Starting phenix.real_space_refine on Sat Jun 7 16:57:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wnq_32633/06_2025/7wnq_32633.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wnq_32633/06_2025/7wnq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wnq_32633/06_2025/7wnq_32633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wnq_32633/06_2025/7wnq_32633.map" model { file = "/net/cci-nas-00/data/ceres_data/7wnq_32633/06_2025/7wnq_32633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wnq_32633/06_2025/7wnq_32633.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B Time building chain proxies: 5.31, per 1000 atoms: 0.60 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: 2.10 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.90 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: 2.20 Time building geometry restraints manager: 2.49 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.070 Find NCS groups from input model: 0.150 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:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.320 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.027 0.004 TRP B 358 HIS 0.009 0.002 HIS B 260 PHE 0.025 0.003 PHE A 285 TYR 0.015 0.003 TYR B 156 ARG 0.009 0.002 ARG A 187 Details of bonding type rmsd hydrogen bonds : bond 0.38278 ( 462) hydrogen bonds : angle 10.11667 ( 1233) covalent geometry : bond 0.01153 ( 9156) covalent geometry : angle 1.19916 (12507) *********************** 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 : 1.051 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: 1.2923 time to fit residues: 199.1736 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 : 0.958 ------------------------------------------------------------------------------- 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 91 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.123855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.097789 restraints weight = 9320.115| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.45 r_work: 0.2887 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2350 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= 0.136 Angle : 0.625 7.322 12507 Z= 0.322 Chirality : 0.041 0.127 1404 Planarity : 0.007 0.043 1521 Dihedral : 5.596 42.713 1190 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.12 % Allowed : 8.68 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.22), residues: 1098 helix: -1.99 (0.16), residues: 675 sheet: None (None), residues: 0 loop : -0.92 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 271 HIS 0.004 0.001 HIS C 364 PHE 0.013 0.001 PHE B 450 TYR 0.008 0.002 TYR C 365 ARG 0.006 0.001 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.07097 ( 462) hydrogen bonds : angle 4.87328 ( 1233) covalent geometry : bond 0.00288 ( 9156) covalent geometry : angle 0.62477 (12507) *********************** 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 152 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.080 Fit side-chains REVERT: B 242 THR cc_start: 0.8949 (t) cc_final: 0.8722 (m) REVERT: B 485 MET cc_start: 0.8358 (mtm) cc_final: 0.7808 (mmp) REVERT: C 384 LYS cc_start: 0.8584 (mmtp) cc_final: 0.8213 (mmtt) REVERT: C 392 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.9042 (mmt) outliers start: 20 outliers final: 4 residues processed: 140 average time/residue: 0.9009 time to fit residues: 137.7932 Evaluate side-chains 94 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 168 VAL 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 23 optimal weight: 0.0270 chunk 21 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.118865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.092217 restraints weight = 9412.659| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.47 r_work: 0.2801 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9156 Z= 0.156 Angle : 0.621 6.913 12507 Z= 0.315 Chirality : 0.042 0.125 1404 Planarity : 0.006 0.037 1521 Dihedral : 5.098 22.401 1185 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.96 % Allowed : 9.74 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1098 helix: -0.42 (0.19), residues: 681 sheet: None (None), residues: 0 loop : -0.14 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 271 HIS 0.007 0.001 HIS A 364 PHE 0.012 0.002 PHE B 450 TYR 0.010 0.002 TYR A 373 ARG 0.005 0.001 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.07301 ( 462) hydrogen bonds : angle 4.54204 ( 1233) covalent geometry : bond 0.00362 ( 9156) covalent geometry : angle 0.62126 (12507) *********************** 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 121 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.916 Fit side-chains REVERT: A 440 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7727 (ttmt) REVERT: A 450 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.6899 (t80) REVERT: A 452 MET cc_start: 0.8512 (mtp) cc_final: 0.8230 (mtp) REVERT: A 485 MET cc_start: 0.8482 (mmp) cc_final: 0.8115 (mmp) REVERT: B 216 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8135 (t0) REVERT: B 314 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8455 (mt0) REVERT: B 477 THR cc_start: 0.8688 (t) cc_final: 0.8479 (p) REVERT: B 485 MET cc_start: 0.8376 (mtm) cc_final: 0.7916 (mmp) REVERT: C 384 LYS cc_start: 0.8669 (mmtp) cc_final: 0.8278 (mmtt) REVERT: C 392 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.9036 (mmt) REVERT: C 450 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7900 (t80) outliers start: 28 outliers final: 10 residues processed: 111 average time/residue: 1.0904 time to fit residues: 130.3325 Evaluate side-chains 101 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 264 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 C residue 264 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.121551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.094809 restraints weight = 9504.049| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.52 r_work: 0.2857 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2925 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= 0.125 Angle : 0.553 5.347 12507 Z= 0.284 Chirality : 0.041 0.123 1404 Planarity : 0.005 0.038 1521 Dihedral : 4.802 21.825 1185 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.12 % Allowed : 10.16 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1098 helix: 0.33 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.15 (0.35), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 271 HIS 0.005 0.001 HIS C 364 PHE 0.011 0.001 PHE B 241 TYR 0.008 0.001 TYR C 365 ARG 0.004 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.06134 ( 462) hydrogen bonds : angle 4.25671 ( 1233) covalent geometry : bond 0.00274 ( 9156) covalent geometry : angle 0.55311 (12507) *********************** 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 113 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.967 Fit side-chains REVERT: A 440 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7587 (ttmt) REVERT: A 450 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.6519 (t80) REVERT: A 452 MET cc_start: 0.8406 (mtp) cc_final: 0.8149 (mtp) REVERT: B 216 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8106 (t0) REVERT: B 314 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8444 (mt0) REVERT: B 376 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.5916 (mt) REVERT: B 477 THR cc_start: 0.8625 (t) cc_final: 0.8393 (p) REVERT: B 485 MET cc_start: 0.8087 (mtm) cc_final: 0.7579 (mmp) REVERT: C 384 LYS cc_start: 0.8524 (mmtp) cc_final: 0.8118 (mmtt) REVERT: C 392 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.8983 (mmt) REVERT: C 450 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7642 (t80) outliers start: 20 outliers final: 6 residues processed: 104 average time/residue: 1.2520 time to fit residues: 139.0328 Evaluate side-chains 102 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP 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 450 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.121678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.094891 restraints weight = 9471.009| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.52 r_work: 0.2865 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3040 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= 0.122 Angle : 0.543 6.578 12507 Z= 0.277 Chirality : 0.041 0.122 1404 Planarity : 0.005 0.039 1521 Dihedral : 4.675 21.480 1185 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.01 % Allowed : 10.69 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 1098 helix: 0.77 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.32 (0.35), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 271 HIS 0.005 0.001 HIS C 364 PHE 0.011 0.001 PHE B 241 TYR 0.008 0.001 TYR A 365 ARG 0.006 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.05961 ( 462) hydrogen bonds : angle 4.13840 ( 1233) covalent geometry : bond 0.00268 ( 9156) covalent geometry : angle 0.54281 (12507) *********************** 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 108 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.057 Fit side-chains REVERT: A 429 LEU cc_start: 0.7859 (tm) cc_final: 0.7649 (tm) REVERT: A 440 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7622 (ttmt) REVERT: A 450 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.6503 (t80) REVERT: A 452 MET cc_start: 0.8456 (mtp) cc_final: 0.8213 (mtp) REVERT: B 314 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8426 (mt0) REVERT: B 376 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.5900 (mt) REVERT: B 477 THR cc_start: 0.8594 (t) cc_final: 0.8381 (p) REVERT: B 485 MET cc_start: 0.8050 (mtm) cc_final: 0.7550 (mmp) REVERT: C 384 LYS cc_start: 0.8531 (mmtp) cc_final: 0.8127 (mmtt) REVERT: C 392 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8987 (mmt) REVERT: C 450 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7599 (t80) outliers start: 19 outliers final: 11 residues processed: 101 average time/residue: 1.2023 time to fit residues: 129.8399 Evaluate side-chains 102 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 0.0170 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 52 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.123887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.097087 restraints weight = 9417.714| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.52 r_work: 0.2898 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9156 Z= 0.105 Angle : 0.508 6.077 12507 Z= 0.260 Chirality : 0.040 0.122 1404 Planarity : 0.005 0.038 1521 Dihedral : 4.464 20.795 1185 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.12 % Allowed : 10.48 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.27), residues: 1098 helix: 1.26 (0.20), residues: 666 sheet: None (None), residues: 0 loop : 0.49 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 271 HIS 0.005 0.001 HIS B 364 PHE 0.011 0.001 PHE B 241 TYR 0.007 0.001 TYR A 156 ARG 0.006 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.05218 ( 462) hydrogen bonds : angle 3.97982 ( 1233) covalent geometry : bond 0.00218 ( 9156) covalent geometry : angle 0.50799 (12507) *********************** 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 114 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.983 Fit side-chains REVERT: A 376 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.5780 (mt) REVERT: A 440 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7622 (ttmt) REVERT: A 450 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.6591 (t80) REVERT: A 485 MET cc_start: 0.8398 (mmp) cc_final: 0.8095 (mmp) REVERT: A 514 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7742 (tttp) REVERT: B 314 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8369 (mt0) REVERT: B 376 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.5927 (mt) REVERT: B 485 MET cc_start: 0.7976 (mtm) cc_final: 0.7477 (mmp) REVERT: C 376 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6153 (mt) REVERT: C 384 LYS cc_start: 0.8473 (mmtp) cc_final: 0.8086 (mmtt) REVERT: C 392 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8750 (mmt) REVERT: C 450 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7434 (t80) REVERT: C 485 MET cc_start: 0.8127 (mtp) cc_final: 0.7665 (mmm) outliers start: 20 outliers final: 8 residues processed: 106 average time/residue: 1.2802 time to fit residues: 144.7104 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 : 0.975 ------------------------------------------------------------------------------- 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 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 A residue 514 LYS Chi-restraints excluded: chain B residue 168 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 34 optimal weight: 0.6980 chunk 49 optimal weight: 0.0040 chunk 26 optimal weight: 0.2980 chunk 100 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.3590 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.125940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.098926 restraints weight = 9520.791| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.55 r_work: 0.2927 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3392 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= 0.097 Angle : 0.490 7.297 12507 Z= 0.250 Chirality : 0.039 0.120 1404 Planarity : 0.005 0.037 1521 Dihedral : 4.284 20.096 1185 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.90 % Allowed : 11.22 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.27), residues: 1098 helix: 1.44 (0.20), residues: 681 sheet: None (None), residues: 0 loop : 0.64 (0.36), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 229 HIS 0.005 0.001 HIS B 364 PHE 0.012 0.001 PHE B 241 TYR 0.006 0.001 TYR A 156 ARG 0.008 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.04721 ( 462) hydrogen bonds : angle 3.85791 ( 1233) covalent geometry : bond 0.00196 ( 9156) covalent geometry : angle 0.48988 (12507) *********************** 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 108 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.093 Fit side-chains REVERT: A 376 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.5779 (mt) REVERT: A 440 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7543 (ttmt) REVERT: A 514 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7737 (tttp) REVERT: B 314 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8401 (mt0) REVERT: B 376 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.5881 (mt) REVERT: B 485 MET cc_start: 0.7914 (mtm) cc_final: 0.7462 (mmp) REVERT: C 284 MET cc_start: 0.8219 (mtp) cc_final: 0.8015 (mtp) REVERT: C 376 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6053 (mt) REVERT: C 384 LYS cc_start: 0.8449 (mmtp) cc_final: 0.8070 (mmtt) REVERT: C 392 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8947 (mmt) REVERT: C 450 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7245 (t80) REVERT: C 485 MET cc_start: 0.8126 (mtp) cc_final: 0.7685 (mmm) outliers start: 18 outliers final: 5 residues processed: 102 average time/residue: 1.4297 time to fit residues: 155.4043 Evaluate side-chains 99 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL 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 514 LYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 376 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.0870 chunk 74 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.121191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.093844 restraints weight = 9549.940| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.56 r_work: 0.2843 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3184 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= 0.133 Angle : 0.548 5.281 12507 Z= 0.279 Chirality : 0.042 0.122 1404 Planarity : 0.005 0.038 1521 Dihedral : 4.530 21.135 1185 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 10.48 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.27), residues: 1098 helix: 1.28 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.66 (0.35), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 271 HIS 0.006 0.001 HIS C 364 PHE 0.012 0.001 PHE A 450 TYR 0.010 0.001 TYR A 365 ARG 0.008 0.001 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.06224 ( 462) hydrogen bonds : angle 4.05486 ( 1233) covalent geometry : bond 0.00304 ( 9156) covalent geometry : angle 0.54780 (12507) *********************** 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 107 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.995 Fit side-chains REVERT: A 376 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.5872 (mt) REVERT: A 440 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7536 (ttmt) REVERT: A 450 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.6535 (t80) REVERT: A 514 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7782 (tttp) REVERT: B 314 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8438 (mt0) REVERT: B 376 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.5911 (mt) REVERT: B 477 THR cc_start: 0.8507 (t) cc_final: 0.8296 (p) REVERT: B 485 MET cc_start: 0.8032 (mtm) cc_final: 0.7572 (mmp) REVERT: C 376 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6138 (mt) REVERT: C 384 LYS cc_start: 0.8475 (mmtp) cc_final: 0.8076 (mmtt) REVERT: C 392 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.8696 (mmt) REVERT: C 450 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7610 (t80) REVERT: C 485 MET cc_start: 0.8135 (mtp) cc_final: 0.7703 (mmm) outliers start: 21 outliers final: 7 residues processed: 97 average time/residue: 1.4773 time to fit residues: 152.9856 Evaluate side-chains 101 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL 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 A residue 514 LYS Chi-restraints excluded: chain B residue 168 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.121969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.094711 restraints weight = 9495.032| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.55 r_work: 0.2864 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3254 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= 0.122 Angle : 0.535 7.315 12507 Z= 0.272 Chirality : 0.041 0.125 1404 Planarity : 0.005 0.043 1521 Dihedral : 4.482 21.141 1185 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.80 % Allowed : 10.90 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.27), residues: 1098 helix: 1.31 (0.20), residues: 690 sheet: None (None), residues: 0 loop : 0.75 (0.36), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 271 HIS 0.005 0.001 HIS C 364 PHE 0.011 0.001 PHE A 450 TYR 0.008 0.001 TYR A 365 ARG 0.009 0.001 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.05849 ( 462) hydrogen bonds : angle 4.02105 ( 1233) covalent geometry : bond 0.00269 ( 9156) covalent geometry : angle 0.53526 (12507) *********************** 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 103 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.943 Fit side-chains REVERT: A 376 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.5844 (mt) REVERT: A 440 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7575 (ttmt) REVERT: A 450 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.6494 (t80) REVERT: A 514 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7794 (tttp) REVERT: B 314 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8394 (mt0) REVERT: B 376 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.5892 (mt) REVERT: B 477 THR cc_start: 0.8508 (t) cc_final: 0.8302 (p) REVERT: B 485 MET cc_start: 0.8007 (mtm) cc_final: 0.7558 (mmp) REVERT: C 376 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6093 (mt) REVERT: C 384 LYS cc_start: 0.8471 (mmtp) cc_final: 0.8069 (mmtt) REVERT: C 392 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8692 (mmt) REVERT: C 450 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7541 (t80) REVERT: C 485 MET cc_start: 0.8182 (mtp) cc_final: 0.7753 (mmm) outliers start: 17 outliers final: 7 residues processed: 96 average time/residue: 1.5055 time to fit residues: 154.0617 Evaluate side-chains 102 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL 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 A residue 514 LYS Chi-restraints excluded: chain B residue 168 VAL 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 0 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.118272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.091054 restraints weight = 9468.670| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.54 r_work: 0.2793 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9156 Z= 0.179 Angle : 0.616 5.899 12507 Z= 0.312 Chirality : 0.045 0.125 1404 Planarity : 0.005 0.045 1521 Dihedral : 4.809 22.473 1185 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.01 % Allowed : 10.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1098 helix: 1.07 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.55 (0.35), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 271 HIS 0.008 0.002 HIS A 364 PHE 0.012 0.002 PHE A 266 TYR 0.012 0.002 TYR A 365 ARG 0.010 0.001 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.07406 ( 462) hydrogen bonds : angle 4.25332 ( 1233) covalent geometry : bond 0.00432 ( 9156) covalent geometry : angle 0.61560 (12507) ********************** 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 105 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.950 Fit side-chains REVERT: A 376 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.5871 (mt) REVERT: A 440 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7606 (ttmt) REVERT: A 472 ARG cc_start: 0.7537 (mmt90) cc_final: 0.6496 (mtp180) REVERT: A 514 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7840 (tttp) REVERT: B 314 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8540 (mt0) REVERT: B 376 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.5903 (mt) REVERT: B 485 MET cc_start: 0.8064 (mtm) cc_final: 0.7588 (mmp) REVERT: C 376 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6077 (mt) REVERT: C 384 LYS cc_start: 0.8478 (mmtp) cc_final: 0.8198 (mmtt) REVERT: C 392 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.9035 (mmt) REVERT: C 450 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7962 (t80) REVERT: C 485 MET cc_start: 0.8231 (mtp) cc_final: 0.7744 (mmm) outliers start: 19 outliers final: 8 residues processed: 97 average time/residue: 1.2844 time to fit residues: 132.7087 Evaluate side-chains 102 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 376 LEU Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain B residue 168 VAL 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 81 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.121938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.094748 restraints weight = 9446.994| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.54 r_work: 0.2858 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3261 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= 0.117 Angle : 0.525 5.105 12507 Z= 0.269 Chirality : 0.041 0.122 1404 Planarity : 0.005 0.043 1521 Dihedral : 4.522 21.570 1185 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.90 % Allowed : 10.90 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.27), residues: 1098 helix: 1.50 (0.20), residues: 657 sheet: None (None), residues: 0 loop : 0.59 (0.33), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 271 HIS 0.005 0.001 HIS B 364 PHE 0.012 0.001 PHE A 450 TYR 0.008 0.001 TYR A 365 ARG 0.009 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.05709 ( 462) hydrogen bonds : angle 4.03957 ( 1233) covalent geometry : bond 0.00254 ( 9156) covalent geometry : angle 0.52479 (12507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6001.25 seconds wall clock time: 104 minutes 28.01 seconds (6268.01 seconds total)