Starting phenix.real_space_refine on Fri Aug 22 18:04:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unr_42414/08_2025/8unr_42414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unr_42414/08_2025/8unr_42414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8unr_42414/08_2025/8unr_42414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unr_42414/08_2025/8unr_42414.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8unr_42414/08_2025/8unr_42414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unr_42414/08_2025/8unr_42414.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.023 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 38 5.16 5 C 4286 2.51 5 N 1157 2.21 5 O 1186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6670 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1740 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 240, 1728 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 10, 'GLN:plan1': 7, 'ARG:plan': 8, 'ASN:plan1': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 183 Conformer: "B" Number of residues, atoms: 240, 1728 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 10, 'GLN:plan1': 7, 'ARG:plan': 8, 'ASN:plan1': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 183 bond proxies already assigned to first conformer: 1747 Chain: "B" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2418 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 13, 'GLN:plan1': 4, 'ARG:plan': 8, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 138 Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 351 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2112 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3, 'GLN:plan1': 4, 'ASP:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 110 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 2.22, per 1000 atoms: 0.33 Number of scatterers: 6670 At special positions: 0 Unit cell: (85.9023, 135.361, 99.7855, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 3 15.00 O 1186 8.00 N 1157 7.00 C 4286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 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: 0.59 Conformation dependent library (CDL) restraints added in 432.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1742 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 48.6% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.967A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.540A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.757A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.591A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.753A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.366A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.906A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.502A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.521A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 4.624A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.626A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.801A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.558A pdb=" N TYR R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 4.020A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.592A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.548A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 175 removed outlier: 3.509A pdb=" N ARG R 175 " --> pdb=" O HIS R 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 172 through 175' Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.721A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.774A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 287 removed outlier: 3.693A pdb=" N LYS R 273 " --> pdb=" O HIS R 269 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE R 277 " --> pdb=" O LYS R 273 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.887A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.599A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 341 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 7.174A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL A 287 " --> pdb=" O ATYR A 360 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.834A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.114A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.999A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.536A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.865A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.647A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.957A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1035 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: 1.08 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1600 1.33 - 1.45: 1437 1.45 - 1.57: 3720 1.57 - 1.69: 5 1.69 - 1.82: 51 Bond restraints: 6813 Sorted by residual: bond pdb=" N VAL A 256 " pdb=" CA VAL A 256 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.17e-02 7.31e+03 9.70e+00 bond pdb=" N ARG B 129 " pdb=" CA ARG B 129 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.06e+00 bond pdb=" N VAL B 133 " pdb=" CA VAL B 133 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.22e-02 6.72e+03 7.88e+00 bond pdb=" N VAL G 16 " pdb=" CA VAL G 16 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.83e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.452 -0.055 2.00e-02 2.50e+03 7.66e+00 ... (remaining 6808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 9010 2.12 - 4.25: 278 4.25 - 6.37: 28 6.37 - 8.49: 10 8.49 - 10.61: 4 Bond angle restraints: 9330 Sorted by residual: angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 103.91 7.37 1.09e+00 8.42e-01 4.57e+01 angle pdb=" N SER G 8 " pdb=" CA SER G 8 " pdb=" C SER G 8 " ideal model delta sigma weight residual 112.38 104.62 7.76 1.22e+00 6.72e-01 4.05e+01 angle pdb=" N GLU A 16 " pdb=" CA GLU A 16 " pdb=" C GLU A 16 " ideal model delta sigma weight residual 111.28 104.82 6.46 1.09e+00 8.42e-01 3.51e+01 angle pdb=" N HIS R 269 " pdb=" CA HIS R 269 " pdb=" C HIS R 269 " ideal model delta sigma weight residual 113.88 106.94 6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N ASP A 11 " pdb=" CA ASP A 11 " pdb=" C ASP A 11 " ideal model delta sigma weight residual 111.28 106.23 5.05 1.09e+00 8.42e-01 2.15e+01 ... (remaining 9325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.92: 3808 28.92 - 57.85: 119 57.85 - 86.77: 6 86.77 - 115.69: 0 115.69 - 144.61: 2 Dihedral angle restraints: 3935 sinusoidal: 1250 harmonic: 2685 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 155.75 -62.75 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -146.12 -144.61 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -34.69 139.28 1 2.00e+01 2.50e-03 4.22e+01 ... (remaining 3932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 817 0.046 - 0.093: 202 0.093 - 0.139: 79 0.139 - 0.186: 17 0.186 - 0.232: 7 Chirality restraints: 1122 Sorted by residual: chirality pdb=" CA GLN A 12 " pdb=" N GLN A 12 " pdb=" C GLN A 12 " pdb=" CB GLN A 12 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ILE R 38 " pdb=" N ILE R 38 " pdb=" C ILE R 38 " pdb=" CB ILE R 38 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL R 33 " pdb=" N VAL R 33 " pdb=" C VAL R 33 " pdb=" CB VAL R 33 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1119 not shown) Planarity restraints: 1169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 239 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C ARG R 239 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG R 239 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE R 240 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 12 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C GLN A 12 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN A 12 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 13 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 19 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C GLN A 19 " -0.035 2.00e-02 2.50e+03 pdb=" O GLN A 19 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 20 " 0.012 2.00e-02 2.50e+03 ... (remaining 1166 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 29 2.54 - 3.13: 4958 3.13 - 3.72: 9727 3.72 - 4.31: 12697 4.31 - 4.90: 22385 Nonbonded interactions: 49796 Sorted by model distance: nonbonded pdb=" NH1 ARG A 231 " pdb=" O ARG A 232 " model vdw 1.950 3.120 nonbonded pdb=" OD1 ASN B 295 " pdb=" NH2 ARG B 304 " model vdw 2.200 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.214 3.040 nonbonded pdb=" N GLU A 309 " pdb=" OE1 GLU A 309 " model vdw 2.260 3.120 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.268 3.120 ... (remaining 49791 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.660 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6815 Z= 0.329 Angle : 0.787 10.613 9334 Z= 0.521 Chirality : 0.051 0.232 1122 Planarity : 0.004 0.039 1169 Dihedral : 13.749 144.614 2187 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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 aren not related in a simple way. whole: 0.99 (0.29), residues: 908 helix: 1.93 (0.27), residues: 412 sheet: 0.44 (0.41), residues: 172 loop : -0.89 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 239 TYR 0.015 0.001 TYR A 339 PHE 0.011 0.001 PHE B 234 TRP 0.005 0.001 TRP R 313 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 6813) covalent geometry : angle 0.78704 ( 9330) SS BOND : bond 0.00221 ( 2) SS BOND : angle 0.64690 ( 4) hydrogen bonds : bond 0.21064 ( 357) hydrogen bonds : angle 6.77419 ( 1035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0842 time to fit residues: 13.6508 Evaluate side-chains 86 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN R 93 HIS R 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.091126 restraints weight = 41337.013| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 5.27 r_work: 0.2863 rms_B_bonded: 5.25 restraints_weight: 2.0000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6815 Z= 0.202 Angle : 0.555 6.194 9334 Z= 0.300 Chirality : 0.044 0.137 1122 Planarity : 0.004 0.042 1169 Dihedral : 8.034 141.494 1010 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.18 % Allowed : 9.40 % Favored : 88.42 % 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 aren not related in a simple way. whole: 1.19 (0.29), residues: 908 helix: 2.14 (0.27), residues: 410 sheet: 0.50 (0.41), residues: 173 loop : -0.81 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 231 TYR 0.015 0.002 TYR A 311 PHE 0.013 0.001 PHE R 217 TRP 0.008 0.001 TRP A 234 HIS 0.010 0.002 HIS R 93 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 6813) covalent geometry : angle 0.55468 ( 9330) SS BOND : bond 0.00261 ( 2) SS BOND : angle 0.71519 ( 4) hydrogen bonds : bond 0.05642 ( 357) hydrogen bonds : angle 4.58301 ( 1035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7228 (mtm) outliers start: 13 outliers final: 12 residues processed: 96 average time/residue: 0.0783 time to fit residues: 10.3797 Evaluate side-chains 94 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 0.0070 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 292 ASN B 88 ASN R 93 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.093215 restraints weight = 39146.580| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 5.19 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6815 Z= 0.116 Angle : 0.469 6.585 9334 Z= 0.255 Chirality : 0.041 0.147 1122 Planarity : 0.003 0.040 1169 Dihedral : 7.667 139.557 1010 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.18 % Allowed : 11.74 % Favored : 86.07 % 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 aren not related in a simple way. whole: 1.41 (0.29), residues: 908 helix: 2.48 (0.27), residues: 410 sheet: 0.48 (0.41), residues: 174 loop : -0.86 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 221 TYR 0.012 0.001 TYR A 358 PHE 0.011 0.001 PHE B 241 TRP 0.005 0.001 TRP B 297 HIS 0.011 0.001 HIS R 93 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6813) covalent geometry : angle 0.46879 ( 9330) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.57393 ( 4) hydrogen bonds : bond 0.04154 ( 357) hydrogen bonds : angle 4.11229 ( 1035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 ASN cc_start: 0.8610 (t0) cc_final: 0.8319 (t0) outliers start: 13 outliers final: 10 residues processed: 95 average time/residue: 0.0780 time to fit residues: 10.3179 Evaluate side-chains 89 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 159 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 37 optimal weight: 0.0050 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 213 GLN A 292 ASN R 93 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.093905 restraints weight = 37265.204| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 4.90 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6815 Z= 0.095 Angle : 0.446 7.011 9334 Z= 0.242 Chirality : 0.040 0.169 1122 Planarity : 0.003 0.038 1169 Dihedral : 7.479 140.135 1010 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.52 % Allowed : 12.92 % Favored : 84.56 % 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 aren not related in a simple way. whole: 1.55 (0.29), residues: 908 helix: 2.59 (0.27), residues: 411 sheet: 0.45 (0.40), residues: 181 loop : -0.76 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 221 TYR 0.012 0.001 TYR A 358 PHE 0.010 0.001 PHE A 212 TRP 0.005 0.001 TRP A 277 HIS 0.010 0.001 HIS R 93 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 6813) covalent geometry : angle 0.44602 ( 9330) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.56643 ( 4) hydrogen bonds : bond 0.03555 ( 357) hydrogen bonds : angle 3.85968 ( 1035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 ASN cc_start: 0.8567 (t0) cc_final: 0.8249 (t0) REVERT: B 259 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7677 (pt0) outliers start: 15 outliers final: 11 residues processed: 100 average time/residue: 0.0799 time to fit residues: 11.0405 Evaluate side-chains 97 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.092504 restraints weight = 40143.335| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 5.00 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6815 Z= 0.127 Angle : 0.474 7.209 9334 Z= 0.256 Chirality : 0.041 0.193 1122 Planarity : 0.003 0.040 1169 Dihedral : 7.465 140.352 1010 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.52 % Allowed : 14.60 % Favored : 82.89 % 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 aren not related in a simple way. whole: 1.49 (0.29), residues: 908 helix: 2.53 (0.27), residues: 411 sheet: 0.44 (0.39), residues: 180 loop : -0.77 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 221 TYR 0.020 0.001 TYR A 358 PHE 0.011 0.001 PHE B 241 TRP 0.005 0.001 TRP B 63 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6813) covalent geometry : angle 0.47382 ( 9330) SS BOND : bond 0.00238 ( 2) SS BOND : angle 0.57013 ( 4) hydrogen bonds : bond 0.03915 ( 357) hydrogen bonds : angle 3.84039 ( 1035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 237 ASN cc_start: 0.8592 (t0) cc_final: 0.8260 (t0) REVERT: B 259 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7720 (pt0) outliers start: 15 outliers final: 13 residues processed: 97 average time/residue: 0.0716 time to fit residues: 9.8976 Evaluate side-chains 96 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 7.9990 chunk 64 optimal weight: 0.0370 chunk 42 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 39 optimal weight: 0.0170 chunk 36 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.0470 chunk 87 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.094010 restraints weight = 37016.007| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 4.80 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6815 Z= 0.089 Angle : 0.440 7.245 9334 Z= 0.239 Chirality : 0.040 0.172 1122 Planarity : 0.003 0.041 1169 Dihedral : 7.372 141.279 1010 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.52 % Allowed : 15.27 % Favored : 82.21 % 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 aren not related in a simple way. whole: 1.60 (0.29), residues: 908 helix: 2.67 (0.27), residues: 405 sheet: 0.52 (0.40), residues: 180 loop : -0.76 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 221 TYR 0.018 0.001 TYR A 358 PHE 0.011 0.001 PHE A 212 TRP 0.005 0.001 TRP B 297 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00176 ( 6813) covalent geometry : angle 0.44036 ( 9330) SS BOND : bond 0.00221 ( 2) SS BOND : angle 0.54032 ( 4) hydrogen bonds : bond 0.03247 ( 357) hydrogen bonds : angle 3.70829 ( 1035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7411 (tpp-160) cc_final: 0.7138 (mmp-170) REVERT: B 237 ASN cc_start: 0.8539 (t0) cc_final: 0.8208 (t0) REVERT: B 259 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7725 (pt0) outliers start: 15 outliers final: 12 residues processed: 105 average time/residue: 0.0745 time to fit residues: 10.8962 Evaluate side-chains 101 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.087300 restraints weight = 42659.319| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 5.07 r_work: 0.2818 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 6815 Z= 0.271 Angle : 0.618 7.271 9334 Z= 0.334 Chirality : 0.046 0.189 1122 Planarity : 0.004 0.060 1169 Dihedral : 7.835 141.370 1010 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.86 % Allowed : 15.27 % Favored : 80.87 % 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 aren not related in a simple way. whole: 1.09 (0.29), residues: 908 helix: 2.21 (0.27), residues: 410 sheet: 0.35 (0.41), residues: 171 loop : -1.03 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 221 TYR 0.020 0.002 TYR A 358 PHE 0.015 0.002 PHE R 282 TRP 0.011 0.002 TRP B 63 HIS 0.007 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00662 ( 6813) covalent geometry : angle 0.61813 ( 9330) SS BOND : bond 0.00310 ( 2) SS BOND : angle 0.62241 ( 4) hydrogen bonds : bond 0.06031 ( 357) hydrogen bonds : angle 4.32785 ( 1035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8373 (p0) REVERT: B 197 ARG cc_start: 0.7812 (tpp-160) cc_final: 0.7561 (mmp-170) REVERT: B 234 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8289 (t80) REVERT: B 237 ASN cc_start: 0.8881 (t0) cc_final: 0.8657 (t0) REVERT: B 259 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7986 (pt0) outliers start: 23 outliers final: 17 residues processed: 91 average time/residue: 0.0687 time to fit residues: 9.0365 Evaluate side-chains 93 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 15 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 80 optimal weight: 0.0170 chunk 10 optimal weight: 4.9990 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.093701 restraints weight = 41974.367| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 5.31 r_work: 0.2908 rms_B_bonded: 5.29 restraints_weight: 2.0000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6815 Z= 0.093 Angle : 0.452 7.210 9334 Z= 0.247 Chirality : 0.040 0.141 1122 Planarity : 0.003 0.063 1169 Dihedral : 7.497 142.671 1010 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.68 % Allowed : 17.11 % Favored : 81.21 % 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 aren not related in a simple way. whole: 1.40 (0.29), residues: 908 helix: 2.55 (0.27), residues: 409 sheet: 0.37 (0.40), residues: 180 loop : -0.93 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 221 TYR 0.014 0.001 TYR A 358 PHE 0.011 0.001 PHE B 241 TRP 0.007 0.001 TRP R 313 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00177 ( 6813) covalent geometry : angle 0.45238 ( 9330) SS BOND : bond 0.00213 ( 2) SS BOND : angle 0.63541 ( 4) hydrogen bonds : bond 0.03335 ( 357) hydrogen bonds : angle 3.76922 ( 1035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7797 (tpp-160) cc_final: 0.7564 (mmp-170) REVERT: B 237 ASN cc_start: 0.8693 (t0) cc_final: 0.8297 (t0) REVERT: B 259 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7895 (pt0) REVERT: G 50 LEU cc_start: 0.8844 (mp) cc_final: 0.8587 (mt) REVERT: R 40 MET cc_start: 0.7529 (mtm) cc_final: 0.7210 (mtt) outliers start: 10 outliers final: 9 residues processed: 100 average time/residue: 0.0754 time to fit residues: 10.4497 Evaluate side-chains 96 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.092547 restraints weight = 37480.456| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.85 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6815 Z= 0.106 Angle : 0.473 7.281 9334 Z= 0.256 Chirality : 0.041 0.138 1122 Planarity : 0.004 0.078 1169 Dihedral : 7.443 143.187 1010 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.01 % Allowed : 17.62 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.29), residues: 908 helix: 2.55 (0.27), residues: 410 sheet: 0.44 (0.40), residues: 180 loop : -0.91 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 221 TYR 0.011 0.001 TYR A 358 PHE 0.015 0.001 PHE A 212 TRP 0.005 0.001 TRP A 277 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 6813) covalent geometry : angle 0.46855 ( 9330) SS BOND : bond 0.00319 ( 2) SS BOND : angle 3.12690 ( 4) hydrogen bonds : bond 0.03561 ( 357) hydrogen bonds : angle 3.72324 ( 1035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7496 (tpp-160) cc_final: 0.7178 (mmp-170) REVERT: B 237 ASN cc_start: 0.8560 (t0) cc_final: 0.8129 (t0) REVERT: B 259 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7643 (pt0) REVERT: R 40 MET cc_start: 0.7498 (mtm) cc_final: 0.7235 (mtt) outliers start: 12 outliers final: 10 residues processed: 94 average time/residue: 0.0722 time to fit residues: 9.6680 Evaluate side-chains 89 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.093044 restraints weight = 31601.772| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 4.48 r_work: 0.2922 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6815 Z= 0.106 Angle : 0.468 7.299 9334 Z= 0.253 Chirality : 0.041 0.134 1122 Planarity : 0.004 0.085 1169 Dihedral : 7.415 143.358 1010 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.18 % Allowed : 17.28 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.29), residues: 908 helix: 2.53 (0.27), residues: 410 sheet: 0.44 (0.40), residues: 180 loop : -0.90 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 221 TYR 0.011 0.001 TYR A 358 PHE 0.016 0.001 PHE A 212 TRP 0.005 0.001 TRP A 277 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6813) covalent geometry : angle 0.46354 ( 9330) SS BOND : bond 0.00264 ( 2) SS BOND : angle 3.08272 ( 4) hydrogen bonds : bond 0.03535 ( 357) hydrogen bonds : angle 3.69771 ( 1035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8549 (tm-30) REVERT: B 197 ARG cc_start: 0.7803 (tpp-160) cc_final: 0.7539 (mmp-170) REVERT: B 237 ASN cc_start: 0.8758 (t0) cc_final: 0.8349 (t0) REVERT: B 259 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7869 (pt0) REVERT: R 40 MET cc_start: 0.7598 (mtm) cc_final: 0.7300 (mtt) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.0669 time to fit residues: 8.8416 Evaluate side-chains 91 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 76 optimal weight: 0.0970 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.092640 restraints weight = 38788.011| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 4.89 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 6815 Z= 0.187 Angle : 1.001 59.200 9334 Z= 0.590 Chirality : 0.041 0.271 1122 Planarity : 0.006 0.137 1169 Dihedral : 7.412 143.354 1010 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.85 % Allowed : 17.95 % Favored : 80.20 % Cbeta Deviations : 0.11 % 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 aren not related in a simple way. whole: 1.46 (0.29), residues: 908 helix: 2.56 (0.27), residues: 409 sheet: 0.44 (0.40), residues: 180 loop : -0.87 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 221 TYR 0.010 0.001 TYR A 358 PHE 0.014 0.001 PHE A 212 TRP 0.004 0.001 TRP A 277 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6813) covalent geometry : angle 0.99906 ( 9330) SS BOND : bond 0.00318 ( 2) SS BOND : angle 3.02185 ( 4) hydrogen bonds : bond 0.03522 ( 357) hydrogen bonds : angle 3.69881 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1706.19 seconds wall clock time: 30 minutes 0.24 seconds (1800.24 seconds total)