Starting phenix.real_space_refine on Wed Feb 4 04:15:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wnq_32633/02_2026/7wnq_32633.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wnq_32633/02_2026/7wnq_32633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wnq_32633/02_2026/7wnq_32633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wnq_32633/02_2026/7wnq_32633.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wnq_32633/02_2026/7wnq_32633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wnq_32633/02_2026/7wnq_32633.map" } resolution = 2.7 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= 0.005 sd= 0.172 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 5964 2.51 5 N 1398 2.21 5 O 1440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8847 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2949 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 22, 'TRANS': 345} Restraints were copied for chains: B, C Time building chain proxies: 1.53, per 1000 atoms: 0.17 Number of scatterers: 8847 At special positions: 0 Unit cell: (105.6, 100.1, 80.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1440 8.00 N 1398 7.00 C 5964 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: 0.81 Conformation dependent library (CDL) restraints added in 341.0 milliseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 75.0% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.534A pdb=" N TYR A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 201 through 209 removed outlier: 3.589A pdb=" N LEU A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 removed outlier: 3.785A pdb=" N ASN A 216 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N PHE A 217 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 250 removed outlier: 3.844A pdb=" N LEU A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 241 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.513A pdb=" N ARG A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 277 removed outlier: 3.586A pdb=" N VAL A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 275 " --> pdb=" O TRP A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 removed outlier: 4.185A pdb=" N TRP A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.500A pdb=" N LEU A 307 " --> pdb=" O PRO A 303 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 328 through 335 removed outlier: 3.526A pdb=" N HIS A 332 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 350 through 372 removed outlier: 3.530A pdb=" N ALA A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 391 through 409 removed outlier: 4.019A pdb=" N ALA A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA A 396 " --> pdb=" O MET A 392 " (cutoff:3.500A) Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 412 through 431 removed outlier: 3.586A pdb=" N THR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS A 418 " --> pdb=" O CYS A 414 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 442 through 448 Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.538A pdb=" N ALA A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 456 " --> pdb=" O MET A 452 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 499 removed outlier: 3.515A pdb=" N LEU A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 491 " --> pdb=" O CYS A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 removed outlier: 3.705A pdb=" N ILE A 510 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.533A pdb=" N TYR B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 190 through 192 No H-bonds generated for 'chain 'B' and resid 190 through 192' Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 201 through 209 removed outlier: 3.589A pdb=" N LEU B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 removed outlier: 3.784A pdb=" N ASN B 216 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N PHE B 217 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 250 removed outlier: 3.844A pdb=" N LEU B 226 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 241 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 removed outlier: 3.513A pdb=" N ARG B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.586A pdb=" N VAL B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 275 " --> pdb=" O TRP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 301 removed outlier: 4.185A pdb=" N TRP B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.500A pdb=" N LEU B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 316 " --> pdb=" O TYR B 312 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'B' and resid 328 through 335 removed outlier: 3.526A pdb=" N HIS B 332 " --> pdb=" O PRO B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 350 through 372 removed outlier: 3.529A pdb=" N ALA B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 391 through 409 removed outlier: 4.018A pdb=" N ALA B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA B 396 " --> pdb=" O MET B 392 " (cutoff:3.500A) Proline residue: B 397 - end of helix Processing helix chain 'B' and resid 412 through 431 removed outlier: 3.586A pdb=" N THR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 442 through 448 Processing helix chain 'B' and resid 449 through 466 removed outlier: 3.538A pdb=" N ALA B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 456 " --> pdb=" O MET B 452 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 499 removed outlier: 3.514A pdb=" N LEU B 474 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 491 " --> pdb=" O CYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 511 removed outlier: 3.705A pdb=" N ILE B 510 " --> pdb=" O ASP B 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.534A pdb=" N TYR C 156 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 201 through 209 removed outlier: 3.590A pdb=" N LEU C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 removed outlier: 3.784A pdb=" N ASN C 216 " --> pdb=" O PRO C 213 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N PHE C 217 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 218 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 250 removed outlier: 3.843A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 removed outlier: 3.514A pdb=" N ARG C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 277 removed outlier: 3.586A pdb=" N VAL C 272 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 275 " --> pdb=" O TRP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 301 removed outlier: 4.184A pdb=" N TRP C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE C 300 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 317 removed outlier: 3.500A pdb=" N LEU C 307 " --> pdb=" O PRO C 303 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 316 " --> pdb=" O TYR C 312 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 326 Processing helix chain 'C' and resid 328 through 335 removed outlier: 3.526A pdb=" N HIS C 332 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 350 through 372 removed outlier: 3.530A pdb=" N ALA C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 367 " --> pdb=" O ALA C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 391 through 409 removed outlier: 4.019A pdb=" N ALA C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA C 396 " --> pdb=" O MET C 392 " (cutoff:3.500A) Proline residue: C 397 - end of helix Processing helix chain 'C' and resid 412 through 431 removed outlier: 3.585A pdb=" N THR C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 449 through 466 removed outlier: 3.538A pdb=" N ALA C 455 " --> pdb=" O PRO C 451 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 456 " --> pdb=" O MET C 452 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 465 " --> pdb=" O LYS C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 499 removed outlier: 3.514A pdb=" N LEU C 474 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 481 " --> pdb=" O THR C 477 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR C 483 " --> pdb=" O SER C 479 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 491 " --> pdb=" O CYS C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 511 removed outlier: 3.705A pdb=" N ILE C 510 " --> pdb=" O ASP C 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 161 462 hydrogen bonds defined for protein. 1233 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: 0.98 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1257 1.25 - 1.39: 2558 1.39 - 1.53: 4706 1.53 - 1.67: 572 1.67 - 1.81: 63 Bond restraints: 9156 Sorted by residual: bond pdb=" N SER A 442 " pdb=" CA SER A 442 " ideal model delta sigma weight residual 1.455 1.342 0.113 1.25e-02 6.40e+03 8.22e+01 bond pdb=" N SER C 442 " pdb=" CA SER C 442 " ideal model delta sigma weight residual 1.455 1.342 0.113 1.25e-02 6.40e+03 8.22e+01 bond pdb=" N SER B 442 " pdb=" CA SER B 442 " ideal model delta sigma weight residual 1.455 1.342 0.113 1.25e-02 6.40e+03 8.18e+01 bond pdb=" C THR A 449 " pdb=" O THR A 449 " ideal model delta sigma weight residual 1.235 1.109 0.126 1.40e-02 5.10e+03 8.10e+01 bond pdb=" C THR C 449 " pdb=" O THR C 449 " ideal model delta sigma weight residual 1.235 1.109 0.126 1.40e-02 5.10e+03 8.05e+01 ... (remaining 9151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 12021 2.63 - 5.25: 348 5.25 - 7.88: 102 7.88 - 10.51: 27 10.51 - 13.13: 9 Bond angle restraints: 12507 Sorted by residual: angle pdb=" N THR C 449 " pdb=" CA THR C 449 " pdb=" C THR C 449 " ideal model delta sigma weight residual 113.12 103.94 9.18 1.25e+00 6.40e-01 5.39e+01 angle pdb=" N THR B 449 " pdb=" CA THR B 449 " pdb=" C THR B 449 " ideal model delta sigma weight residual 113.12 103.94 9.18 1.25e+00 6.40e-01 5.39e+01 angle pdb=" N THR A 449 " pdb=" CA THR A 449 " pdb=" C THR A 449 " ideal model delta sigma weight residual 113.12 104.00 9.12 1.25e+00 6.40e-01 5.32e+01 angle pdb=" N SER B 447 " pdb=" CA SER B 447 " pdb=" CB SER B 447 " ideal model delta sigma weight residual 110.44 100.79 9.65 1.53e+00 4.27e-01 3.98e+01 angle pdb=" N SER C 447 " pdb=" CA SER C 447 " pdb=" CB SER C 447 " ideal model delta sigma weight residual 110.44 100.79 9.65 1.53e+00 4.27e-01 3.98e+01 ... (remaining 12502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.31: 4592 10.31 - 20.63: 523 20.63 - 30.94: 86 30.94 - 41.26: 25 41.26 - 51.57: 3 Dihedral angle restraints: 5229 sinusoidal: 1977 harmonic: 3252 Sorted by residual: dihedral pdb=" CA CYS B 192 " pdb=" C CYS B 192 " pdb=" N PHE B 193 " pdb=" CA PHE B 193 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N PHE A 193 " pdb=" CA PHE A 193 " ideal model delta harmonic sigma weight residual 180.00 152.57 27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA CYS C 192 " pdb=" C CYS C 192 " pdb=" N PHE C 193 " pdb=" CA PHE C 193 " ideal model delta harmonic sigma weight residual 180.00 152.58 27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 5226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1295 0.112 - 0.223: 106 0.223 - 0.335: 0 0.335 - 0.447: 0 0.447 - 0.558: 3 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CA LEU C 165 " pdb=" N LEU C 165 " pdb=" C LEU C 165 " pdb=" CB LEU C 165 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" CA LEU B 165 " pdb=" N LEU B 165 " pdb=" C LEU B 165 " pdb=" CB LEU B 165 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" CA LEU A 165 " pdb=" N LEU A 165 " pdb=" C LEU A 165 " pdb=" CB LEU A 165 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.62e+00 ... (remaining 1401 not shown) Planarity restraints: 1521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 387 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO C 388 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 388 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 388 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 387 " -0.042 5.00e-02 4.00e+02 6.30e-02 6.36e+00 pdb=" N PRO B 388 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 388 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 388 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 387 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO A 388 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " 0.035 5.00e-02 4.00e+02 ... (remaining 1518 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 209 2.70 - 3.25: 8155 3.25 - 3.80: 12834 3.80 - 4.35: 18472 4.35 - 4.90: 30221 Nonbonded interactions: 69891 Sorted by model distance: nonbonded pdb=" O ASP B 166 " pdb=" OD1 ASP B 166 " model vdw 2.155 3.040 nonbonded pdb=" O ASP A 166 " pdb=" OD1 ASP A 166 " model vdw 2.155 3.040 nonbonded pdb=" O ASP C 166 " pdb=" OD1 ASP C 166 " model vdw 2.155 3.040 nonbonded pdb=" O LYS C 440 " pdb=" NE1 TRP C 445 " model vdw 2.390 3.120 nonbonded pdb=" O LYS A 440 " pdb=" NE1 TRP A 445 " model vdw 2.390 3.120 ... (remaining 69886 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 1.100 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.270 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.012 0.126 9156 Z= 0.681 Angle : 1.199 13.134 12507 Z= 0.661 Chirality : 0.067 0.558 1404 Planarity : 0.009 0.063 1521 Dihedral : 9.169 51.569 3123 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.63 % Allowed : 3.81 % Favored : 95.56 % Cbeta Deviations : 0.57 % 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: -5.53 (0.17), residues: 1098 helix: -4.62 (0.06), residues: 654 sheet: None (None), residues: 0 loop : -1.75 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 187 TYR 0.015 0.003 TYR B 156 PHE 0.025 0.003 PHE A 285 TRP 0.027 0.004 TRP B 358 HIS 0.009 0.002 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.01153 ( 9156) covalent geometry : angle 1.19916 (12507) hydrogen bonds : bond 0.38278 ( 462) hydrogen bonds : angle 10.11667 ( 1233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.333 Fit side-chains REVERT: A 472 ARG cc_start: 0.7623 (mmt90) cc_final: 0.6724 (mtp180) REVERT: B 172 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7389 (mm-30) REVERT: B 216 ASN cc_start: 0.8573 (t0) cc_final: 0.8344 (t0) outliers start: 6 outliers final: 4 residues processed: 145 average time/residue: 0.6078 time to fit residues: 93.3461 Evaluate side-chains 87 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 443 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 314 GLN A 328 ASN B 225 ASN B 328 ASN C 216 ASN C 314 GLN C 328 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.124691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.098700 restraints weight = 9363.835| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.45 r_work: 0.2899 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9156 Z= 0.133 Angle : 0.617 7.311 12507 Z= 0.319 Chirality : 0.041 0.128 1404 Planarity : 0.007 0.043 1521 Dihedral : 5.551 40.910 1190 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.01 % Allowed : 8.68 % Favored : 89.31 % 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: -2.58 (0.22), residues: 1098 helix: -1.98 (0.16), residues: 675 sheet: None (None), residues: 0 loop : -0.91 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 161 TYR 0.008 0.002 TYR C 250 PHE 0.012 0.001 PHE B 450 TRP 0.013 0.002 TRP A 358 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9156) covalent geometry : angle 0.61650 (12507) hydrogen bonds : bond 0.06776 ( 462) hydrogen bonds : angle 4.85882 ( 1233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.347 Fit side-chains REVERT: B 242 THR cc_start: 0.8943 (t) cc_final: 0.8711 (m) REVERT: C 384 LYS cc_start: 0.8573 (mmtp) cc_final: 0.8204 (mmtt) REVERT: C 392 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.9046 (mmt) outliers start: 19 outliers final: 3 residues processed: 140 average time/residue: 0.4030 time to fit residues: 61.5408 Evaluate side-chains 98 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 392 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 106 optimal weight: 0.0000 chunk 107 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 314 GLN C 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.122846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.096399 restraints weight = 9314.252| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.46 r_work: 0.2855 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9156 Z= 0.119 Angle : 0.557 5.959 12507 Z= 0.284 Chirality : 0.040 0.123 1404 Planarity : 0.005 0.038 1521 Dihedral : 4.834 21.452 1185 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.43 % Allowed : 10.48 % Favored : 87.09 % 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: -0.26 (0.26), residues: 1098 helix: -0.12 (0.20), residues: 660 sheet: None (None), residues: 0 loop : 0.00 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 161 TYR 0.009 0.001 TYR A 373 PHE 0.011 0.001 PHE B 450 TRP 0.009 0.001 TRP A 271 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9156) covalent geometry : angle 0.55725 (12507) hydrogen bonds : bond 0.06020 ( 462) hydrogen bonds : angle 4.33541 ( 1233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.337 Fit side-chains REVERT: A 440 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7716 (ttmt) REVERT: A 450 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.6824 (t80) REVERT: A 452 MET cc_start: 0.8475 (mtp) cc_final: 0.8211 (mtp) REVERT: B 216 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8231 (t0) REVERT: B 242 THR cc_start: 0.8980 (t) cc_final: 0.8757 (m) REVERT: B 314 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8404 (mt0) REVERT: B 376 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6132 (mt) REVERT: B 485 MET cc_start: 0.8257 (mtm) cc_final: 0.7763 (mmp) REVERT: C 242 THR cc_start: 0.8987 (t) cc_final: 0.8764 (t) REVERT: C 384 LYS cc_start: 0.8547 (mmtp) cc_final: 0.8183 (mmtt) REVERT: C 392 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.9036 (mmt) REVERT: C 450 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7735 (t80) outliers start: 23 outliers final: 7 residues processed: 122 average time/residue: 0.4707 time to fit residues: 61.6345 Evaluate side-chains 100 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 PHE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 1 optimal weight: 0.3980 chunk 95 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 314 GLN C 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.124142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.097676 restraints weight = 9410.202| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.46 r_work: 0.2898 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9156 Z= 0.103 Angle : 0.508 5.350 12507 Z= 0.260 Chirality : 0.039 0.121 1404 Planarity : 0.005 0.036 1521 Dihedral : 4.525 20.590 1185 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.12 % Allowed : 10.79 % Favored : 87.09 % 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: 0.71 (0.27), residues: 1098 helix: 0.72 (0.21), residues: 666 sheet: None (None), residues: 0 loop : 0.29 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 161 TYR 0.007 0.001 TYR A 156 PHE 0.010 0.001 PHE B 241 TRP 0.008 0.001 TRP A 271 HIS 0.004 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 9156) covalent geometry : angle 0.50835 (12507) hydrogen bonds : bond 0.05088 ( 462) hydrogen bonds : angle 4.02287 ( 1233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.361 Fit side-chains REVERT: A 440 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7736 (ttmt) REVERT: A 450 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.6892 (t80) REVERT: A 452 MET cc_start: 0.8475 (mtp) cc_final: 0.8259 (mtp) REVERT: A 485 MET cc_start: 0.8514 (mmp) cc_final: 0.8194 (mmp) REVERT: B 242 THR cc_start: 0.8918 (t) cc_final: 0.8689 (m) REVERT: B 314 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8427 (mt0) REVERT: B 376 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6088 (mt) REVERT: B 485 MET cc_start: 0.8274 (mtm) cc_final: 0.7774 (mmp) REVERT: C 384 LYS cc_start: 0.8569 (mmtp) cc_final: 0.8227 (mmtt) REVERT: C 392 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8798 (mmt) REVERT: C 450 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7523 (t80) outliers start: 20 outliers final: 7 residues processed: 110 average time/residue: 0.6013 time to fit residues: 70.5534 Evaluate side-chains 100 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 314 GLN C 216 ASN C 314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.117704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.090597 restraints weight = 9579.067| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.55 r_work: 0.2801 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9156 Z= 0.193 Angle : 0.645 7.763 12507 Z= 0.326 Chirality : 0.045 0.125 1404 Planarity : 0.006 0.036 1521 Dihedral : 5.011 23.168 1185 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.86 % Allowed : 10.48 % Favored : 86.67 % 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: 0.47 (0.26), residues: 1098 helix: 0.53 (0.20), residues: 681 sheet: None (None), residues: 0 loop : 0.19 (0.34), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 161 TYR 0.012 0.002 TYR B 365 PHE 0.014 0.002 PHE A 266 TRP 0.014 0.002 TRP A 271 HIS 0.008 0.002 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 9156) covalent geometry : angle 0.64488 (12507) hydrogen bonds : bond 0.07800 ( 462) hydrogen bonds : angle 4.40706 ( 1233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.355 Fit side-chains REVERT: A 376 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6212 (pp) REVERT: A 440 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7591 (ttmt) REVERT: A 472 ARG cc_start: 0.7638 (mmt90) cc_final: 0.6479 (mtp180) REVERT: B 216 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8022 (t0) REVERT: B 242 THR cc_start: 0.8925 (t) cc_final: 0.8682 (m) REVERT: B 314 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8621 (mt0) REVERT: B 376 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.5875 (mt) REVERT: B 485 MET cc_start: 0.8152 (mtm) cc_final: 0.7541 (mmp) REVERT: C 384 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8273 (mmtt) REVERT: C 392 MET cc_start: 0.9311 (OUTLIER) cc_final: 0.8739 (mmt) outliers start: 27 outliers final: 11 residues processed: 105 average time/residue: 0.6576 time to fit residues: 73.3029 Evaluate side-chains 100 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 392 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 chunk 84 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN C 216 ASN C 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.094564 restraints weight = 9583.914| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.54 r_work: 0.2860 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9156 Z= 0.119 Angle : 0.537 5.932 12507 Z= 0.275 Chirality : 0.041 0.122 1404 Planarity : 0.005 0.038 1521 Dihedral : 4.642 21.888 1185 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.22 % Allowed : 11.11 % Favored : 86.67 % 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: 1.01 (0.27), residues: 1098 helix: 0.97 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.38 (0.35), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 161 TYR 0.008 0.001 TYR C 365 PHE 0.013 0.001 PHE A 450 TRP 0.010 0.001 TRP A 271 HIS 0.005 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9156) covalent geometry : angle 0.53686 (12507) hydrogen bonds : bond 0.05797 ( 462) hydrogen bonds : angle 4.10920 ( 1233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.362 Fit side-chains REVERT: A 376 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6218 (pp) REVERT: A 384 LYS cc_start: 0.8631 (mmtm) cc_final: 0.8304 (mmtt) REVERT: A 440 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7602 (ttmt) REVERT: A 450 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.6497 (t80) REVERT: B 242 THR cc_start: 0.8904 (t) cc_final: 0.8649 (m) REVERT: B 314 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8463 (mt0) REVERT: B 376 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.5879 (mt) REVERT: B 485 MET cc_start: 0.8116 (mtm) cc_final: 0.7552 (mmp) REVERT: C 320 LYS cc_start: 0.7884 (mmpt) cc_final: 0.7235 (pttm) REVERT: C 384 LYS cc_start: 0.8502 (mmtp) cc_final: 0.8078 (mmtt) REVERT: C 392 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.9007 (mmt) REVERT: C 450 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7610 (t80) REVERT: C 485 MET cc_start: 0.8137 (mtp) cc_final: 0.7674 (mmm) outliers start: 21 outliers final: 10 residues processed: 103 average time/residue: 0.6448 time to fit residues: 70.5049 Evaluate side-chains 103 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN C 216 ASN C 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.093406 restraints weight = 9566.569| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.54 r_work: 0.2839 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9156 Z= 0.132 Angle : 0.553 7.347 12507 Z= 0.281 Chirality : 0.041 0.122 1404 Planarity : 0.005 0.039 1521 Dihedral : 4.641 21.841 1185 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 11.11 % Favored : 86.67 % 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: 1.19 (0.27), residues: 1098 helix: 1.10 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.47 (0.35), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 161 TYR 0.009 0.001 TYR C 365 PHE 0.013 0.001 PHE A 450 TRP 0.010 0.001 TRP A 271 HIS 0.006 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9156) covalent geometry : angle 0.55295 (12507) hydrogen bonds : bond 0.06196 ( 462) hydrogen bonds : angle 4.12070 ( 1233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.373 Fit side-chains REVERT: A 376 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6212 (pp) REVERT: A 384 LYS cc_start: 0.8621 (mmtm) cc_final: 0.8286 (mmtt) REVERT: A 440 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7611 (ttmt) REVERT: A 450 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.6520 (t80) REVERT: B 242 THR cc_start: 0.8907 (t) cc_final: 0.8664 (m) REVERT: B 314 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8461 (mt0) REVERT: B 376 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.5883 (mt) REVERT: B 485 MET cc_start: 0.8180 (mtm) cc_final: 0.7602 (mmp) REVERT: C 320 LYS cc_start: 0.7837 (mmpt) cc_final: 0.7226 (pttm) REVERT: C 384 LYS cc_start: 0.8504 (mmtp) cc_final: 0.8080 (mmtt) REVERT: C 392 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.9006 (mmt) REVERT: C 450 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7661 (t80) REVERT: C 485 MET cc_start: 0.8152 (mtp) cc_final: 0.7690 (mmm) outliers start: 21 outliers final: 11 residues processed: 102 average time/residue: 0.6535 time to fit residues: 70.7229 Evaluate side-chains 105 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN C 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.091900 restraints weight = 9484.602| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.55 r_work: 0.2814 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9156 Z= 0.153 Angle : 0.581 5.361 12507 Z= 0.296 Chirality : 0.043 0.123 1404 Planarity : 0.005 0.040 1521 Dihedral : 4.751 22.527 1185 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.33 % Allowed : 10.58 % Favored : 87.09 % 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: 1.17 (0.26), residues: 1098 helix: 1.08 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.46 (0.35), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 161 TYR 0.010 0.001 TYR A 365 PHE 0.014 0.002 PHE A 450 TRP 0.011 0.002 TRP A 271 HIS 0.007 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9156) covalent geometry : angle 0.58084 (12507) hydrogen bonds : bond 0.06774 ( 462) hydrogen bonds : angle 4.19893 ( 1233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.396 Fit side-chains REVERT: A 376 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6216 (pp) REVERT: A 384 LYS cc_start: 0.8632 (mmtm) cc_final: 0.8275 (mmtt) REVERT: A 440 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7616 (ttmt) REVERT: A 450 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.6726 (t80) REVERT: B 242 THR cc_start: 0.8914 (t) cc_final: 0.8679 (m) REVERT: B 314 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8444 (mt0) REVERT: B 376 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6059 (mt) REVERT: B 485 MET cc_start: 0.8115 (mtm) cc_final: 0.7548 (mmp) REVERT: C 384 LYS cc_start: 0.8519 (mmtp) cc_final: 0.8250 (mmtt) REVERT: C 392 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8742 (mmt) REVERT: C 450 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7737 (t80) REVERT: C 485 MET cc_start: 0.8158 (mtp) cc_final: 0.7709 (mmm) outliers start: 22 outliers final: 10 residues processed: 100 average time/residue: 0.6592 time to fit residues: 69.9914 Evaluate side-chains 103 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN C 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.091999 restraints weight = 9474.112| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.54 r_work: 0.2823 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9156 Z= 0.149 Angle : 0.580 7.522 12507 Z= 0.295 Chirality : 0.043 0.125 1404 Planarity : 0.005 0.039 1521 Dihedral : 4.745 22.461 1185 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.90 % Allowed : 11.11 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.26), residues: 1098 helix: 1.13 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.50 (0.35), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 161 TYR 0.010 0.001 TYR C 365 PHE 0.014 0.001 PHE A 450 TRP 0.011 0.001 TRP A 271 HIS 0.006 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9156) covalent geometry : angle 0.58045 (12507) hydrogen bonds : bond 0.06683 ( 462) hydrogen bonds : angle 4.19366 ( 1233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.425 Fit side-chains REVERT: A 376 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6197 (pp) REVERT: A 384 LYS cc_start: 0.8632 (mmtm) cc_final: 0.8266 (mmtt) REVERT: A 440 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7646 (ttmt) REVERT: A 450 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.6646 (t80) REVERT: B 242 THR cc_start: 0.8912 (t) cc_final: 0.8673 (m) REVERT: B 314 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8440 (mt0) REVERT: B 376 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6036 (mt) REVERT: B 485 MET cc_start: 0.8120 (mtm) cc_final: 0.7539 (mmp) REVERT: C 384 LYS cc_start: 0.8489 (mmtp) cc_final: 0.8212 (mmtt) REVERT: C 392 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8734 (mmt) REVERT: C 450 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7774 (t80) REVERT: C 485 MET cc_start: 0.8182 (mtp) cc_final: 0.7737 (mmm) outliers start: 18 outliers final: 10 residues processed: 97 average time/residue: 0.6547 time to fit residues: 67.5359 Evaluate side-chains 103 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN C 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.093338 restraints weight = 9458.465| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.55 r_work: 0.2838 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9156 Z= 0.127 Angle : 0.546 5.137 12507 Z= 0.279 Chirality : 0.041 0.123 1404 Planarity : 0.005 0.040 1521 Dihedral : 4.629 21.907 1185 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.90 % Allowed : 11.11 % Favored : 86.98 % 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: 1.41 (0.27), residues: 1098 helix: 1.27 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.57 (0.35), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 161 TYR 0.009 0.001 TYR C 365 PHE 0.013 0.001 PHE A 450 TRP 0.012 0.001 TRP C 271 HIS 0.005 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9156) covalent geometry : angle 0.54564 (12507) hydrogen bonds : bond 0.06106 ( 462) hydrogen bonds : angle 4.11358 ( 1233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.340 Fit side-chains REVERT: A 376 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.5794 (mt) REVERT: A 384 LYS cc_start: 0.8668 (mmtm) cc_final: 0.8327 (mmtt) REVERT: A 440 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7640 (ttmt) REVERT: A 450 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.6506 (t80) REVERT: B 242 THR cc_start: 0.8897 (t) cc_final: 0.8652 (m) REVERT: B 314 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8409 (mt0) REVERT: B 376 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6020 (mt) REVERT: B 485 MET cc_start: 0.8114 (mtm) cc_final: 0.7550 (mmp) REVERT: C 376 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6159 (mt) REVERT: C 384 LYS cc_start: 0.8475 (mmtp) cc_final: 0.8045 (mmtt) REVERT: C 392 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8735 (mmt) REVERT: C 450 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7623 (t80) REVERT: C 485 MET cc_start: 0.8176 (mtp) cc_final: 0.7737 (mmm) outliers start: 18 outliers final: 10 residues processed: 100 average time/residue: 0.6798 time to fit residues: 72.1368 Evaluate side-chains 106 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 72 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 0.0170 chunk 94 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN C 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.119627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.092747 restraints weight = 9409.640| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.52 r_work: 0.2826 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9156 Z= 0.141 Angle : 0.564 5.233 12507 Z= 0.288 Chirality : 0.042 0.124 1404 Planarity : 0.005 0.039 1521 Dihedral : 4.674 22.025 1185 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.33 % Allowed : 10.90 % Favored : 86.77 % 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: 1.37 (0.26), residues: 1098 helix: 1.24 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.55 (0.35), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 161 TYR 0.009 0.001 TYR C 365 PHE 0.014 0.001 PHE A 450 TRP 0.012 0.001 TRP C 271 HIS 0.006 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9156) covalent geometry : angle 0.56362 (12507) hydrogen bonds : bond 0.06456 ( 462) hydrogen bonds : angle 4.14493 ( 1233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2827.45 seconds wall clock time: 48 minutes 57.88 seconds (2937.88 seconds total)