Starting phenix.real_space_refine on Fri Jul 3 06:06:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fm9_50550/07_2026/9fm9_50550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fm9_50550/07_2026/9fm9_50550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fm9_50550/07_2026/9fm9_50550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fm9_50550/07_2026/9fm9_50550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fm9_50550/07_2026/9fm9_50550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fm9_50550/07_2026/9fm9_50550.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 71 5.16 5 C 8109 2.51 5 N 2192 2.21 5 O 2390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12764 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3847 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 23, 'TRANS': 475} Chain: "B" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3837 Classifications: {'peptide': 498} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 474} Chain: "C" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3504 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 22, 'TRANS': 432} Chain breaks: 2 Chain: "D" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1574 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain breaks: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Time building chain proxies: 2.82, per 1000 atoms: 0.22 Number of scatterers: 12764 At special positions: 0 Unit cell: (108.68, 113.696, 103.664, 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) K 2 19.00 S 71 16.00 O 2390 8.00 N 2192 7.00 C 8109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 461.8 milliseconds 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3002 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 43.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 56 through 75 removed outlier: 3.748A pdb=" N ILE A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 95 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 111 through 136 removed outlier: 5.476A pdb=" N LEU A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 168 through 183 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 196 through 207 removed outlier: 3.894A pdb=" N MET A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 282 through 294 Processing helix chain 'A' and resid 295 through 301 removed outlier: 6.068A pdb=" N ASN A 298 " --> pdb=" O PHE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 347 through 364 Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.584A pdb=" N GLY A 383 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.574A pdb=" N CYS A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 489 Processing helix chain 'B' and resid 58 through 76 removed outlier: 4.463A pdb=" N GLU B 72 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LYS B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.517A pdb=" N ASN B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 118 through 137 removed outlier: 3.759A pdb=" N ARG B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 183 removed outlier: 3.767A pdb=" N LYS B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 178 " --> pdb=" O CYS B 174 " (cutoff:3.500A) Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 243 through 255 Processing helix chain 'B' and resid 282 through 293 removed outlier: 3.551A pdb=" N THR B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 removed outlier: 5.342A pdb=" N ASN B 298 " --> pdb=" O PHE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 4.458A pdb=" N GLN B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.625A pdb=" N LYS B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'C' and resid 58 through 75 removed outlier: 5.038A pdb=" N GLU C 72 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LYS C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 96 removed outlier: 3.661A pdb=" N ASN C 96 " --> pdb=" O ARG C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.699A pdb=" N ALA C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 114 through 119' Processing helix chain 'C' and resid 119 through 137 removed outlier: 3.660A pdb=" N ARG C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 183 Proline residue: C 179 - end of helix Processing helix chain 'C' and resid 197 through 207 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 225 through 231 removed outlier: 3.610A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 283 through 293 Processing helix chain 'C' and resid 297 through 301 removed outlier: 3.662A pdb=" N GLY C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 328 Processing helix chain 'C' and resid 347 through 365 removed outlier: 3.615A pdb=" N LYS C 351 " --> pdb=" O SER C 347 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 364 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 365 " --> pdb=" O GLY C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 426 Processing helix chain 'C' and resid 440 through 451 Processing helix chain 'D' and resid 59 through 75 removed outlier: 4.281A pdb=" N LYS D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY D 75 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 96 Processing helix chain 'D' and resid 119 through 137 Processing helix chain 'D' and resid 170 through 184 Proline residue: D 179 - end of helix Processing helix chain 'D' and resid 200 through 210 removed outlier: 3.664A pdb=" N LEU D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP D 208 " --> pdb=" O ASN D 204 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 210 " --> pdb=" O ILE D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 425 Processing helix chain 'D' and resid 443 through 450 Processing helix chain 'D' and resid 483 through 487 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 42 removed outlier: 6.220A pdb=" N PHE A 38 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLN A 51 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN A 40 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 47 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 140 through 143 removed outlier: 7.941A pdb=" N VAL B 456 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN A 495 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR B 458 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 497 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY B 433 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER B 269 " --> pdb=" O ARG B 308 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B 310 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASN B 271 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLN B 312 " --> pdb=" O ASN B 271 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE B 273 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N CYS B 305 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N SER B 411 " --> pdb=" O CYS B 305 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N SER B 307 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR B 413 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL B 309 " --> pdb=" O THR B 413 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N PHE B 415 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 311 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR B 390 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL B 412 " --> pdb=" O THR B 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 217 removed outlier: 6.463A pdb=" N VAL A 160 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LYS A 190 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN A 162 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 241 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 367 through 370 removed outlier: 6.268A pdb=" N ILE A 391 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 309 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE A 415 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE A 311 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 141 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL D 456 " --> pdb=" O THR C 493 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN C 495 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR D 458 " --> pdb=" O ASN C 495 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU C 497 " --> pdb=" O THR D 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 20 through 21 removed outlier: 8.005A pdb=" N TYR B 21 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN B 40 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN B 51 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE B 38 " --> pdb=" O GLN B 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 25 Processing sheet with id=AA7, first strand: chain 'B' and resid 215 through 217 removed outlier: 6.643A pdb=" N VAL B 160 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS B 190 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN B 162 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS B 237 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.208A pdb=" N PHE C 38 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN C 51 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN C 40 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 159 through 164 Processing sheet with id=AB1, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.766A pdb=" N ILE C 272 " --> pdb=" O TRP C 437 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA C 434 " --> pdb=" O TRP C 457 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR D 148 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA D 150 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN D 143 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 308 through 312 removed outlier: 6.376A pdb=" N VAL C 309 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N PHE C 415 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE C 311 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 412 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 159 through 161 removed outlier: 3.613A pdb=" N VAL D 160 " --> pdb=" O CYS D 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 272 through 273 removed outlier: 6.805A pdb=" N ILE D 272 " --> pdb=" O TRP D 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 310 through 311 555 hydrogen bonds defined for protein. 1578 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: 1.59 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4247 1.34 - 1.46: 2765 1.46 - 1.58: 5904 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 13036 Sorted by residual: bond pdb=" N LEU D 170 " pdb=" CA LEU D 170 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.32e-02 5.74e+03 7.35e+00 bond pdb=" N CYS D 174 " pdb=" CA CYS D 174 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.20e-02 6.94e+03 6.66e+00 bond pdb=" N LYS D 176 " pdb=" CA LYS D 176 " ideal model delta sigma weight residual 1.460 1.490 -0.030 1.22e-02 6.72e+03 6.11e+00 bond pdb=" N MET D 172 " pdb=" CA MET D 172 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.28e+00 bond pdb=" N LEU D 177 " pdb=" CA LEU D 177 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.09e+00 ... (remaining 13031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 17339 2.34 - 4.68: 263 4.68 - 7.03: 37 7.03 - 9.37: 5 9.37 - 11.71: 3 Bond angle restraints: 17647 Sorted by residual: angle pdb=" C GLU C 18 " pdb=" N GLU C 19 " pdb=" CA GLU C 19 " ideal model delta sigma weight residual 121.54 133.25 -11.71 1.91e+00 2.74e-01 3.76e+01 angle pdb=" C ARG B 336 " pdb=" N GLU B 337 " pdb=" CA GLU B 337 " ideal model delta sigma weight residual 121.54 113.24 8.30 1.91e+00 2.74e-01 1.89e+01 angle pdb=" C GLU A 280 " pdb=" N ASP A 281 " pdb=" CA ASP A 281 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C PHE C 17 " pdb=" N GLU C 18 " pdb=" CA GLU C 18 " ideal model delta sigma weight residual 121.71 116.35 5.36 1.39e+00 5.18e-01 1.49e+01 angle pdb=" N LYS B 474 " pdb=" CA LYS B 474 " pdb=" C LYS B 474 " ideal model delta sigma weight residual 108.23 103.25 4.98 1.38e+00 5.25e-01 1.30e+01 ... (remaining 17642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6891 17.99 - 35.98: 699 35.98 - 53.97: 125 53.97 - 71.96: 24 71.96 - 89.95: 11 Dihedral angle restraints: 7750 sinusoidal: 3055 harmonic: 4695 Sorted by residual: dihedral pdb=" CA SER B 338 " pdb=" C SER B 338 " pdb=" N ASP B 339 " pdb=" CA ASP B 339 " ideal model delta harmonic sigma weight residual 180.00 -154.94 -25.06 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA PRO C 196 " pdb=" C PRO C 196 " pdb=" N ALA C 197 " pdb=" CA ALA C 197 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ARG A 20 " pdb=" C ARG A 20 " pdb=" N TYR A 21 " pdb=" CA TYR A 21 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 7747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1480 0.054 - 0.107: 384 0.107 - 0.161: 48 0.161 - 0.215: 6 0.215 - 0.269: 1 Chirality restraints: 1919 Sorted by residual: chirality pdb=" CB ILE B 141 " pdb=" CA ILE B 141 " pdb=" CG1 ILE B 141 " pdb=" CG2 ILE B 141 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE B 206 " pdb=" CA ILE B 206 " pdb=" CG1 ILE B 206 " pdb=" CG2 ILE B 206 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.76e-01 chirality pdb=" CB ILE B 342 " pdb=" CA ILE B 342 " pdb=" CG1 ILE B 342 " pdb=" CG2 ILE B 342 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 1916 not shown) Planarity restraints: 2308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 253 " -0.018 2.00e-02 2.50e+03 1.93e-02 7.49e+00 pdb=" CG TYR A 253 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 253 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 253 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 253 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 253 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 253 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 253 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 211 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO B 212 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 212 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 212 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 305 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO B 306 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 306 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 306 " 0.030 5.00e-02 4.00e+02 ... (remaining 2305 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 3009 2.79 - 3.37: 14079 3.37 - 3.96: 25645 3.96 - 4.55: 37406 4.55 - 5.14: 54506 Nonbonded interactions: 134645 Sorted by model distance: nonbonded pdb=" O ILE A 44 " pdb=" OH TYR A 386 " model vdw 2.197 3.040 nonbonded pdb=" NH1 ARG B 135 " pdb=" OD1 ASP D 125 " model vdw 2.212 3.120 nonbonded pdb=" OG1 THR A 304 " pdb=" OH TYR A 464 " model vdw 2.224 3.040 nonbonded pdb=" OD2 ASP C 276 " pdb=" OG SER C 438 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR C 357 " pdb=" OE1 GLU C 403 " model vdw 2.238 3.040 ... (remaining 134640 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 238 or resid 266 through 469 or resid 482 throu \ gh 504)) selection = (chain 'B' and (resid 11 through 238 or resid 266 through 469 or resid 482 throu \ gh 504)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.990 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 0.055 13036 Z= 0.245 Angle : 0.735 11.709 17647 Z= 0.414 Chirality : 0.047 0.269 1919 Planarity : 0.005 0.055 2308 Dihedral : 15.081 89.951 4748 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.23 % Allowed : 0.84 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.20), residues: 1627 helix: -0.83 (0.19), residues: 655 sheet: -1.35 (0.29), residues: 335 loop : -1.73 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 36 TYR 0.048 0.003 TYR A 253 PHE 0.028 0.002 PHE A 130 TRP 0.036 0.002 TRP D 437 HIS 0.022 0.003 HIS C 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 (13036) covalent geometry : angle 0.73516 / 0.41 (17647) hydrogen bonds : bond 0.15984 / 10.52 ( 555) hydrogen bonds : angle 7.31058 / 5.27 ( 1578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.391 Fit side-chains REVERT: B 36 ARG cc_start: 0.7326 (mtm-85) cc_final: 0.6780 (mtm180) REVERT: B 392 PHE cc_start: 0.8017 (m-80) cc_final: 0.7775 (m-80) REVERT: C 107 ASP cc_start: 0.7371 (t70) cc_final: 0.7115 (t70) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 0.1062 time to fit residues: 29.1400 Evaluate side-chains 153 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0060 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 GLN A 491 GLN B 325 GLN B 495 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 GLN D 126 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121136 restraints weight = 16152.404| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.77 r_work: 0.3336 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13036 Z= 0.138 Angle : 0.604 8.930 17647 Z= 0.317 Chirality : 0.044 0.189 1919 Planarity : 0.005 0.048 2308 Dihedral : 5.327 72.379 1772 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.84 % Allowed : 7.49 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.21), residues: 1627 helix: 0.01 (0.20), residues: 648 sheet: -1.21 (0.29), residues: 343 loop : -1.41 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 36 TYR 0.040 0.002 TYR A 253 PHE 0.023 0.002 PHE A 130 TRP 0.016 0.001 TRP A 74 HIS 0.012 0.002 HIS C 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (13036) covalent geometry : angle 0.60381 / 0.32 (17647) hydrogen bonds : bond 0.04603 / 3.20 ( 555) hydrogen bonds : angle 5.40591 / 4.00 ( 1578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.440 Fit side-chains REVERT: A 104 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6834 (mm-30) REVERT: B 351 LYS cc_start: 0.6891 (mttt) cc_final: 0.6520 (mttt) REVERT: B 503 LYS cc_start: 0.8398 (mtmt) cc_final: 0.8129 (mmtm) REVERT: C 65 ASP cc_start: 0.7396 (m-30) cc_final: 0.7122 (m-30) REVERT: C 107 ASP cc_start: 0.8214 (t70) cc_final: 0.8009 (t70) REVERT: D 88 LYS cc_start: 0.7657 (mttm) cc_final: 0.7376 (mttt) outliers start: 11 outliers final: 7 residues processed: 188 average time/residue: 0.1027 time to fit residues: 27.7412 Evaluate side-chains 162 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 0 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 120 optimal weight: 0.0000 chunk 5 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.147754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122846 restraints weight = 16270.283| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.79 r_work: 0.3360 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13036 Z= 0.117 Angle : 0.541 7.109 17647 Z= 0.284 Chirality : 0.043 0.143 1919 Planarity : 0.004 0.046 2308 Dihedral : 4.962 69.458 1772 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.15 % Allowed : 10.09 % Favored : 88.76 % 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: -0.85 (0.21), residues: 1627 helix: 0.50 (0.20), residues: 655 sheet: -1.04 (0.29), residues: 343 loop : -1.31 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 36 TYR 0.042 0.001 TYR A 253 PHE 0.020 0.001 PHE C 153 TRP 0.017 0.001 TRP A 74 HIS 0.009 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (13036) covalent geometry : angle 0.54136 / 0.28 (17647) hydrogen bonds : bond 0.04048 / 2.82 ( 555) hydrogen bonds : angle 5.07266 / 3.75 ( 1578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 404 GLU cc_start: 0.7185 (tt0) cc_final: 0.6395 (pt0) REVERT: B 36 ARG cc_start: 0.7572 (mtm-85) cc_final: 0.7241 (mtm-85) REVERT: B 503 LYS cc_start: 0.8368 (mtmt) cc_final: 0.8128 (mmtm) REVERT: C 65 ASP cc_start: 0.7249 (m-30) cc_final: 0.6893 (m-30) REVERT: C 107 ASP cc_start: 0.8123 (t70) cc_final: 0.7884 (t70) REVERT: C 276 ASP cc_start: 0.8118 (m-30) cc_final: 0.7280 (m-30) REVERT: D 88 LYS cc_start: 0.7639 (mttm) cc_final: 0.7370 (mttt) REVERT: D 172 MET cc_start: 0.6261 (mmp) cc_final: 0.5904 (ptm) outliers start: 15 outliers final: 7 residues processed: 194 average time/residue: 0.1051 time to fit residues: 29.1297 Evaluate side-chains 173 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 107 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.142290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116956 restraints weight = 16433.912| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.69 r_work: 0.3278 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 13036 Z= 0.245 Angle : 0.638 7.824 17647 Z= 0.333 Chirality : 0.047 0.171 1919 Planarity : 0.005 0.046 2308 Dihedral : 5.352 77.085 1772 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.53 % Allowed : 12.54 % Favored : 85.93 % 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: -1.05 (0.21), residues: 1627 helix: 0.30 (0.20), residues: 650 sheet: -1.20 (0.28), residues: 345 loop : -1.33 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 455 TYR 0.043 0.002 TYR A 253 PHE 0.025 0.002 PHE A 130 TRP 0.014 0.002 TRP A 74 HIS 0.013 0.002 HIS C 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.24 (13036) covalent geometry : angle 0.63833 / 0.33 (17647) hydrogen bonds : bond 0.05009 / 3.47 ( 555) hydrogen bonds : angle 5.24539 / 3.89 ( 1578) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7322 (m-80) cc_final: 0.6677 (m-80) REVERT: A 104 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6858 (mm-30) REVERT: B 36 ARG cc_start: 0.7583 (mtm-85) cc_final: 0.7349 (mtm-85) REVERT: B 403 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5619 (mt-10) REVERT: C 65 ASP cc_start: 0.7419 (m-30) cc_final: 0.7045 (m-30) REVERT: C 107 ASP cc_start: 0.8251 (t0) cc_final: 0.8020 (t70) REVERT: D 172 MET cc_start: 0.6253 (mmp) cc_final: 0.6011 (ptm) outliers start: 20 outliers final: 14 residues processed: 180 average time/residue: 0.1022 time to fit residues: 26.4876 Evaluate side-chains 179 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 129 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.145602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.120333 restraints weight = 16332.211| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.72 r_work: 0.3322 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13036 Z= 0.131 Angle : 0.547 7.293 17647 Z= 0.287 Chirality : 0.043 0.147 1919 Planarity : 0.004 0.045 2308 Dihedral : 5.010 73.245 1772 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.91 % Allowed : 14.45 % Favored : 83.64 % 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 (0.21), residues: 1627 helix: 0.62 (0.20), residues: 654 sheet: -1.10 (0.29), residues: 343 loop : -1.24 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 36 TYR 0.042 0.001 TYR A 253 PHE 0.021 0.002 PHE A 130 TRP 0.016 0.001 TRP A 74 HIS 0.008 0.001 HIS C 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (13036) covalent geometry : angle 0.54654 / 0.29 (17647) hydrogen bonds : bond 0.04098 / 2.85 ( 555) hydrogen bonds : angle 5.02810 / 3.73 ( 1578) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7260 (m-80) cc_final: 0.6640 (m-80) REVERT: B 36 ARG cc_start: 0.7513 (mtm-85) cc_final: 0.7275 (mtm-85) REVERT: B 403 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5615 (mt-10) REVERT: B 406 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7712 (t80) REVERT: B 503 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8162 (mmtm) REVERT: C 65 ASP cc_start: 0.7360 (m-30) cc_final: 0.6964 (m-30) REVERT: D 172 MET cc_start: 0.6268 (mmp) cc_final: 0.6009 (ptm) outliers start: 25 outliers final: 19 residues processed: 196 average time/residue: 0.1058 time to fit residues: 29.9134 Evaluate side-chains 183 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 142 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.141687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116378 restraints weight = 16372.933| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.69 r_work: 0.3271 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 13036 Z= 0.259 Angle : 0.653 8.768 17647 Z= 0.340 Chirality : 0.047 0.172 1919 Planarity : 0.005 0.045 2308 Dihedral : 5.381 76.662 1772 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.22 % Allowed : 14.83 % Favored : 82.95 % 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: -1.07 (0.21), residues: 1627 helix: 0.26 (0.20), residues: 650 sheet: -1.25 (0.28), residues: 345 loop : -1.28 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 455 TYR 0.046 0.002 TYR A 253 PHE 0.036 0.003 PHE A 285 TRP 0.013 0.002 TRP D 74 HIS 0.011 0.002 HIS C 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.26 (13036) covalent geometry : angle 0.65306 / 0.34 (17647) hydrogen bonds : bond 0.05036 / 3.49 ( 555) hydrogen bonds : angle 5.21654 / 3.86 ( 1578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.450 Fit side-chains REVERT: A 37 TYR cc_start: 0.7331 (m-80) cc_final: 0.6748 (m-80) REVERT: A 104 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6925 (mm-30) REVERT: B 36 ARG cc_start: 0.7530 (mtm-85) cc_final: 0.7286 (mtm-85) REVERT: B 227 LYS cc_start: 0.7735 (tttm) cc_final: 0.7315 (mtpt) REVERT: B 403 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5702 (mt-10) REVERT: B 406 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7709 (t80) REVERT: C 65 ASP cc_start: 0.7436 (m-30) cc_final: 0.7035 (m-30) REVERT: C 402 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6283 (mp10) REVERT: D 172 MET cc_start: 0.6298 (mmp) cc_final: 0.6062 (ptm) REVERT: D 174 CYS cc_start: 0.7649 (m) cc_final: 0.7308 (m) outliers start: 29 outliers final: 18 residues processed: 186 average time/residue: 0.1167 time to fit residues: 30.9206 Evaluate side-chains 181 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 86 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 5 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 149 optimal weight: 0.0040 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121325 restraints weight = 16235.364| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.71 r_work: 0.3339 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13036 Z= 0.117 Angle : 0.541 7.658 17647 Z= 0.284 Chirality : 0.042 0.144 1919 Planarity : 0.004 0.045 2308 Dihedral : 4.908 70.448 1772 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.76 % Allowed : 15.90 % Favored : 82.34 % 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: -0.67 (0.21), residues: 1627 helix: 0.69 (0.20), residues: 654 sheet: -1.06 (0.29), residues: 343 loop : -1.17 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 95 TYR 0.046 0.001 TYR A 253 PHE 0.030 0.002 PHE A 285 TRP 0.016 0.001 TRP A 74 HIS 0.006 0.001 HIS C 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (13036) covalent geometry : angle 0.54112 / 0.28 (17647) hydrogen bonds : bond 0.03889 / 2.70 ( 555) hydrogen bonds : angle 4.96721 / 3.68 ( 1578) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.481 Fit side-chains REVERT: A 37 TYR cc_start: 0.7168 (m-80) cc_final: 0.6691 (m-80) REVERT: B 18 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.5986 (mp0) REVERT: B 36 ARG cc_start: 0.7458 (mtm-85) cc_final: 0.7218 (mtm-85) REVERT: B 227 LYS cc_start: 0.7606 (tttm) cc_final: 0.7168 (mtpt) REVERT: B 351 LYS cc_start: 0.6755 (mttt) cc_final: 0.6521 (mttt) REVERT: B 403 GLU cc_start: 0.5894 (OUTLIER) cc_final: 0.5530 (mt-10) REVERT: B 406 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7698 (t80) REVERT: B 503 LYS cc_start: 0.8366 (mtmt) cc_final: 0.8128 (mmtm) REVERT: C 65 ASP cc_start: 0.7315 (m-30) cc_final: 0.6887 (m-30) REVERT: C 402 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6342 (mm110) REVERT: D 88 LYS cc_start: 0.7699 (mttm) cc_final: 0.7398 (mttt) REVERT: D 122 LEU cc_start: 0.6429 (mt) cc_final: 0.6151 (tt) REVERT: D 172 MET cc_start: 0.6408 (mmp) cc_final: 0.6119 (ptm) REVERT: D 174 CYS cc_start: 0.7643 (m) cc_final: 0.7258 (m) outliers start: 23 outliers final: 15 residues processed: 191 average time/residue: 0.1068 time to fit residues: 29.6661 Evaluate side-chains 185 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 272 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 33 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.145828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120563 restraints weight = 16174.807| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.72 r_work: 0.3330 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13036 Z= 0.137 Angle : 0.549 7.369 17647 Z= 0.287 Chirality : 0.043 0.183 1919 Planarity : 0.004 0.045 2308 Dihedral : 4.886 70.094 1772 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.76 % Allowed : 16.67 % Favored : 81.57 % 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: -0.60 (0.21), residues: 1627 helix: 0.77 (0.20), residues: 653 sheet: -1.04 (0.29), residues: 345 loop : -1.15 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 95 TYR 0.047 0.001 TYR A 253 PHE 0.028 0.002 PHE A 285 TRP 0.017 0.001 TRP A 74 HIS 0.007 0.001 HIS C 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (13036) covalent geometry : angle 0.54942 / 0.29 (17647) hydrogen bonds : bond 0.04011 / 2.78 ( 555) hydrogen bonds : angle 4.92931 / 3.66 ( 1578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7132 (m-80) cc_final: 0.6693 (m-80) REVERT: B 36 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.7233 (mtm-85) REVERT: B 227 LYS cc_start: 0.7584 (tttm) cc_final: 0.7145 (mtpt) REVERT: B 313 GLU cc_start: 0.7748 (tt0) cc_final: 0.7432 (mt-10) REVERT: B 403 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5601 (mt-10) REVERT: B 406 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7694 (t80) REVERT: B 503 LYS cc_start: 0.8369 (mtmt) cc_final: 0.8138 (mmtm) REVERT: C 19 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6270 (mm-30) REVERT: C 65 ASP cc_start: 0.7289 (m-30) cc_final: 0.6871 (m-30) REVERT: C 402 GLN cc_start: 0.6675 (OUTLIER) cc_final: 0.6246 (mm110) REVERT: D 88 LYS cc_start: 0.7711 (mttm) cc_final: 0.7400 (mttt) REVERT: D 122 LEU cc_start: 0.6327 (mt) cc_final: 0.6079 (tt) REVERT: D 172 MET cc_start: 0.6334 (mmp) cc_final: 0.5989 (ptm) REVERT: D 174 CYS cc_start: 0.7605 (m) cc_final: 0.7233 (m) outliers start: 23 outliers final: 17 residues processed: 185 average time/residue: 0.1069 time to fit residues: 28.5973 Evaluate side-chains 186 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 272 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 126 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 78 optimal weight: 0.0370 chunk 66 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.148169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123669 restraints weight = 16111.269| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.76 r_work: 0.3352 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13036 Z= 0.122 Angle : 0.537 7.225 17647 Z= 0.280 Chirality : 0.043 0.158 1919 Planarity : 0.004 0.044 2308 Dihedral : 4.767 68.542 1772 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.91 % Allowed : 16.90 % Favored : 81.19 % 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: -0.46 (0.21), residues: 1627 helix: 0.90 (0.21), residues: 654 sheet: -1.00 (0.29), residues: 345 loop : -1.08 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 95 TYR 0.045 0.001 TYR A 253 PHE 0.027 0.002 PHE A 285 TRP 0.017 0.001 TRP A 74 HIS 0.006 0.001 HIS C 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (13036) covalent geometry : angle 0.53727 / 0.28 (17647) hydrogen bonds : bond 0.03825 / 2.64 ( 555) hydrogen bonds : angle 4.84216 / 3.59 ( 1578) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7103 (m-80) cc_final: 0.6695 (m-80) REVERT: B 18 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.5911 (mp0) REVERT: B 36 ARG cc_start: 0.7532 (mtm-85) cc_final: 0.7303 (mtm-85) REVERT: B 168 PHE cc_start: 0.8772 (m-80) cc_final: 0.8546 (m-80) REVERT: B 227 LYS cc_start: 0.7597 (tttm) cc_final: 0.7158 (mtpt) REVERT: B 313 GLU cc_start: 0.7795 (tt0) cc_final: 0.7501 (mt-10) REVERT: B 406 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7780 (t80) REVERT: B 503 LYS cc_start: 0.8426 (mtmt) cc_final: 0.8179 (mmtm) REVERT: C 65 ASP cc_start: 0.7256 (m-30) cc_final: 0.6834 (m-30) REVERT: C 402 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6250 (mm110) REVERT: D 74 TRP cc_start: 0.8494 (t-100) cc_final: 0.8235 (t-100) REVERT: D 88 LYS cc_start: 0.7725 (mttm) cc_final: 0.7434 (mttt) REVERT: D 96 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7667 (t0) REVERT: D 122 LEU cc_start: 0.6317 (mt) cc_final: 0.6066 (tt) REVERT: D 172 MET cc_start: 0.6275 (mmp) cc_final: 0.5959 (ptm) REVERT: D 174 CYS cc_start: 0.7623 (m) cc_final: 0.7227 (m) outliers start: 25 outliers final: 19 residues processed: 191 average time/residue: 0.1014 time to fit residues: 28.3823 Evaluate side-chains 192 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 71 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.146618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.121833 restraints weight = 16242.116| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.77 r_work: 0.3326 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13036 Z= 0.160 Angle : 0.564 7.524 17647 Z= 0.294 Chirality : 0.044 0.165 1919 Planarity : 0.004 0.044 2308 Dihedral : 4.890 70.916 1772 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.06 % Allowed : 16.97 % Favored : 80.96 % 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: -0.52 (0.21), residues: 1627 helix: 0.82 (0.20), residues: 654 sheet: -1.04 (0.29), residues: 345 loop : -1.08 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 455 TYR 0.046 0.002 TYR A 253 PHE 0.025 0.002 PHE A 285 TRP 0.016 0.002 TRP A 74 HIS 0.007 0.001 HIS C 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (13036) covalent geometry : angle 0.56412 / 0.29 (17647) hydrogen bonds : bond 0.04137 / 2.86 ( 555) hydrogen bonds : angle 4.89202 / 3.63 ( 1578) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.484 Fit side-chains REVERT: A 37 TYR cc_start: 0.7172 (m-80) cc_final: 0.6759 (m-80) REVERT: B 18 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.5854 (mp0) REVERT: B 36 ARG cc_start: 0.7524 (mtm-85) cc_final: 0.7297 (mtm-85) REVERT: B 227 LYS cc_start: 0.7603 (tttm) cc_final: 0.7164 (mtpt) REVERT: B 313 GLU cc_start: 0.7793 (tt0) cc_final: 0.7494 (mt-10) REVERT: B 403 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5703 (mt-10) REVERT: B 406 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7766 (t80) REVERT: B 503 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8192 (mmtm) REVERT: C 65 ASP cc_start: 0.7317 (m-30) cc_final: 0.6915 (m-30) REVERT: C 112 ILE cc_start: 0.8243 (tp) cc_final: 0.7787 (tp) REVERT: C 402 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6255 (mm110) REVERT: D 74 TRP cc_start: 0.8511 (t-100) cc_final: 0.8192 (t-100) REVERT: D 88 LYS cc_start: 0.7756 (mttm) cc_final: 0.7437 (mttt) REVERT: D 96 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7600 (t0) REVERT: D 122 LEU cc_start: 0.6388 (mt) cc_final: 0.6139 (tt) REVERT: D 172 MET cc_start: 0.6219 (mmp) cc_final: 0.5890 (ptm) REVERT: D 174 CYS cc_start: 0.7641 (m) cc_final: 0.7240 (m) outliers start: 27 outliers final: 20 residues processed: 187 average time/residue: 0.1057 time to fit residues: 28.7937 Evaluate side-chains 189 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 5 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.145004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.120120 restraints weight = 16267.900| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.76 r_work: 0.3300 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 13036 Z= 0.192 Angle : 0.597 8.123 17647 Z= 0.311 Chirality : 0.045 0.177 1919 Planarity : 0.004 0.044 2308 Dihedral : 5.086 74.654 1772 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.06 % Allowed : 17.20 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.21), residues: 1627 helix: 0.65 (0.20), residues: 653 sheet: -1.08 (0.29), residues: 345 loop : -1.10 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 95 TYR 0.048 0.002 TYR A 253 PHE 0.025 0.002 PHE A 285 TRP 0.016 0.002 TRP A 74 HIS 0.008 0.001 HIS C 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (13036) covalent geometry : angle 0.59672 / 0.31 (17647) hydrogen bonds : bond 0.04466 / 3.08 ( 555) hydrogen bonds : angle 4.98939 / 3.70 ( 1578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2785.75 seconds wall clock time: 48 minutes 29.25 seconds (2909.25 seconds total)