z= 0.114 Angle : 0.578 11.611 26800 Z= 0.301 Chirality : 0.044 0.195 3178 Planarity : 0.004 0.053 3493 Dihedral : 4.645 21.714 2669 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.68 % Favored : 92.20 % Rotamer: Outliers : 3.43 % Allowed : 17.78 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.16), residues: 2501 helix: 1.85 (0.23), residues: 571 sheet: -0.60 (0.21), residues: 624 loop : -2.07 (0.15), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 209 TYR 0.012 0.001 TYR D 174 PHE 0.012 0.001 PHE D 204 TRP 0.015 0.001 TRP C 299 HIS 0.004 0.001 HIS G 155 Details of bonding type rmsd covalent geometry : bond 0.00237 (19705) covalent geometry : angle 0.57754 (26800) hydrogen bonds : bond 0.03751 ( 597) hydrogen bonds : angle 4.38972 ( 1626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 325 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 82 ASP cc_start: 0.8502 (t70) cc_final: 0.8216 (t0) REVERT: G 124 LYS cc_start: 0.8980 (tppt) cc_final: 0.8302 (mttt) REVERT: G 186 GLN cc_start: 0.8634 (tt0) cc_final: 0.8375 (tm-30) REVERT: G 190 GLU cc_start: 0.8045 (mp0) cc_final: 0.7504 (tt0) REVERT: G 325 SER cc_start: 0.9208 (t) cc_final: 0.8992 (p) REVERT: A 52 THR cc_start: 0.9010 (m) cc_final: 0.8646 (p) REVERT: A 195 ASP cc_start: 0.8463 (p0) cc_final: 0.8169 (p0) REVERT: A 240 VAL cc_start: 0.9340 (t) cc_final: 0.9102 (m) REVERT: B 17 GLU cc_start: 0.5410 (pt0) cc_final: 0.4459 (mm-30) REVERT: B 195 ASP cc_start: 0.8073 (p0) cc_final: 0.7763 (p0) REVERT: B 301 LYS cc_start: 0.5430 (tttt) cc_final: 0.4986 (tmtt) REVERT: C 80 LYS cc_start: 0.8667 (mmtp) cc_final: 0.7809 (mmmt) REVERT: C 181 TYR cc_start: 0.8972 (t80) cc_final: 0.8302 (t80) REVERT: C 210 ASP cc_start: 0.8064 (t0) cc_final: 0.7859 (m-30) REVERT: C 221 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9280 (pp) REVERT: C 282 MET cc_start: 0.8625 (tmm) cc_final: 0.8126 (tmm) REVERT: C 283 ASP cc_start: 0.8635 (p0) cc_final: 0.8397 (p0) REVERT: C 311 TYR cc_start: 0.8947 (p90) cc_final: 0.8612 (p90) REVERT: C 358 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8898 (tt) REVERT: D 149 ASN cc_start: 0.8200 (p0) cc_final: 0.7909 (p0) REVERT: D 224 GLU cc_start: 0.7552 (tt0) cc_final: 0.7238 (tt0) REVERT: E 6 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7651 (m) REVERT: E 89 ASP cc_start: 0.6759 (t0) cc_final: 0.6388 (t0) REVERT: E 105 GLN cc_start: 0.3062 (tt0) cc_final: 0.2789 (tp-100) REVERT: E 130 MET cc_start: 0.8897 (tmm) cc_final: 0.8577 (tmm) REVERT: E 221 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8817 (pp) REVERT: E 302 LYS cc_start: 0.5378 (mmtt) cc_final: 0.4899 (mmtm) REVERT: F 208 LEU cc_start: 0.9511 (tp) cc_final: 0.9308 (tt) REVERT: F 283 ASP cc_start: 0.8231 (p0) cc_final: 0.8014 (p0) outliers start: 73 outliers final: 41 residues processed: 373 average time/residue: 0.1130 time to fit residues: 69.8437 Evaluate side-chains 346 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 301 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 321 TRP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 228 optimal weight: 4.9990 chunk 136 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 245 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN C 33 GLN D 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.104486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.095648 restraints weight = 32991.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.097345 restraints weight = 20741.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.098561 restraints weight = 14408.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.099429 restraints weight = 10771.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.100054 restraints weight = 8468.842| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19705 Z= 0.147 Angle : 0.618 11.766 26800 Z= 0.321 Chirality : 0.046 0.208 3178 Planarity : 0.004 0.053 3493 Dihedral : 4.746 21.071 2669 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.40 % Favored : 91.48 % Rotamer: Outliers : 3.20 % Allowed : 18.30 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.16), residues: 2501 helix: 1.69 (0.22), residues: 576 sheet: -0.68 (0.21), residues: 625 loop : -2.13 (0.15), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 209 TYR 0.014 0.001 TYR D 174 PHE 0.012 0.001 PHE C 204 TRP 0.012 0.001 TRP C 299 HIS 0.003 0.001 HIS F 155 Details of bonding type rmsd covalent geometry : bond 0.00339 (19705) covalent geometry : angle 0.61787 (26800) hydrogen bonds : bond 0.04409 ( 597) hydrogen bonds : angle 4.48982 ( 1626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 303 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: G 124 LYS cc_start: 0.9017 (tppt) cc_final: 0.8239 (mttt) REVERT: G 127 GLU cc_start: 0.6899 (tt0) cc_final: 0.6605 (tt0) REVERT: G 186 GLN cc_start: 0.8653 (tt0) cc_final: 0.8170 (tm-30) REVERT: G 190 GLU cc_start: 0.8030 (mp0) cc_final: 0.7495 (tt0) REVERT: G 210 ASP cc_start: 0.6997 (m-30) cc_final: 0.6765 (m-30) REVERT: G 325 SER cc_start: 0.9195 (t) cc_final: 0.8995 (p) REVERT: A 52 THR cc_start: 0.9070 (m) cc_final: 0.8735 (p) REVERT: A 195 ASP cc_start: 0.8453 (p0) cc_final: 0.8176 (p0) REVERT: A 240 VAL cc_start: 0.9357 (t) cc_final: 0.9126 (m) REVERT: B 17 GLU cc_start: 0.5560 (pt0) cc_final: 0.4493 (mm-30) REVERT: B 195 ASP cc_start: 0.8085 (p0) cc_final: 0.7753 (p0) REVERT: B 301 LYS cc_start: 0.5473 (tttt) cc_final: 0.5044 (tmtt) REVERT: B 311 TYR cc_start: 0.9175 (p90) cc_final: 0.8390 (p90) REVERT: C 80 LYS cc_start: 0.8756 (mmtp) cc_final: 0.7859 (mmmt) REVERT: C 181 TYR cc_start: 0.8937 (t80) cc_final: 0.8306 (t80) REVERT: C 221 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9269 (pp) REVERT: C 282 MET cc_start: 0.8674 (tmm) cc_final: 0.8152 (tmm) REVERT: C 283 ASP cc_start: 0.8643 (p0) cc_final: 0.8416 (p0) REVERT: C 311 TYR cc_start: 0.9035 (p90) cc_final: 0.8639 (p90) REVERT: C 358 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8946 (tt) REVERT: D 149 ASN cc_start: 0.8250 (p0) cc_final: 0.7955 (p0) REVERT: D 244 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7823 (ptp-110) REVERT: E 6 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7728 (m) REVERT: E 89 ASP cc_start: 0.6831 (t0) cc_final: 0.6474 (t0) REVERT: E 105 GLN cc_start: 0.3019 (tt0) cc_final: 0.2664 (tp-100) REVERT: E 130 MET cc_start: 0.8942 (tmm) cc_final: 0.8608 (tmm) REVERT: E 133 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8731 (tm-30) REVERT: E 221 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8896 (pp) REVERT: E 302 LYS cc_start: 0.5223 (mmtt) cc_final: 0.4687 (tttt) REVERT: F 283 ASP cc_start: 0.8198 (p0) cc_final: 0.7968 (p0) outliers start: 68 outliers final: 48 residues processed: 348 average time/residue: 0.1158 time to fit residues: 66.5733 Evaluate side-chains 347 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 294 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 321 TRP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 341 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 233 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN E 118 ASN F 250 GLN F 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.101286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.091722 restraints weight = 33569.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.093616 restraints weight = 20630.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.094958 restraints weight = 14120.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.095893 restraints weight = 10390.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.096480 restraints weight = 8129.086| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19705 Z= 0.192 Angle : 0.662 11.628 26800 Z= 0.346 Chirality : 0.047 0.201 3178 Planarity : 0.004 0.054 3493 Dihedral : 5.030 22.882 2669 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.76 % Favored : 91.12 % Rotamer: Outliers : 3.25 % Allowed : 18.86 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.16), residues: 2501 helix: 1.45 (0.22), residues: 583 sheet: -0.87 (0.21), residues: 623 loop : -2.15 (0.15), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 265 TYR 0.015 0.001 TYR D 174 PHE 0.015 0.002 PHE B 248 TRP 0.012 0.001 TRP A 299 HIS 0.004 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00458 (19705) covalent geometry : angle 0.66177 (26800) hydrogen bonds : bond 0.05155 ( 597) hydrogen bonds : angle 4.71825 ( 1626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 293 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: G 103 ASP cc_start: 0.8884 (t70) cc_final: 0.8622 (t0) REVERT: G 124 LYS cc_start: 0.9095 (tppt) cc_final: 0.8488 (ttmt) REVERT: G 157 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7152 (p90) REVERT: G 190 GLU cc_start: 0.8089 (mp0) cc_final: 0.7445 (tt0) REVERT: G 210 ASP cc_start: 0.7030 (m-30) cc_final: 0.6760 (m-30) REVERT: A 52 THR cc_start: 0.9150 (m) cc_final: 0.8836 (p) REVERT: A 195 ASP cc_start: 0.8479 (p0) cc_final: 0.8237 (p0) REVERT: A 240 VAL cc_start: 0.9385 (t) cc_final: 0.9139 (m) REVERT: B 17 GLU cc_start: 0.5630 (pt0) cc_final: 0.4460 (mm-30) REVERT: B 195 ASP cc_start: 0.8093 (p0) cc_final: 0.7743 (p0) REVERT: B 301 LYS cc_start: 0.5543 (tttt) cc_final: 0.5084 (tmtt) REVERT: C 125 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8320 (ttm170) REVERT: C 181 TYR cc_start: 0.9048 (t80) cc_final: 0.8333 (t80) REVERT: C 221 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9252 (pp) REVERT: C 282 MET cc_start: 0.8664 (tmm) cc_final: 0.8122 (tmm) REVERT: C 283 ASP cc_start: 0.8654 (p0) cc_final: 0.8423 (p0) REVERT: C 311 TYR cc_start: 0.9092 (p90) cc_final: 0.8689 (p90) REVERT: D 244 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7849 (ptp-110) REVERT: E 89 ASP cc_start: 0.6865 (t0) cc_final: 0.6532 (t0) REVERT: E 105 GLN cc_start: 0.3602 (tt0) cc_final: 0.2900 (tp-100) REVERT: E 130 MET cc_start: 0.8882 (tmm) cc_final: 0.8531 (tmm) REVERT: E 133 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8900 (tm-30) REVERT: E 221 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8902 (pp) REVERT: E 302 LYS cc_start: 0.5129 (mmtt) cc_final: 0.4477 (tttt) REVERT: F 184 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8150 (tm-30) outliers start: 69 outliers final: 54 residues processed: 344 average time/residue: 0.1172 time to fit residues: 66.5235 Evaluate side-chains 344 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 285 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 321 TRP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 341 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 154 optimal weight: 0.9980 chunk 176 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 79 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 125 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN D 33 GLN D 118 ASN F 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.102996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.094128 restraints weight = 33029.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.095812 restraints weight = 20855.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.097000 restraints weight = 14615.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.097884 restraints weight = 10958.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.098321 restraints weight = 8618.421| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19705 Z= 0.150 Angle : 0.623 9.642 26800 Z= 0.324 Chirality : 0.046 0.198 3178 Planarity : 0.004 0.057 3493 Dihedral : 4.930 22.951 2669 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.32 % Favored : 91.64 % Rotamer: Outliers : 3.01 % Allowed : 19.24 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.16), residues: 2501 helix: 1.55 (0.22), residues: 583 sheet: -0.80 (0.21), residues: 612 loop : -2.18 (0.15), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 151 TYR 0.016 0.001 TYR B 34 PHE 0.013 0.001 PHE E 26 TRP 0.014 0.001 TRP C 299 HIS 0.004 0.001 HIS G 155 Details of bonding type rmsd covalent geometry : bond 0.00345 (19705) covalent geometry : angle 0.62287 (26800) hydrogen bonds : bond 0.04587 ( 597) hydrogen bonds : angle 4.59223 ( 1626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 295 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: G 103 ASP cc_start: 0.8860 (t70) cc_final: 0.8566 (t0) REVERT: G 124 LYS cc_start: 0.9049 (tppt) cc_final: 0.8383 (mttt) REVERT: G 157 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7175 (p90) REVERT: G 186 GLN cc_start: 0.8697 (tt0) cc_final: 0.8233 (tm-30) REVERT: G 190 GLU cc_start: 0.8077 (mp0) cc_final: 0.7522 (tt0) REVERT: G 210 ASP cc_start: 0.6973 (m-30) cc_final: 0.6690 (m-30) REVERT: A 52 THR cc_start: 0.9126 (m) cc_final: 0.8808 (p) REVERT: A 195 ASP cc_start: 0.8455 (p0) cc_final: 0.8168 (p0) REVERT: A 240 VAL cc_start: 0.9375 (t) cc_final: 0.9143 (m) REVERT: B 17 GLU cc_start: 0.5572 (pt0) cc_final: 0.4458 (mm-30) REVERT: B 190 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7525 (mt-10) REVERT: B 195 ASP cc_start: 0.8058 (p0) cc_final: 0.7575 (p0) REVERT: B 301 LYS cc_start: 0.5515 (tttt) cc_final: 0.5035 (tmtt) REVERT: B 320 ARG cc_start: 0.9057 (tpt90) cc_final: 0.8819 (tpt170) REVERT: C 125 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8313 (ttm170) REVERT: C 181 TYR cc_start: 0.9020 (t80) cc_final: 0.8326 (t80) REVERT: C 282 MET cc_start: 0.8668 (tmm) cc_final: 0.8135 (tmm) REVERT: C 283 ASP cc_start: 0.8622 (p0) cc_final: 0.8387 (p0) REVERT: C 311 TYR cc_start: 0.9064 (p90) cc_final: 0.8656 (p90) REVERT: C 358 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8983 (tt) REVERT: D 244 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7857 (ptp-110) REVERT: E 6 VAL cc_start: 0.8034 (OUTLIER) cc_final: 0.7784 (m) REVERT: E 89 ASP cc_start: 0.6828 (t0) cc_final: 0.6500 (t0) REVERT: E 105 GLN cc_start: 0.3339 (tt0) cc_final: 0.2827 (tp-100) REVERT: E 130 MET cc_start: 0.8895 (tmm) cc_final: 0.8521 (tmm) REVERT: E 133 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8936 (tm-30) REVERT: E 221 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8892 (pp) REVERT: E 302 LYS cc_start: 0.5095 (mmtt) cc_final: 0.4483 (tttt) REVERT: F 184 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8176 (tm-30) REVERT: F 283 ASP cc_start: 0.8319 (p0) cc_final: 0.8037 (p0) outliers start: 64 outliers final: 50 residues processed: 341 average time/residue: 0.1185 time to fit residues: 66.6042 Evaluate side-chains 341 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 285 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain G residue 321 TRP Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 321 TRP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 341 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 141 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 118 optimal weight: 0.0010 chunk 41 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN D 118 ASN D 259 ASN F 250 GLN F 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.105616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.096510 restraints weight = 32955.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.098320 restraints weight = 20681.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.099595 restraints weight = 14300.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.100477 restraints weight = 10581.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.101130 restraints weight = 8327.497| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19705 Z= 0.121 Angle : 0.603 9.731 26800 Z= 0.312 Chirality : 0.045 0.226 3178 Planarity : 0.004 0.057 3493 Dihedral : 4.725 21.358 2669 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.20 % Favored : 91.76 % Rotamer: Outliers : 2.40 % Allowed : 19.94 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.16), residues: 2501 helix: 1.84 (0.23), residues: 569 sheet: -0.67 (0.21), residues: 615 loop : -2.11 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 354 TYR 0.012 0.001 TYR D 174 PHE 0.020 0.001 PHE B 248 TRP 0.017 0.001 TRP C 299 HIS 0.004 0.000 HIS G 155 Details of bonding type rmsd covalent geometry : bond 0.00260 (19705) covalent geometry : angle 0.60337 (26800) hydrogen bonds : bond 0.03930 ( 597) hydrogen bonds : angle 4.40186 ( 1626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5002 Ramachandran restraints generated. 2501 Oldfield, 0 Emsley, 2501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 308 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: G 82 ASP cc_start: 0.8473 (t70) cc_final: 0.8147 (t0) REVERT: G 124 LYS cc_start: 0.8999 (tppt) cc_final: 0.8210 (mttt) REVERT: G 157 PHE cc_start: 0.7737 (p90) cc_final: 0.7481 (p90) REVERT: G 186 GLN cc_start: 0.8566 (tt0) cc_final: 0.8348 (tm-30) REVERT: G 190 GLU cc_start: 0.8105 (mp0) cc_final: 0.7561 (tt0) REVERT: G 210 ASP cc_start: 0.6926 (m-30) cc_final: 0.6644 (m-30) REVERT: A 52 THR cc_start: 0.9067 (m) cc_final: 0.8735 (p) REVERT: A 195 ASP cc_start: 0.8430 (p0) cc_final: 0.8149 (p0) REVERT: A 240 VAL cc_start: 0.9359 (t) cc_final: 0.9155 (m) REVERT: B 17 GLU cc_start: 0.5498 (pt0) cc_final: 0.4464 (mm-30) REVERT: B 190 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7500 (mt-10) REVERT: B 195 ASP cc_start: 0.7996 (p0) cc_final: 0.7505 (p0) REVERT: B 301 LYS cc_start: 0.5439 (tttt) cc_final: 0.4899 (tmtt) REVERT: B 311 TYR cc_start: 0.9123 (p90) cc_final: 0.8601 (p90) REVERT: C 80 LYS cc_start: 0.8729 (mmtp) cc_final: 0.7778 (mmmt) REVERT: C 125 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8243 (ttm170) REVERT: C 181 TYR cc_start: 0.8962 (t80) cc_final: 0.8207 (t80) REVERT: C 282 MET cc_start: 0.8676 (tmm) cc_final: 0.8156 (tmm) REVERT: C 283 ASP cc_start: 0.8584 (p0) cc_final: 0.8348 (p0) REVERT: C 311 TYR cc_start: 0.9004 (p90) cc_final: 0.8593 (p90) REVERT: C 358 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8939 (tt) REVERT: D 149 ASN cc_start: 0.8281 (p0) cc_final: 0.7993 (p0) REVERT: D 244 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7782 (ptp-110) REVERT: E 6 VAL cc_start: 0.7943 (OUTLIER) cc_final: 0.7689 (m) REVERT: E 89 ASP cc_start: 0.6844 (t0) cc_final: 0.6487 (t0) REVERT: E 105 GLN cc_start: 0.3303 (tt0) cc_final: 0.3066 (tp-100) REVERT: E 130 MET cc_start: 0.8947 (tmm) cc_final: 0.8627 (tmm) REVERT: E 133 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8704 (tm-30) REVERT: E 221 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8860 (pp) REVERT: E 302 LYS cc_start: 0.5001 (mmtt) cc_final: 0.4503 (tttt) REVERT: F 184 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8167 (tm-30) REVERT: F 283 ASP cc_start: 0.8289 (p0) cc_final: 0.8070 (p0) outliers start: 51 outliers final: 42 residues processed: 343 average time/residue: 0.1231 time to fit residues: 69.1828 Evaluate side-chains 340 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 293 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 321 TRP Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 321 TRP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 157 PHE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 99 optimal weight: 0.0000 chunk 101 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN D 134 GLN F 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.105221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.096556 restraints weight = 32878.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.098194 restraints weight = 20902.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.099411 restraints weight = 14659.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.100201 restraints weight = 10988.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.100858 restraints weight = 8763.632| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19705 Z= 0.132 Angle : 0.617 9.985 26800 Z= 0.318 Chirality : 0.045 0.232 3178 Planarity : 0.004 0.057 3493 Dihedral : 4.695 21.785 2669 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.40 % Favored : 91.56 % Rotamer: Outliers : 2.59 % Allowed : 19.90 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.16), residues: 2501 helix: 1.79 (0.22), residues: 573 sheet: -0.64 (0.21), residues: 613 loop : -2.09 (0.15), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 209 TYR 0.013 0.001 TYR D 174 PHE 0.012 0.001 PHE E 26 TRP 0.014 0.001 TRP C 299 HIS 0.003 0.001 HIS G 155 Details of bonding type rmsd covalent geometry : bond 0.00297 (19705) covalent geometry : angle 0.61719 (26800) hydrogen bonds : bond 0.04087 ( 597) hydrogen bonds : angle 4.41190 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4527.00 seconds wall clock time: 79 minutes 3.71 seconds (4743.71 seconds total)