Starting phenix.real_space_refine on Fri Sep 11 18:28:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x1a_21994/09_2026/6x1a_21994.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x1a_21994/09_2026/6x1a_21994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x1a_21994/09_2026/6x1a_21994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x1a_21994/09_2026/6x1a_21994.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x1a_21994/09_2026/6x1a_21994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x1a_21994/09_2026/6x1a_21994.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6x1a_21994/09_2026/6x1a_21994.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x1a_21994/09_2026/6x1a_21994.cif" } resolution = 2.5 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 849 atoms to isotropic. 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 S 59 5.16 5 C 6444 2.51 5 N 1746 2.21 5 O 1890 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10140 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2873 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 337} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3206 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 64 Unusual residues: {'UK4': 1} Classifications: {'undetermined': 1, 'water': 23} Link IDs: {None: 23} Time building chain proxies: 2.17, per 1000 atoms: 0.21 Number of scatterers: 10140 At special positions: 0 Unit cell: (112.05, 99.6, 164.34, 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 59 16.00 F 1 9.00 O 1890 8.00 N 1746 7.00 C 6444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 0.92 Conformation dependent library (CDL) restraints added in 350.7 milliseconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 43.2% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 4.071A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 90 through 113 removed outlier: 4.130A pdb=" N ASP A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 143 through 154 removed outlier: 4.359A pdb=" N TYR A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.541A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.752A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.622A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.892A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.875A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 16 removed outlier: 3.633A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.658A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 44 through 48 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.629A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.619A pdb=" N GLU R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER R 49 " --> pdb=" O GLN R 45 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 167 Processing helix chain 'R' and resid 174 through 201 removed outlier: 3.544A pdb=" N LEU R 201 " --> pdb=" O LYS R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 212 No H-bonds generated for 'chain 'R' and resid 210 through 212' Processing helix chain 'R' and resid 213 through 223 removed outlier: 3.814A pdb=" N TYR R 220 " --> pdb=" O GLY R 216 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP R 222 " --> pdb=" O LEU R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 256 Processing helix chain 'R' and resid 261 through 274 removed outlier: 3.766A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 removed outlier: 3.692A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.671A pdb=" N VAL R 287 " --> pdb=" O PRO R 283 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR R 289 " --> pdb=" O GLY R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 337 Proline residue: R 312 - end of helix removed outlier: 3.696A pdb=" N LEU R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER R 333 " --> pdb=" O CYS R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 361 removed outlier: 3.519A pdb=" N LEU R 349 " --> pdb=" O ILE R 345 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 371 removed outlier: 3.819A pdb=" N PHE R 369 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 392 removed outlier: 3.835A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 402 Processing helix chain 'R' and resid 406 through 419 removed outlier: 3.513A pdb=" N TRP R 417 " --> pdb=" O PHE R 413 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG R 419 " --> pdb=" O LYS R 415 " (cutoff:3.500A) Processing helix chain 'R' and resid 420 through 423 removed outlier: 3.651A pdb=" N GLU R 423 " --> pdb=" O TRP R 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 420 through 423' Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.326A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.864A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.093A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.664A 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: 6.397A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.296A 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: 4.104A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.679A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.817A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.408A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.728A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 79 through 80 removed outlier: 3.503A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 83 through 84 removed outlier: 4.085A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1299 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: 1.51 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1656 1.27 - 1.40: 2709 1.40 - 1.54: 5847 1.54 - 1.68: 61 1.68 - 1.81: 79 Bond restraints: 10352 Sorted by residual: bond pdb=" C27 UK4 R 501 " pdb=" C28 UK4 R 501 " ideal model delta sigma weight residual 1.535 1.424 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C38 UK4 R 501 " pdb=" C39 UK4 R 501 " ideal model delta sigma weight residual 1.427 1.529 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C PRO A 115 " pdb=" N PRO A 116 " ideal model delta sigma weight residual 1.330 1.381 -0.051 1.19e-02 7.06e+03 1.82e+01 bond pdb=" C ASP B 27 " pdb=" N ALA B 28 " ideal model delta sigma weight residual 1.332 1.383 -0.051 1.25e-02 6.40e+03 1.66e+01 bond pdb=" C PHE A 142 " pdb=" N PRO A 143 " ideal model delta sigma weight residual 1.329 1.377 -0.048 1.18e-02 7.18e+03 1.64e+01 ... (remaining 10347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 13909 3.57 - 7.14: 126 7.14 - 10.70: 8 10.70 - 14.27: 0 14.27 - 17.84: 1 Bond angle restraints: 14044 Sorted by residual: angle pdb=" N ILE A 308 " pdb=" CA ILE A 308 " pdb=" C ILE A 308 " ideal model delta sigma weight residual 112.04 101.46 10.58 1.40e+00 5.10e-01 5.71e+01 angle pdb=" N PRO A 138 " pdb=" CA PRO A 138 " pdb=" C PRO A 138 " ideal model delta sigma weight residual 113.53 103.10 10.43 1.39e+00 5.18e-01 5.63e+01 angle pdb=" C08 UK4 R 501 " pdb=" C09 UK4 R 501 " pdb=" C32 UK4 R 501 " ideal model delta sigma weight residual 110.26 92.42 17.84 3.00e+00 1.11e-01 3.54e+01 angle pdb=" C VAL A 114 " pdb=" N PRO A 115 " pdb=" CA PRO A 115 " ideal model delta sigma weight residual 120.38 125.97 -5.59 1.03e+00 9.43e-01 2.95e+01 angle pdb=" C VAL A 191 " pdb=" N PRO A 192 " pdb=" CA PRO A 192 " ideal model delta sigma weight residual 119.76 125.25 -5.49 1.03e+00 9.43e-01 2.84e+01 ... (remaining 14039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5451 17.47 - 34.95: 511 34.95 - 52.42: 137 52.42 - 69.89: 27 69.89 - 87.36: 13 Dihedral angle restraints: 6139 sinusoidal: 2443 harmonic: 3696 Sorted by residual: dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual 93.00 173.00 -80.00 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CA VAL A 114 " pdb=" C VAL A 114 " pdb=" N PRO A 115 " pdb=" CA PRO A 115 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ASN A 292 " pdb=" C ASN A 292 " pdb=" N LYS A 293 " pdb=" CA LYS A 293 " ideal model delta harmonic sigma weight residual -180.00 -157.75 -22.25 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 6136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1262 0.071 - 0.143: 201 0.143 - 0.214: 55 0.214 - 0.286: 20 0.286 - 0.357: 5 Chirality restraints: 1543 Sorted by residual: chirality pdb=" CA ILE A 308 " pdb=" N ILE A 308 " pdb=" C ILE A 308 " pdb=" CB ILE A 308 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA VAL A 214 " pdb=" N VAL A 214 " pdb=" C VAL A 214 " pdb=" CB VAL A 214 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA LYS A 100 " pdb=" N LYS A 100 " pdb=" C LYS A 100 " pdb=" CB LYS A 100 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 1540 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 364 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C THR A 364 " 0.068 2.00e-02 2.50e+03 pdb=" O THR A 364 " -0.026 2.00e-02 2.50e+03 pdb=" N CYS A 365 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 322 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C GLU A 322 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU A 322 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP A 323 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 61 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C PHE G 61 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE G 61 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG G 62 " 0.014 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 285 2.69 - 3.24: 10042 3.24 - 3.80: 16022 3.80 - 4.35: 22922 4.35 - 4.90: 35848 Nonbonded interactions: 85119 Sorted by model distance: nonbonded pdb=" O THR A 325 " pdb=" OG1 THR A 325 " model vdw 2.140 3.040 nonbonded pdb=" O HOH R 603 " pdb=" O HOH R 617 " model vdw 2.230 3.040 nonbonded pdb=" O GLN R 234 " pdb=" O HOH R 601 " model vdw 2.233 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR R 152 " pdb=" O HOH R 602 " model vdw 2.261 3.040 ... (remaining 85114 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.040 Find NCS groups from input model: 0.060 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 : 0.006 0.111 10358 Z= 0.428 Angle : 0.926 17.839 14056 Z= 0.655 Chirality : 0.066 0.357 1543 Planarity : 0.004 0.051 1794 Dihedral : 15.412 87.364 3729 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.79 % Allowed : 15.97 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.21), residues: 1246 helix: -2.54 (0.18), residues: 498 sheet: -1.43 (0.34), residues: 193 loop : -1.72 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.025 0.001 TYR B 145 PHE 0.012 0.001 PHE A 219 TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.43 (10352) covalent geometry : angle 0.92575 / 0.66 (14044) SS BOND : bond 0.00268 / 0.14 ( 6) SS BOND : angle 0.63604 / 0.33 ( 12) hydrogen bonds : bond 0.25123 / 16.65 ( 457) hydrogen bonds : angle 8.80283 / 6.30 ( 1299) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.2248 (ptt) cc_final: 0.1891 (mtm) REVERT: A 222 PHE cc_start: 0.7406 (m-80) cc_final: 0.7150 (m-80) REVERT: A 265 ARG cc_start: 0.7206 (mtp85) cc_final: 0.6997 (ttt-90) REVERT: A 358 TYR cc_start: 0.6807 (m-80) cc_final: 0.6163 (m-80) REVERT: B 38 ASP cc_start: 0.5869 (OUTLIER) cc_final: 0.5043 (p0) REVERT: B 44 GLN cc_start: 0.6341 (mp10) cc_final: 0.5987 (mp10) REVERT: B 75 GLN cc_start: 0.7394 (mm-40) cc_final: 0.7182 (tp40) REVERT: B 142 HIS cc_start: 0.6783 (OUTLIER) cc_final: 0.5731 (m-70) REVERT: B 228 ASP cc_start: 0.7773 (m-30) cc_final: 0.7539 (m-30) REVERT: B 322 ASP cc_start: 0.5199 (OUTLIER) cc_final: 0.4932 (t70) REVERT: G 32 LYS cc_start: 0.6958 (mmmt) cc_final: 0.6483 (tptt) REVERT: N 43 LYS cc_start: 0.6071 (tmtt) cc_final: 0.5806 (tmtt) REVERT: N 78 THR cc_start: 0.7667 (OUTLIER) cc_final: 0.7367 (m) REVERT: R 62 CYS cc_start: 0.1138 (OUTLIER) cc_final: 0.0588 (m) REVERT: R 67 ASP cc_start: 0.7114 (p0) cc_final: 0.6785 (p0) REVERT: R 170 ARG cc_start: 0.5551 (ttt180) cc_final: 0.5301 (tpp80) REVERT: R 414 ARG cc_start: 0.5815 (mmt-90) cc_final: 0.5337 (mmm160) outliers start: 41 outliers final: 17 residues processed: 197 average time/residue: 0.4964 time to fit residues: 106.0303 Evaluate side-chains 145 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 142 HIS 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 277 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 126 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 23 ASN A 64 HIS A 112 ASN A 136 ASN A 170 GLN A 187 GLN A 218 ASN A 236 GLN A 377 ASN A 390 GLN B 16 ASN B 36 ASN B 88 ASN B 110 ASN B 125 ASN B 155 ASN B 176 GLN B 183 HIS B 268 ASN B 295 ASN B 340 ASN G 18 GLN G 24 ASN N 1 GLN N 3 GLN N 31 ASN N 77 ASN R 45 GLN R 177 ASN R 263 GLN R 304 ASN R 394 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.222872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.185267 restraints weight = 11332.688| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.39 r_work: 0.3955 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10358 Z= 0.138 Angle : 0.608 10.364 14056 Z= 0.323 Chirality : 0.043 0.144 1543 Planarity : 0.004 0.051 1794 Dihedral : 6.237 59.811 1425 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.36 % Allowed : 16.44 % Favored : 78.21 % 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 are not related in a simple way. whole: -1.43 (0.22), residues: 1246 helix: -0.56 (0.22), residues: 496 sheet: -0.85 (0.33), residues: 218 loop : -1.22 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 374 TYR 0.029 0.002 TYR R 148 PHE 0.010 0.001 PHE A 212 TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS R 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (10352) covalent geometry : angle 0.60674 / 0.32 (14044) SS BOND : bond 0.00596 / 0.29 ( 6) SS BOND : angle 1.60600 / 1.25 ( 12) hydrogen bonds : bond 0.05222 / 3.40 ( 457) hydrogen bonds : angle 5.38966 / 3.84 ( 1299) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 128 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7503 (OUTLIER) cc_final: 0.7298 (t0) REVERT: A 135 MET cc_start: 0.1701 (ptt) cc_final: 0.1459 (mtm) REVERT: A 265 ARG cc_start: 0.7457 (mtp85) cc_final: 0.6432 (ttt-90) REVERT: A 358 TYR cc_start: 0.7338 (m-80) cc_final: 0.6604 (m-80) REVERT: B 44 GLN cc_start: 0.6622 (mp10) cc_final: 0.6246 (mp10) REVERT: B 59 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.6099 (t80) REVERT: B 124 TYR cc_start: 0.5541 (m-80) cc_final: 0.5233 (m-80) REVERT: B 142 HIS cc_start: 0.6939 (OUTLIER) cc_final: 0.4949 (m-70) REVERT: B 197 ARG cc_start: 0.4476 (OUTLIER) cc_final: 0.4264 (ttm170) REVERT: B 261 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7859 (mp) REVERT: G 32 LYS cc_start: 0.7069 (mmmt) cc_final: 0.6701 (tptt) REVERT: N 1 GLN cc_start: 0.6340 (pt0) cc_final: 0.6121 (pt0) REVERT: N 43 LYS cc_start: 0.6193 (tmtt) cc_final: 0.5879 (mmtp) REVERT: N 46 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7381 (mm-30) REVERT: R 50 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5500 (mp) REVERT: R 127 GLU cc_start: 0.6155 (mm-30) cc_final: 0.5903 (tp30) REVERT: R 346 LYS cc_start: 0.5891 (mttp) cc_final: 0.5477 (mtmt) REVERT: R 371 MET cc_start: 0.7692 (tpp) cc_final: 0.7363 (tpp) REVERT: R 414 ARG cc_start: 0.5700 (mmt-90) cc_final: 0.5246 (mmm160) outliers start: 58 outliers final: 26 residues processed: 179 average time/residue: 0.5627 time to fit residues: 108.4183 Evaluate side-chains 140 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 34 optimal weight: 4.9990 chunk 47 optimal weight: 0.0670 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 101 optimal weight: 0.5980 overall best weight: 1.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 23 ASN A 187 GLN A 390 GLN B 110 ASN B 125 ASN B 155 ASN B 268 ASN G 18 GLN N 3 GLN R 45 GLN R 212 HIS R 302 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.220774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.182644 restraints weight = 11271.568| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 1.41 r_work: 0.3941 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10358 Z= 0.147 Angle : 0.612 9.215 14056 Z= 0.322 Chirality : 0.043 0.145 1543 Planarity : 0.004 0.057 1794 Dihedral : 5.751 55.450 1409 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.72 % Allowed : 18.01 % Favored : 76.27 % 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: -0.76 (0.23), residues: 1246 helix: 0.19 (0.23), residues: 489 sheet: -0.52 (0.33), residues: 220 loop : -1.04 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.029 0.002 TYR R 148 PHE 0.012 0.002 PHE B 199 TRP 0.014 0.002 TRP R 72 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (10352) covalent geometry : angle 0.61134 / 0.32 (14044) SS BOND : bond 0.00329 / 0.16 ( 6) SS BOND : angle 1.32811 / 0.78 ( 12) hydrogen bonds : bond 0.04978 / 3.23 ( 457) hydrogen bonds : angle 5.11766 / 3.63 ( 1299) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 117 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.1983 (ptt) cc_final: 0.1742 (mtm) REVERT: A 265 ARG cc_start: 0.7419 (mtp85) cc_final: 0.6311 (ttt-90) REVERT: A 267 GLN cc_start: 0.8039 (tp-100) cc_final: 0.7759 (tp40) REVERT: A 390 GLN cc_start: 0.7071 (mt0) cc_final: 0.6792 (mt0) REVERT: B 44 GLN cc_start: 0.6626 (mp10) cc_final: 0.6233 (mp10) REVERT: B 59 TYR cc_start: 0.6946 (OUTLIER) cc_final: 0.6067 (t80) REVERT: B 124 TYR cc_start: 0.5578 (m-80) cc_final: 0.5260 (m-80) REVERT: B 142 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.5747 (m-70) REVERT: B 217 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6442 (pmm) REVERT: B 261 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7882 (mp) REVERT: B 266 HIS cc_start: 0.6302 (t-170) cc_final: 0.5974 (t70) REVERT: G 32 LYS cc_start: 0.7185 (mmmt) cc_final: 0.6742 (tptt) REVERT: N 43 LYS cc_start: 0.6216 (tmtt) cc_final: 0.5906 (mmtp) REVERT: N 46 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7374 (mm-30) REVERT: N 78 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7479 (m) REVERT: R 50 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5618 (mp) REVERT: R 67 ASP cc_start: 0.7312 (p0) cc_final: 0.7070 (p0) REVERT: R 127 GLU cc_start: 0.6168 (mm-30) cc_final: 0.5826 (tp30) REVERT: R 346 LYS cc_start: 0.5892 (mttp) cc_final: 0.5440 (mtmt) REVERT: R 371 MET cc_start: 0.7552 (tpp) cc_final: 0.7341 (tpp) REVERT: R 411 LEU cc_start: 0.6741 (mt) cc_final: 0.6498 (mt) REVERT: R 414 ARG cc_start: 0.5694 (mmt-90) cc_final: 0.5310 (mmm160) outliers start: 62 outliers final: 29 residues processed: 169 average time/residue: 0.4601 time to fit residues: 84.6839 Evaluate side-chains 144 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 293 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.0870 chunk 56 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 23 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN B 110 ASN B 125 ASN B 155 ASN B 259 GLN B 268 ASN N 3 GLN R 45 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.222829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.184536 restraints weight = 11323.325| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 1.40 r_work: 0.3966 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10358 Z= 0.122 Angle : 0.560 8.317 14056 Z= 0.296 Chirality : 0.042 0.143 1543 Planarity : 0.004 0.059 1794 Dihedral : 5.625 57.482 1409 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.54 % Allowed : 18.56 % Favored : 75.90 % 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: -0.39 (0.24), residues: 1246 helix: 0.62 (0.24), residues: 486 sheet: -0.49 (0.33), residues: 230 loop : -0.88 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 20 TYR 0.028 0.002 TYR R 148 PHE 0.012 0.001 PHE B 199 TRP 0.013 0.002 TRP A 234 HIS 0.012 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10352) covalent geometry : angle 0.55786 / 0.30 (14044) SS BOND : bond 0.00252 / 0.12 ( 6) SS BOND : angle 1.65454 / 1.26 ( 12) hydrogen bonds : bond 0.04299 / 2.80 ( 457) hydrogen bonds : angle 4.81909 / 3.40 ( 1299) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 115 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.1834 (ptt) cc_final: 0.1632 (mtm) REVERT: A 265 ARG cc_start: 0.7416 (mtp85) cc_final: 0.6330 (ttt-90) REVERT: A 390 GLN cc_start: 0.6998 (mt0) cc_final: 0.6741 (mt0) REVERT: B 44 GLN cc_start: 0.6589 (mp10) cc_final: 0.6213 (mp10) REVERT: B 59 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.5957 (t80) REVERT: B 124 TYR cc_start: 0.5483 (m-80) cc_final: 0.5150 (m-80) REVERT: B 142 HIS cc_start: 0.7263 (OUTLIER) cc_final: 0.5738 (m-70) REVERT: B 217 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.6389 (pmm) REVERT: B 261 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7843 (mp) REVERT: B 304 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6369 (mtm180) REVERT: G 32 LYS cc_start: 0.7044 (mmmt) cc_final: 0.6722 (tptt) REVERT: N 43 LYS cc_start: 0.6318 (tmtt) cc_final: 0.5970 (mmtt) REVERT: N 46 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7365 (mm-30) REVERT: R 50 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5733 (mp) REVERT: R 67 ASP cc_start: 0.7133 (p0) cc_final: 0.6897 (p0) REVERT: R 292 GLU cc_start: 0.5632 (OUTLIER) cc_final: 0.5285 (mt-10) REVERT: R 346 LYS cc_start: 0.5965 (mttp) cc_final: 0.5556 (ttmt) REVERT: R 371 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7283 (tpp) REVERT: R 411 LEU cc_start: 0.6717 (mt) cc_final: 0.6469 (mt) REVERT: R 414 ARG cc_start: 0.5684 (mmt-90) cc_final: 0.5246 (mmm-85) outliers start: 60 outliers final: 37 residues processed: 161 average time/residue: 0.5011 time to fit residues: 87.7537 Evaluate side-chains 146 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 101 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 267 ARG Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 371 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 24 optimal weight: 0.4980 chunk 91 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 23 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 155 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.221316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.182801 restraints weight = 11254.202| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 1.38 r_work: 0.3949 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10358 Z= 0.142 Angle : 0.609 11.822 14056 Z= 0.318 Chirality : 0.043 0.188 1543 Planarity : 0.004 0.060 1794 Dihedral : 5.821 58.758 1407 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 6.09 % Allowed : 19.30 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.24), residues: 1246 helix: 0.65 (0.24), residues: 488 sheet: -0.35 (0.35), residues: 216 loop : -0.87 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 20 TYR 0.030 0.002 TYR R 148 PHE 0.020 0.002 PHE A 222 TRP 0.013 0.002 TRP A 234 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (10352) covalent geometry : angle 0.60287 / 0.32 (14044) SS BOND : bond 0.00735 / 0.35 ( 6) SS BOND : angle 3.02002 / 1.38 ( 12) hydrogen bonds : bond 0.04471 / 2.91 ( 457) hydrogen bonds : angle 4.85862 / 3.42 ( 1299) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 109 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7711 (mp) REVERT: A 265 ARG cc_start: 0.7374 (mtp85) cc_final: 0.6314 (ttt-90) REVERT: B 44 GLN cc_start: 0.6604 (mp10) cc_final: 0.6225 (mp10) REVERT: B 59 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.5954 (t80) REVERT: B 142 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.5994 (m-70) REVERT: B 175 GLN cc_start: 0.7571 (pm20) cc_final: 0.7147 (mp10) REVERT: B 217 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6438 (pmm) REVERT: B 261 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7954 (mp) REVERT: B 304 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6344 (mtm180) REVERT: G 32 LYS cc_start: 0.7106 (mmmt) cc_final: 0.6737 (tptt) REVERT: N 43 LYS cc_start: 0.6357 (tmtt) cc_final: 0.5963 (mmtt) REVERT: N 46 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7361 (mm-30) REVERT: R 50 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5724 (mp) REVERT: R 67 ASP cc_start: 0.7165 (p0) cc_final: 0.6935 (p0) REVERT: R 292 GLU cc_start: 0.5627 (OUTLIER) cc_final: 0.5234 (mt-10) REVERT: R 346 LYS cc_start: 0.5844 (mttp) cc_final: 0.5462 (OUTLIER) REVERT: R 371 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7217 (tpp) REVERT: R 411 LEU cc_start: 0.6794 (mt) cc_final: 0.6549 (mt) REVERT: R 414 ARG cc_start: 0.5723 (mmt-90) cc_final: 0.5269 (mmm-85) outliers start: 66 outliers final: 36 residues processed: 161 average time/residue: 0.4968 time to fit residues: 87.2047 Evaluate side-chains 149 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 371 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 8 optimal weight: 30.0000 chunk 46 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 110 ASN B 125 ASN B 155 ASN B 259 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.223028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.184417 restraints weight = 11317.231| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 1.44 r_work: 0.3962 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3869 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10358 Z= 0.117 Angle : 0.564 11.394 14056 Z= 0.296 Chirality : 0.042 0.152 1543 Planarity : 0.004 0.058 1794 Dihedral : 5.666 59.824 1407 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.17 % Allowed : 21.14 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.24), residues: 1246 helix: 0.92 (0.24), residues: 486 sheet: -0.38 (0.33), residues: 232 loop : -0.74 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 20 TYR 0.028 0.002 TYR R 148 PHE 0.037 0.001 PHE A 222 TRP 0.018 0.002 TRP R 72 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (10352) covalent geometry : angle 0.55935 / 0.29 (14044) SS BOND : bond 0.00444 / 0.22 ( 6) SS BOND : angle 2.59844 / 1.26 ( 12) hydrogen bonds : bond 0.04060 / 2.65 ( 457) hydrogen bonds : angle 4.64476 / 3.27 ( 1299) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 104 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7363 (mtp85) cc_final: 0.6283 (ttt-90) REVERT: B 44 GLN cc_start: 0.6619 (mp10) cc_final: 0.6248 (mp10) REVERT: B 59 TYR cc_start: 0.6798 (OUTLIER) cc_final: 0.5897 (t80) REVERT: B 142 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.5815 (m-70) REVERT: B 175 GLN cc_start: 0.7444 (pm20) cc_final: 0.6999 (mp10) REVERT: B 217 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6473 (pmm) REVERT: B 261 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7907 (mp) REVERT: B 304 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6408 (mtm180) REVERT: B 325 MET cc_start: 0.5458 (mpp) cc_final: 0.4392 (ptt) REVERT: G 32 LYS cc_start: 0.7082 (mmmt) cc_final: 0.6679 (tptt) REVERT: N 43 LYS cc_start: 0.6405 (tmtt) cc_final: 0.5935 (mmtt) REVERT: N 46 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7345 (mm-30) REVERT: N 91 THR cc_start: 0.7887 (OUTLIER) cc_final: 0.7395 (t) REVERT: R 50 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5699 (mp) REVERT: R 67 ASP cc_start: 0.7008 (p0) cc_final: 0.6760 (p0) REVERT: R 292 GLU cc_start: 0.5534 (OUTLIER) cc_final: 0.5111 (mt-10) REVERT: R 346 LYS cc_start: 0.5830 (mttp) cc_final: 0.5459 (OUTLIER) REVERT: R 371 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7350 (tpp) REVERT: R 411 LEU cc_start: 0.6733 (mt) cc_final: 0.6488 (mt) REVERT: R 414 ARG cc_start: 0.5590 (mmt-90) cc_final: 0.5145 (mmm-85) outliers start: 56 outliers final: 31 residues processed: 145 average time/residue: 0.4776 time to fit residues: 75.6691 Evaluate side-chains 137 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 371 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 125 ASN B 155 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.224262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.186107 restraints weight = 11257.546| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 1.39 r_work: 0.3981 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10358 Z= 0.107 Angle : 0.543 11.868 14056 Z= 0.284 Chirality : 0.041 0.174 1543 Planarity : 0.004 0.056 1794 Dihedral : 5.477 59.003 1406 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.17 % Allowed : 21.05 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.24), residues: 1246 helix: 1.08 (0.24), residues: 490 sheet: -0.28 (0.33), residues: 232 loop : -0.64 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 20 TYR 0.029 0.001 TYR R 148 PHE 0.037 0.001 PHE A 222 TRP 0.017 0.001 TRP R 72 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (10352) covalent geometry : angle 0.53995 / 0.28 (14044) SS BOND : bond 0.00282 / 0.13 ( 6) SS BOND : angle 2.03729 / 1.03 ( 12) hydrogen bonds : bond 0.03751 / 2.45 ( 457) hydrogen bonds : angle 4.46496 / 3.14 ( 1299) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 111 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7656 (mp) REVERT: A 265 ARG cc_start: 0.7336 (mtp85) cc_final: 0.6276 (ttt-90) REVERT: A 376 PHE cc_start: 0.7611 (t80) cc_final: 0.7407 (t80) REVERT: B 44 GLN cc_start: 0.6606 (mp10) cc_final: 0.6247 (mp10) REVERT: B 59 TYR cc_start: 0.6769 (OUTLIER) cc_final: 0.5842 (t80) REVERT: B 101 MET cc_start: 0.7861 (mtp) cc_final: 0.7605 (mtm) REVERT: B 142 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.5698 (m-70) REVERT: B 175 GLN cc_start: 0.7265 (pm20) cc_final: 0.6947 (mp10) REVERT: B 261 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7893 (mp) REVERT: B 304 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6374 (mtm180) REVERT: B 325 MET cc_start: 0.5365 (mpp) cc_final: 0.4480 (ptt) REVERT: G 32 LYS cc_start: 0.7046 (mmmt) cc_final: 0.6633 (tptt) REVERT: N 43 LYS cc_start: 0.6404 (tmtt) cc_final: 0.5955 (mmtt) REVERT: N 46 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7326 (mm-30) REVERT: N 65 LYS cc_start: 0.6796 (OUTLIER) cc_final: 0.6429 (mtpt) REVERT: N 91 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7357 (t) REVERT: R 52 GLU cc_start: 0.4433 (tm-30) cc_final: 0.3636 (mm-30) REVERT: R 67 ASP cc_start: 0.6975 (p0) cc_final: 0.6721 (p0) REVERT: R 93 SER cc_start: 0.6213 (OUTLIER) cc_final: 0.5913 (p) REVERT: R 346 LYS cc_start: 0.5888 (mttp) cc_final: 0.5532 (OUTLIER) REVERT: R 371 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7225 (tpp) REVERT: R 411 LEU cc_start: 0.6713 (mt) cc_final: 0.6501 (mt) REVERT: R 414 ARG cc_start: 0.5640 (mmt-90) cc_final: 0.5209 (mmm-85) outliers start: 56 outliers final: 29 residues processed: 153 average time/residue: 0.4934 time to fit residues: 82.3686 Evaluate side-chains 142 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 371 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 125 ASN B 155 ASN B 220 GLN B 259 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.218761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.179372 restraints weight = 11243.289| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 1.45 r_work: 0.3917 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10358 Z= 0.228 Angle : 0.710 13.869 14056 Z= 0.375 Chirality : 0.047 0.188 1543 Planarity : 0.005 0.061 1794 Dihedral : 6.135 57.241 1405 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.17 % Allowed : 21.61 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.24), residues: 1246 helix: 0.55 (0.23), residues: 486 sheet: -0.29 (0.33), residues: 233 loop : -0.87 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 20 TYR 0.032 0.003 TYR R 148 PHE 0.041 0.003 PHE A 222 TRP 0.026 0.003 TRP R 72 HIS 0.008 0.002 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (10352) covalent geometry : angle 0.70566 / 0.37 (14044) SS BOND : bond 0.00433 / 0.22 ( 6) SS BOND : angle 2.67823 / 1.21 ( 12) hydrogen bonds : bond 0.05236 / 3.41 ( 457) hydrogen bonds : angle 5.13559 / 3.61 ( 1299) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 103 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7422 (mtp85) cc_final: 0.6342 (ttt-90) REVERT: A 299 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6947 (mp0) REVERT: A 376 PHE cc_start: 0.7618 (t80) cc_final: 0.7374 (t80) REVERT: B 44 GLN cc_start: 0.6681 (mp10) cc_final: 0.6289 (mp10) REVERT: B 59 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6115 (t80) REVERT: B 142 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.5909 (m-70) REVERT: B 175 GLN cc_start: 0.7582 (pm20) cc_final: 0.7246 (mp10) REVERT: B 217 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6435 (pmm) REVERT: B 261 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7982 (mp) REVERT: B 304 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6445 (mtm180) REVERT: B 325 MET cc_start: 0.5415 (mpp) cc_final: 0.4530 (ptt) REVERT: G 32 LYS cc_start: 0.7154 (mmmt) cc_final: 0.6795 (tptt) REVERT: N 43 LYS cc_start: 0.6456 (tmtt) cc_final: 0.5987 (mmtt) REVERT: N 46 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7401 (mm-30) REVERT: N 77 ASN cc_start: 0.7294 (OUTLIER) cc_final: 0.6998 (m-40) REVERT: R 50 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5552 (mp) REVERT: R 67 ASP cc_start: 0.7176 (p0) cc_final: 0.6939 (p0) REVERT: R 224 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7777 (tt) REVERT: R 346 LYS cc_start: 0.5759 (mttp) cc_final: 0.5400 (mtmt) REVERT: R 371 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7272 (tpp) REVERT: R 411 LEU cc_start: 0.6781 (mt) cc_final: 0.6520 (mt) REVERT: R 414 ARG cc_start: 0.5646 (mmt-90) cc_final: 0.5198 (mmm-85) outliers start: 56 outliers final: 31 residues processed: 148 average time/residue: 0.4420 time to fit residues: 72.0864 Evaluate side-chains 138 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 371 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 125 ASN B 155 ASN B 259 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.220101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.180946 restraints weight = 11309.146| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 1.44 r_work: 0.3922 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10358 Z= 0.192 Angle : 0.675 13.197 14056 Z= 0.356 Chirality : 0.046 0.207 1543 Planarity : 0.005 0.060 1794 Dihedral : 6.120 57.147 1405 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.43 % Allowed : 22.16 % Favored : 73.41 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.24), residues: 1246 helix: 0.47 (0.23), residues: 486 sheet: -0.30 (0.33), residues: 234 loop : -0.90 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 20 TYR 0.033 0.003 TYR R 148 PHE 0.057 0.002 PHE A 222 TRP 0.027 0.003 TRP R 72 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (10352) covalent geometry : angle 0.67124 / 0.35 (14044) SS BOND : bond 0.00395 / 0.20 ( 6) SS BOND : angle 2.51101 / 1.14 ( 12) hydrogen bonds : bond 0.04915 / 3.20 ( 457) hydrogen bonds : angle 5.05326 / 3.55 ( 1299) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 102 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.4794 (mtm-85) cc_final: 0.3378 (ptt180) REVERT: A 265 ARG cc_start: 0.7439 (mtp85) cc_final: 0.6353 (ttt-90) REVERT: A 299 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6912 (mp0) REVERT: A 376 PHE cc_start: 0.7616 (t80) cc_final: 0.7384 (t80) REVERT: B 44 GLN cc_start: 0.6696 (mp10) cc_final: 0.6303 (mp10) REVERT: B 59 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6034 (t80) REVERT: B 142 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.5787 (m-70) REVERT: B 175 GLN cc_start: 0.7580 (pm20) cc_final: 0.7244 (mp10) REVERT: B 217 MET cc_start: 0.6684 (pmt) cc_final: 0.6393 (pmm) REVERT: B 261 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7964 (mp) REVERT: B 304 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7252 (ttm170) REVERT: B 325 MET cc_start: 0.5192 (mpp) cc_final: 0.4608 (ptt) REVERT: G 32 LYS cc_start: 0.7143 (mmmt) cc_final: 0.6759 (tptt) REVERT: N 43 LYS cc_start: 0.6429 (tmtt) cc_final: 0.5957 (mmtt) REVERT: N 46 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7373 (mm-30) REVERT: N 77 ASN cc_start: 0.7289 (OUTLIER) cc_final: 0.6995 (m-40) REVERT: R 50 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5605 (mp) REVERT: R 67 ASP cc_start: 0.7200 (p0) cc_final: 0.6949 (p0) REVERT: R 224 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7734 (tt) REVERT: R 292 GLU cc_start: 0.5630 (OUTLIER) cc_final: 0.5215 (mt-10) REVERT: R 303 MET cc_start: 0.6916 (mmm) cc_final: 0.6609 (mmt) REVERT: R 346 LYS cc_start: 0.5748 (mttp) cc_final: 0.5361 (mtmt) REVERT: R 371 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7277 (tpp) REVERT: R 397 MET cc_start: 0.7686 (mmp) cc_final: 0.7415 (mmt) REVERT: R 411 LEU cc_start: 0.6716 (mt) cc_final: 0.6470 (mt) REVERT: R 414 ARG cc_start: 0.5628 (mmt-90) cc_final: 0.5169 (mmm-85) outliers start: 48 outliers final: 30 residues processed: 140 average time/residue: 0.4513 time to fit residues: 69.5352 Evaluate side-chains 137 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 371 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 7 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 27 optimal weight: 0.0470 chunk 96 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 125 ASN B 155 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.222190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.183101 restraints weight = 11179.401| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.67 r_work: 0.3942 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10358 Z= 0.120 Angle : 0.579 12.031 14056 Z= 0.306 Chirality : 0.042 0.153 1543 Planarity : 0.004 0.057 1794 Dihedral : 5.700 59.104 1405 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.97 % Allowed : 22.71 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.24), residues: 1246 helix: 0.92 (0.24), residues: 485 sheet: -0.20 (0.34), residues: 223 loop : -0.78 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 20 TYR 0.028 0.002 TYR R 148 PHE 0.056 0.002 PHE A 222 TRP 0.026 0.002 TRP R 72 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (10352) covalent geometry : angle 0.57615 / 0.30 (14044) SS BOND : bond 0.00270 / 0.13 ( 6) SS BOND : angle 2.07127 / 1.01 ( 12) hydrogen bonds : bond 0.04108 / 2.67 ( 457) hydrogen bonds : angle 4.68112 / 3.27 ( 1299) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.4809 (mtm-85) cc_final: 0.3386 (ptt180) REVERT: A 265 ARG cc_start: 0.7398 (mtp85) cc_final: 0.6342 (ttt-90) REVERT: A 376 PHE cc_start: 0.7622 (t80) cc_final: 0.7404 (t80) REVERT: B 44 GLN cc_start: 0.6700 (mp10) cc_final: 0.6321 (mp10) REVERT: B 59 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.5949 (t80) REVERT: B 142 HIS cc_start: 0.7152 (OUTLIER) cc_final: 0.5909 (m-70) REVERT: B 175 GLN cc_start: 0.7532 (pm20) cc_final: 0.7193 (mp10) REVERT: B 217 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6474 (pmm) REVERT: B 261 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7940 (mp) REVERT: B 325 MET cc_start: 0.5197 (mpp) cc_final: 0.4684 (ptt) REVERT: G 32 LYS cc_start: 0.7088 (mmmt) cc_final: 0.6683 (tptt) REVERT: N 43 LYS cc_start: 0.6409 (tmtt) cc_final: 0.5937 (mmtt) REVERT: N 46 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7348 (mm-30) REVERT: R 67 ASP cc_start: 0.7097 (p0) cc_final: 0.6843 (p0) REVERT: R 224 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7654 (tt) REVERT: R 303 MET cc_start: 0.6900 (mmm) cc_final: 0.6589 (mmt) REVERT: R 346 LYS cc_start: 0.5744 (mttp) cc_final: 0.5389 (mtmt) REVERT: R 371 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7273 (tpp) REVERT: R 397 MET cc_start: 0.7676 (mmp) cc_final: 0.7404 (mmt) REVERT: R 411 LEU cc_start: 0.6663 (mt) cc_final: 0.6437 (mt) REVERT: R 414 ARG cc_start: 0.5550 (mmt-90) cc_final: 0.5120 (mmm-85) outliers start: 43 outliers final: 26 residues processed: 137 average time/residue: 0.4940 time to fit residues: 74.0945 Evaluate side-chains 130 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 371 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 117 optimal weight: 0.0170 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.3420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 125 ASN B 155 ASN B 259 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.221526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.182308 restraints weight = 11248.442| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 1.46 r_work: 0.3953 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10358 Z= 0.130 Angle : 0.595 12.448 14056 Z= 0.313 Chirality : 0.043 0.157 1543 Planarity : 0.005 0.057 1794 Dihedral : 5.726 59.866 1405 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.88 % Allowed : 22.90 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.24), residues: 1246 helix: 0.97 (0.24), residues: 489 sheet: -0.17 (0.34), residues: 223 loop : -0.77 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 20 TYR 0.029 0.002 TYR R 148 PHE 0.053 0.002 PHE A 222 TRP 0.033 0.002 TRP R 72 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10352) covalent geometry : angle 0.59231 / 0.31 (14044) SS BOND : bond 0.00287 / 0.14 ( 6) SS BOND : angle 2.02280 / 0.96 ( 12) hydrogen bonds : bond 0.04176 / 2.72 ( 457) hydrogen bonds : angle 4.65797 / 3.26 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4690.58 seconds wall clock time: 80 minutes 31.62 seconds (4831.62 seconds total)