Starting phenix.real_space_refine on Thu Feb 13 09:35:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wnq_32633/02_2025/7wnq_32633.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wnq_32633/02_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_32633/02_2025/7wnq_32633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wnq_32633/02_2025/7wnq_32633.map" model { file = "/net/cci-nas-00/data/ceres_data/7wnq_32633/02_2025/7wnq_32633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wnq_32633/02_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-5592/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: 5.41, per 1000 atoms: 0.61 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: 2.11 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: 1.04 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: 2.51 Time building geometry restraints manager: 2.47 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: 0.05 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: 2.350 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.490 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.810 ------------------------------------------------------------------------------- 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= 0.724 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 *********************** 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 : 0.955 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: 1.3093 time to fit residues: 201.8637 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 : 1.019 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.123862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.097907 restraints weight = 9320.753| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.45 r_work: 0.2888 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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= 0.184 Angle : 0.625 7.322 12507 Z= 0.322 Chirality : 0.041 0.127 1404 Planarity : 0.007 0.043 1521 Dihedral : 5.596 42.712 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 *********************** 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 : 0.884 Fit side-chains REVERT: B 242 THR cc_start: 0.8949 (t) cc_final: 0.8720 (m) REVERT: B 485 MET cc_start: 0.8360 (mtm) cc_final: 0.7814 (mmp) REVERT: C 384 LYS cc_start: 0.8590 (mmtp) cc_final: 0.8222 (mmtt) REVERT: C 392 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9043 (mmt) outliers start: 20 outliers final: 4 residues processed: 140 average time/residue: 0.9499 time to fit residues: 145.0736 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 : 0.957 ------------------------------------------------------------------------------- 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: 0.0970 chunk 21 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 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 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 = 0.3335 r_free = 0.3335 target = 0.122053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.095480 restraints weight = 9382.297| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.47 r_work: 0.2843 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2805 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= 0.171 Angle : 0.567 6.006 12507 Z= 0.289 Chirality : 0.040 0.123 1404 Planarity : 0.005 0.038 1521 Dihedral : 4.866 21.565 1185 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.33 % Allowed : 10.48 % 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: -0.32 (0.26), residues: 1098 helix: -0.17 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.01 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 271 HIS 0.005 0.001 HIS A 364 PHE 0.011 0.001 PHE B 450 TYR 0.009 0.001 TYR B 373 ARG 0.005 0.000 ARG C 161 *********************** 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 124 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.961 Fit side-chains REVERT: A 440 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7742 (ttmt) REVERT: A 450 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.6706 (t80) REVERT: A 452 MET cc_start: 0.8470 (mtp) cc_final: 0.8231 (mtp) REVERT: B 242 THR cc_start: 0.8987 (t) cc_final: 0.8767 (m) REVERT: B 314 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8414 (mt0) REVERT: B 376 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6088 (mt) REVERT: B 485 MET cc_start: 0.8287 (mtm) cc_final: 0.7773 (mmp) REVERT: C 384 LYS cc_start: 0.8564 (mmtp) cc_final: 0.8197 (mmtt) REVERT: C 392 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.9042 (mmt) REVERT: C 450 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7781 (t80) outliers start: 22 outliers final: 6 residues processed: 118 average time/residue: 1.1430 time to fit residues: 145.0056 Evaluate side-chains 100 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 105 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.122828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.096097 restraints weight = 9489.329| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.52 r_work: 0.2883 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2990 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= 0.165 Angle : 0.540 5.662 12507 Z= 0.277 Chirality : 0.041 0.154 1404 Planarity : 0.005 0.036 1521 Dihedral : 4.690 21.236 1185 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 10.90 % 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: 0.40 (0.26), residues: 1098 helix: 0.45 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.21 (0.34), 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 0.010 0.001 PHE B 241 TYR 0.008 0.001 TYR C 365 ARG 0.007 0.001 ARG C 161 *********************** 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 111 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.998 Fit side-chains REVERT: A 440 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7608 (ttmt) REVERT: A 450 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.6473 (t80) REVERT: A 452 MET cc_start: 0.8450 (mtp) cc_final: 0.8202 (mtp) REVERT: B 242 THR cc_start: 0.8912 (t) cc_final: 0.8642 (m) REVERT: B 314 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8478 (mt0) REVERT: B 376 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.5867 (mt) REVERT: B 485 MET cc_start: 0.8077 (mtm) cc_final: 0.7527 (mmp) REVERT: C 384 LYS cc_start: 0.8498 (mmtp) cc_final: 0.8098 (mmtt) REVERT: C 392 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8973 (mmt) REVERT: C 450 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7588 (t80) outliers start: 21 outliers final: 10 residues processed: 101 average time/residue: 1.2132 time to fit residues: 131.4658 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 : 0.942 ------------------------------------------------------------------------------- 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 450 PHE Chi-restraints excluded: chain C residue 166 ASP 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 83 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.122830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.095770 restraints weight = 9466.030| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.54 r_work: 0.2882 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3084 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= 0.162 Angle : 0.532 6.335 12507 Z= 0.272 Chirality : 0.041 0.127 1404 Planarity : 0.005 0.037 1521 Dihedral : 4.586 21.363 1185 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.22 % Allowed : 10.58 % 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: 0.98 (0.27), residues: 1098 helix: 0.95 (0.20), residues: 666 sheet: None (None), residues: 0 loop : 0.38 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 271 HIS 0.005 0.001 HIS B 364 PHE 0.010 0.001 PHE B 241 TYR 0.008 0.001 TYR C 365 ARG 0.006 0.000 ARG C 161 *********************** 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 113 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.949 Fit side-chains REVERT: A 376 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6224 (pp) REVERT: A 440 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7596 (ttmt) REVERT: A 450 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.6472 (t80) REVERT: A 452 MET cc_start: 0.8438 (mtp) cc_final: 0.8210 (mtp) REVERT: B 242 THR cc_start: 0.8896 (t) cc_final: 0.8643 (m) REVERT: B 314 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8485 (mt0) REVERT: B 376 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.5901 (mt) REVERT: B 485 MET cc_start: 0.8055 (mtm) cc_final: 0.7505 (mmp) REVERT: C 384 LYS cc_start: 0.8491 (mmtp) cc_final: 0.8099 (mmtt) REVERT: C 392 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8968 (mmt) REVERT: C 450 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7552 (t80) outliers start: 21 outliers final: 11 residues processed: 105 average time/residue: 1.3532 time to fit residues: 151.3256 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 : 0.970 ------------------------------------------------------------------------------- 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 166 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 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 = 0.3340 r_free = 0.3340 target = 0.122075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.095267 restraints weight = 9449.824| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.52 r_work: 0.2871 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3132 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= 0.171 Angle : 0.536 6.284 12507 Z= 0.274 Chirality : 0.041 0.122 1404 Planarity : 0.005 0.037 1521 Dihedral : 4.557 21.299 1185 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.12 % Allowed : 11.53 % Favored : 86.35 % 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: 1.21 (0.27), residues: 1098 helix: 1.15 (0.20), residues: 666 sheet: None (None), residues: 0 loop : 0.44 (0.34), residues: 432 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 0.009 0.001 TYR A 365 ARG 0.008 0.001 ARG C 161 *********************** 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: 20 poor density : 89 time to evaluate : 0.970 Fit side-chains REVERT: A 376 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.5809 (mt) REVERT: A 440 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7631 (ttmt) REVERT: A 450 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.6491 (t80) REVERT: A 452 MET cc_start: 0.8464 (mtp) cc_final: 0.8229 (mtp) REVERT: A 485 MET cc_start: 0.8439 (mmp) cc_final: 0.8121 (mmp) REVERT: B 242 THR cc_start: 0.8910 (t) cc_final: 0.8659 (m) REVERT: B 314 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8455 (mt0) REVERT: B 376 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.5938 (mt) REVERT: B 485 MET cc_start: 0.8065 (mtm) cc_final: 0.7555 (mmp) REVERT: C 384 LYS cc_start: 0.8514 (mmtp) cc_final: 0.8120 (mmtt) REVERT: C 392 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8983 (mmt) REVERT: C 450 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7563 (t80) REVERT: C 485 MET cc_start: 0.8136 (mtp) cc_final: 0.7683 (mmm) outliers start: 20 outliers final: 10 residues processed: 102 average time/residue: 1.3645 time to fit residues: 148.1201 Evaluate side-chains 104 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 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 34 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3294 r_free = 0.3294 target = 0.118497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.091330 restraints weight = 9565.384| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.55 r_work: 0.2806 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9156 Z= 0.262 Angle : 0.609 8.060 12507 Z= 0.309 Chirality : 0.044 0.124 1404 Planarity : 0.005 0.037 1521 Dihedral : 4.849 22.408 1185 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.43 % Allowed : 11.22 % Favored : 86.35 % 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: 0.93 (0.26), residues: 1098 helix: 0.90 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.37 (0.35), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 271 HIS 0.008 0.002 HIS A 364 PHE 0.011 0.002 PHE C 369 TYR 0.011 0.002 TYR B 365 ARG 0.008 0.001 ARG C 161 *********************** 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 114 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.946 Fit side-chains REVERT: A 376 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6226 (pp) REVERT: A 440 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7576 (ttmt) REVERT: A 452 MET cc_start: 0.8464 (mtp) cc_final: 0.8218 (mtp) REVERT: A 472 ARG cc_start: 0.7598 (mmt90) cc_final: 0.6490 (mtp180) REVERT: B 242 THR cc_start: 0.8910 (t) cc_final: 0.8669 (m) REVERT: B 314 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8470 (mt0) REVERT: B 376 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.5941 (mt) REVERT: B 485 MET cc_start: 0.8132 (mtm) cc_final: 0.7634 (mmp) REVERT: C 384 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8260 (mmtt) REVERT: C 392 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.8729 (mmt) REVERT: C 450 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7786 (t80) REVERT: C 485 MET cc_start: 0.8192 (mtp) cc_final: 0.7657 (mmm) outliers start: 23 outliers final: 11 residues processed: 107 average time/residue: 1.2896 time to fit residues: 147.1026 Evaluate side-chains 108 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 B residue 168 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 366 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.118724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.091445 restraints weight = 9616.805| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.56 r_work: 0.2814 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9156 Z= 0.243 Angle : 0.593 5.343 12507 Z= 0.303 Chirality : 0.043 0.124 1404 Planarity : 0.005 0.038 1521 Dihedral : 4.842 22.515 1185 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.75 % Allowed : 10.26 % 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 (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: 1.04 (0.26), residues: 1098 helix: 0.98 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.41 (0.35), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 271 HIS 0.007 0.002 HIS A 364 PHE 0.012 0.002 PHE C 369 TYR 0.010 0.002 TYR C 365 ARG 0.007 0.001 ARG C 161 *********************** 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 118 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.960 Fit side-chains REVERT: A 376 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6240 (pp) REVERT: A 440 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7577 (ttmt) REVERT: A 452 MET cc_start: 0.8470 (mtp) cc_final: 0.8216 (mtp) REVERT: A 472 ARG cc_start: 0.7647 (mmt90) cc_final: 0.6534 (mtp180) REVERT: B 242 THR cc_start: 0.8916 (t) cc_final: 0.8678 (m) REVERT: B 314 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8476 (mt0) REVERT: B 376 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6045 (mt) REVERT: B 485 MET cc_start: 0.8104 (mtm) cc_final: 0.7603 (mmp) REVERT: C 384 LYS cc_start: 0.8533 (mmtp) cc_final: 0.8243 (mmtt) REVERT: C 392 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.8747 (mmt) REVERT: C 450 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7832 (t80) REVERT: C 485 MET cc_start: 0.8200 (mtp) cc_final: 0.7674 (mmm) outliers start: 26 outliers final: 14 residues processed: 108 average time/residue: 1.3080 time to fit residues: 150.7935 Evaluate side-chains 109 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 276 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 366 LEU 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 264 VAL 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 103 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 0.0570 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 53 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.123151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.096043 restraints weight = 9546.639| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.55 r_work: 0.2886 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9156 Z= 0.143 Angle : 0.515 7.243 12507 Z= 0.263 Chirality : 0.040 0.128 1404 Planarity : 0.005 0.040 1521 Dihedral : 4.484 21.314 1185 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.59 % Allowed : 11.43 % 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 (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: 1.52 (0.21), residues: 657 sheet: None (None), residues: 0 loop : 0.56 (0.34), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 271 HIS 0.005 0.001 HIS B 364 PHE 0.012 0.001 PHE A 450 TYR 0.007 0.001 TYR A 156 ARG 0.009 0.000 ARG C 161 *********************** 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: 15 poor density : 89 time to evaluate : 1.081 Fit side-chains REVERT: A 376 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.5805 (mt) REVERT: A 440 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7586 (ttmt) REVERT: A 452 MET cc_start: 0.8453 (mtp) cc_final: 0.8238 (mtp) REVERT: B 242 THR cc_start: 0.8873 (t) cc_final: 0.8622 (m) REVERT: B 314 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8378 (mt0) REVERT: B 376 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6045 (mt) REVERT: B 485 MET cc_start: 0.8052 (mtm) cc_final: 0.7550 (mmp) REVERT: C 320 LYS cc_start: 0.7884 (mmpt) cc_final: 0.7244 (pttm) REVERT: C 376 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6175 (mt) REVERT: C 384 LYS cc_start: 0.8486 (mmtp) cc_final: 0.8071 (mmtt) REVERT: C 392 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8697 (mmt) REVERT: C 450 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7399 (t80) REVERT: C 485 MET cc_start: 0.8173 (mtp) cc_final: 0.7764 (mmm) outliers start: 15 outliers final: 6 residues processed: 98 average time/residue: 1.3835 time to fit residues: 144.3300 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 : 0.993 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 91 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 76 optimal weight: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.121099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.093791 restraints weight = 9494.069| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.56 r_work: 0.2853 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9156 Z= 0.186 Angle : 0.544 7.374 12507 Z= 0.278 Chirality : 0.041 0.125 1404 Planarity : 0.005 0.040 1521 Dihedral : 4.563 21.384 1185 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.69 % Allowed : 11.43 % 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: 1.55 (0.27), residues: 1098 helix: 1.36 (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 C 271 HIS 0.006 0.001 HIS C 364 PHE 0.013 0.001 PHE A 450 TYR 0.009 0.001 TYR C 365 ARG 0.009 0.001 ARG C 161 ********************** 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: 16 poor density : 90 time to evaluate : 0.899 Fit side-chains REVERT: A 376 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.5863 (mt) REVERT: A 440 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7593 (ttmt) REVERT: A 452 MET cc_start: 0.8483 (mtp) cc_final: 0.8248 (mtp) REVERT: A 514 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7781 (tttp) REVERT: B 181 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7755 (tp-100) REVERT: B 242 THR cc_start: 0.8898 (t) cc_final: 0.8648 (m) REVERT: B 314 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8403 (mt0) REVERT: B 376 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.5890 (mt) REVERT: B 485 MET cc_start: 0.8069 (mtm) cc_final: 0.7556 (mmp) REVERT: C 376 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6111 (mt) REVERT: C 384 LYS cc_start: 0.8490 (mmtp) cc_final: 0.8074 (mmtt) REVERT: C 392 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8697 (mmt) REVERT: C 450 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7571 (t80) REVERT: C 485 MET cc_start: 0.8183 (mtp) cc_final: 0.7750 (mmm) outliers start: 16 outliers final: 6 residues processed: 100 average time/residue: 1.4335 time to fit residues: 152.7171 Evaluate side-chains 105 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 514 LYS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 181 GLN 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 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 81 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.120943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.093762 restraints weight = 9493.640| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.54 r_work: 0.2849 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9156 Z= 0.186 Angle : 0.543 5.245 12507 Z= 0.278 Chirality : 0.041 0.122 1404 Planarity : 0.005 0.040 1521 Dihedral : 4.568 21.664 1185 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.90 % Allowed : 11.43 % 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 (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: 1.58 (0.27), residues: 1098 helix: 1.38 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.68 (0.35), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 271 HIS 0.006 0.001 HIS C 364 PHE 0.013 0.001 PHE A 450 TYR 0.009 0.001 TYR C 365 ARG 0.009 0.001 ARG C 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5745.33 seconds wall clock time: 102 minutes 3.57 seconds (6123.57 seconds total)