Starting phenix.real_space_refine on Sun Oct 25 23:30:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/38la_78899/10_2026/38la_78899.cif Found real_map, /net/cci-nas-00/data/ceres_data/38la_78899/10_2026/38la_78899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/38la_78899/10_2026/38la_78899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/38la_78899/10_2026/38la_78899.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/38la_78899/10_2026/38la_78899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/38la_78899/10_2026/38la_78899.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 132 5.16 5 C 11676 2.51 5 N 3132 2.21 5 O 3468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18408 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4602 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 20, 'TRANS': 552} Chain breaks: 2 Restraints were copied for chains: B, C, D Time building chain proxies: 4.63, per 1000 atoms: 0.25 Number of scatterers: 18408 At special positions: 0 Unit cell: (114.46, 121.54, 128.62, 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 132 16.00 O 3468 8.00 N 3132 7.00 C 11676 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: 1.29 Conformation dependent library (CDL) restraints added in 747.5 milliseconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4304 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 54.1% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 10 through 14 Processing helix chain 'A' and resid 17 through 26 Processing helix chain 'A' and resid 40 through 60 Processing helix chain 'A' and resid 107 through 117 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 146 through 156 Processing helix chain 'A' and resid 174 through 180 removed outlier: 4.278A pdb=" N ALA A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 Processing helix chain 'A' and resid 202 through 230 removed outlier: 3.527A pdb=" N TYR A 229 " --> pdb=" O MET A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 258 removed outlier: 3.531A pdb=" N ALA A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 removed outlier: 3.730A pdb=" N ILE A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 275 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 303 removed outlier: 3.534A pdb=" N LEU A 303 " --> pdb=" O MET A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.911A pdb=" N PHE A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 391 through 399 removed outlier: 3.659A pdb=" N ALA A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 459 through 493 removed outlier: 3.724A pdb=" N GLN A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 516 through 530 Processing helix chain 'A' and resid 558 through 577 Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 17 through 26 Processing helix chain 'B' and resid 40 through 60 Processing helix chain 'B' and resid 107 through 117 Processing helix chain 'B' and resid 123 through 133 Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 146 through 156 Processing helix chain 'B' and resid 174 through 180 removed outlier: 4.278A pdb=" N ALA B 178 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 Processing helix chain 'B' and resid 202 through 230 removed outlier: 3.527A pdb=" N TYR B 229 " --> pdb=" O MET B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 258 removed outlier: 3.531A pdb=" N ALA B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 282 removed outlier: 3.730A pdb=" N ILE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR B 275 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 303 removed outlier: 3.534A pdb=" N LEU B 303 " --> pdb=" O MET B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.910A pdb=" N PHE B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU B 349 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 391 through 399 removed outlier: 3.659A pdb=" N ALA B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 Processing helix chain 'B' and resid 459 through 493 removed outlier: 3.724A pdb=" N GLN B 469 " --> pdb=" O GLU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 516 through 530 Processing helix chain 'B' and resid 558 through 577 Processing helix chain 'C' and resid 10 through 14 Processing helix chain 'C' and resid 17 through 26 Processing helix chain 'C' and resid 40 through 60 Processing helix chain 'C' and resid 107 through 117 Processing helix chain 'C' and resid 123 through 133 Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 146 through 156 Processing helix chain 'C' and resid 174 through 180 removed outlier: 4.278A pdb=" N ALA C 178 " --> pdb=" O TYR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 196 Processing helix chain 'C' and resid 202 through 230 removed outlier: 3.527A pdb=" N TYR C 229 " --> pdb=" O MET C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 258 removed outlier: 3.531A pdb=" N ALA C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 282 removed outlier: 3.730A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR C 275 " --> pdb=" O PHE C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 303 removed outlier: 3.534A pdb=" N LEU C 303 " --> pdb=" O MET C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 353 removed outlier: 3.910A pdb=" N PHE C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 383 Processing helix chain 'C' and resid 391 through 399 removed outlier: 3.659A pdb=" N ALA C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 436 Processing helix chain 'C' and resid 459 through 493 removed outlier: 3.724A pdb=" N GLN C 469 " --> pdb=" O GLU C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 500 Processing helix chain 'C' and resid 516 through 530 Processing helix chain 'C' and resid 558 through 577 Processing helix chain 'D' and resid 10 through 14 Processing helix chain 'D' and resid 17 through 26 Processing helix chain 'D' and resid 40 through 60 Processing helix chain 'D' and resid 107 through 117 Processing helix chain 'D' and resid 123 through 133 Processing helix chain 'D' and resid 136 through 145 Processing helix chain 'D' and resid 146 through 156 Processing helix chain 'D' and resid 174 through 180 removed outlier: 4.279A pdb=" N ALA D 178 " --> pdb=" O TYR D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 196 Processing helix chain 'D' and resid 202 through 230 removed outlier: 3.526A pdb=" N TYR D 229 " --> pdb=" O MET D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 258 removed outlier: 3.531A pdb=" N ALA D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 282 removed outlier: 3.730A pdb=" N ILE D 274 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR D 275 " --> pdb=" O PHE D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 303 removed outlier: 3.534A pdb=" N LEU D 303 " --> pdb=" O MET D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 353 removed outlier: 3.910A pdb=" N PHE D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU D 349 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 383 Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.659A pdb=" N ALA D 396 " --> pdb=" O GLU D 392 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU D 397 " --> pdb=" O LEU D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 436 Processing helix chain 'D' and resid 459 through 493 removed outlier: 3.724A pdb=" N GLN D 469 " --> pdb=" O GLU D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'D' and resid 516 through 530 Processing helix chain 'D' and resid 558 through 577 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 71 removed outlier: 4.315A pdb=" N LEU A 102 " --> pdb=" O ASP A 67 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LYS A 69 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 323 through 327 removed outlier: 6.452A pdb=" N VAL A 323 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR A 361 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU A 325 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU A 363 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE A 327 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 387 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA4, first strand: chain 'A' and resid 416 through 419 removed outlier: 6.325A pdb=" N ALA A 424 " --> pdb=" O ALA A 515 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 416 through 419 removed outlier: 6.991A pdb=" N ARG A 508 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR A 588 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE A 510 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N SER A 590 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR A 512 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 531 through 536 removed outlier: 3.758A pdb=" N ASP A 544 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 71 removed outlier: 4.314A pdb=" N LEU B 102 " --> pdb=" O ASP B 67 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LYS B 69 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 323 through 327 removed outlier: 6.452A pdb=" N VAL B 323 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N THR B 361 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU B 325 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU B 363 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE B 327 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 387 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AB1, first strand: chain 'B' and resid 416 through 419 removed outlier: 6.325A pdb=" N ALA B 424 " --> pdb=" O ALA B 515 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 416 through 419 removed outlier: 6.991A pdb=" N ARG B 508 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR B 588 " --> pdb=" O ARG B 508 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE B 510 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N SER B 590 " --> pdb=" O PHE B 510 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR B 512 " --> pdb=" O SER B 590 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 531 through 536 removed outlier: 3.757A pdb=" N ASP B 544 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 71 removed outlier: 4.315A pdb=" N LEU C 102 " --> pdb=" O ASP C 67 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LYS C 69 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 323 through 327 removed outlier: 6.452A pdb=" N VAL C 323 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR C 361 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU C 325 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU C 363 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE C 327 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 387 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB7, first strand: chain 'C' and resid 416 through 419 removed outlier: 6.324A pdb=" N ALA C 424 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 416 through 419 removed outlier: 6.991A pdb=" N ARG C 508 " --> pdb=" O ILE C 586 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR C 588 " --> pdb=" O ARG C 508 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE C 510 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N SER C 590 " --> pdb=" O PHE C 510 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR C 512 " --> pdb=" O SER C 590 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 531 through 536 removed outlier: 3.758A pdb=" N ASP C 544 " --> pdb=" O ILE C 535 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 65 through 71 removed outlier: 4.315A pdb=" N LEU D 102 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LYS D 69 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 323 through 327 removed outlier: 6.452A pdb=" N VAL D 323 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N THR D 361 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU D 325 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU D 363 " --> pdb=" O GLU D 325 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE D 327 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN D 387 " --> pdb=" O LEU D 360 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AC4, first strand: chain 'D' and resid 416 through 419 removed outlier: 6.325A pdb=" N ALA D 424 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 416 through 419 removed outlier: 6.991A pdb=" N ARG D 508 " --> pdb=" O ILE D 586 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR D 588 " --> pdb=" O ARG D 508 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE D 510 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N SER D 590 " --> pdb=" O PHE D 510 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR D 512 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 531 through 536 removed outlier: 3.757A pdb=" N ASP D 544 " --> pdb=" O ILE D 535 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2772 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: 3.01 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6052 1.34 - 1.46: 3990 1.46 - 1.58: 8514 1.58 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 18796 Sorted by residual: bond pdb=" CA VAL A 323 " pdb=" CB VAL A 323 " ideal model delta sigma weight residual 1.530 1.540 -0.009 1.05e-02 9.07e+03 8.11e-01 bond pdb=" CA VAL B 323 " pdb=" CB VAL B 323 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 6.73e-01 bond pdb=" CA VAL D 323 " pdb=" CB VAL D 323 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 6.73e-01 bond pdb=" CA VAL C 323 " pdb=" CB VAL C 323 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 6.73e-01 bond pdb=" C GLU A 357 " pdb=" N PRO A 358 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.39e-01 ... (remaining 18791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 25096 1.46 - 2.92: 208 2.92 - 4.37: 40 4.37 - 5.83: 4 5.83 - 7.29: 4 Bond angle restraints: 25352 Sorted by residual: angle pdb=" N VAL B 446 " pdb=" CA VAL B 446 " pdb=" C VAL B 446 " ideal model delta sigma weight residual 111.48 109.13 2.35 9.40e-01 1.13e+00 6.24e+00 angle pdb=" N VAL D 446 " pdb=" CA VAL D 446 " pdb=" C VAL D 446 " ideal model delta sigma weight residual 111.48 109.18 2.30 9.40e-01 1.13e+00 5.97e+00 angle pdb=" N VAL C 446 " pdb=" CA VAL C 446 " pdb=" C VAL C 446 " ideal model delta sigma weight residual 111.48 109.20 2.28 9.40e-01 1.13e+00 5.91e+00 angle pdb=" CB MET A 488 " pdb=" CG MET A 488 " pdb=" SD MET A 488 " ideal model delta sigma weight residual 112.70 119.99 -7.29 3.00e+00 1.11e-01 5.91e+00 angle pdb=" CB MET C 488 " pdb=" CG MET C 488 " pdb=" SD MET C 488 " ideal model delta sigma weight residual 112.70 119.97 -7.27 3.00e+00 1.11e-01 5.88e+00 ... (remaining 25347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 9411 17.72 - 35.45: 1361 35.45 - 53.17: 456 53.17 - 70.90: 100 70.90 - 88.62: 28 Dihedral angle restraints: 11356 sinusoidal: 4656 harmonic: 6700 Sorted by residual: dihedral pdb=" CA CYS B 407 " pdb=" C CYS B 407 " pdb=" N VAL B 408 " pdb=" CA VAL B 408 " ideal model delta harmonic sigma weight residual -180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA CYS A 407 " pdb=" C CYS A 407 " pdb=" N VAL A 408 " pdb=" CA VAL A 408 " ideal model delta harmonic sigma weight residual -180.00 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA CYS D 407 " pdb=" C CYS D 407 " pdb=" N VAL D 408 " pdb=" CA VAL D 408 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 11353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1741 0.026 - 0.051: 602 0.051 - 0.077: 240 0.077 - 0.103: 86 0.103 - 0.128: 63 Chirality restraints: 2732 Sorted by residual: chirality pdb=" CA ILE B 89 " pdb=" N ILE B 89 " pdb=" C ILE B 89 " pdb=" CB ILE B 89 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE A 514 " pdb=" N ILE A 514 " pdb=" C ILE A 514 " pdb=" CB ILE A 514 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE C 514 " pdb=" N ILE C 514 " pdb=" C ILE C 514 " pdb=" CB ILE C 514 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 2729 not shown) Planarity restraints: 3272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 357 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO A 358 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 358 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 358 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 357 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO B 358 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 357 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO D 358 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 358 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 358 " -0.026 5.00e-02 4.00e+02 ... (remaining 3269 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 8206 2.99 - 3.47: 17172 3.47 - 3.94: 30712 3.94 - 4.42: 36287 4.42 - 4.90: 57819 Nonbonded interactions: 150196 Sorted by model distance: nonbonded pdb=" O SER B 384 " pdb=" OG SER B 384 " model vdw 2.509 3.040 nonbonded pdb=" O SER A 384 " pdb=" OG SER A 384 " model vdw 2.509 3.040 nonbonded pdb=" O SER C 384 " pdb=" OG SER C 384 " model vdw 2.509 3.040 nonbonded pdb=" O SER D 384 " pdb=" OG SER D 384 " model vdw 2.510 3.040 nonbonded pdb=" N ASP A 65 " pdb=" O ASP A 65 " model vdw 2.628 2.496 ... (remaining 150191 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 'B' selection = chain 'C' selection = chain 'D' } 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: 1.560 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.230 Find NCS groups from input model: 0.160 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:7.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.002 0.028 18796 Z= 0.081 Angle : 0.398 7.291 25352 Z= 0.223 Chirality : 0.036 0.128 2732 Planarity : 0.003 0.048 3272 Dihedral : 18.983 88.620 7052 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.28 % Allowed : 23.67 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 2268 helix: -0.68 (0.12), residues: 1168 sheet: 0.57 (0.43), residues: 188 loop : -0.79 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 284 TYR 0.006 0.001 TYR D 478 PHE 0.006 0.001 PHE C 510 TRP 0.009 0.001 TRP C 246 HIS 0.009 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.08 (18796) covalent geometry : angle 0.39822 / 0.22 (25352) hydrogen bonds : bond 0.25718 / 17.02 ( 924) hydrogen bonds : angle 7.15524 / 5.05 ( 2772) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 4 residues processed: 236 average time/residue: 0.6973 time to fit residues: 180.8018 Evaluate side-chains 163 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 159 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain D residue 145 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 200] chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 387 GLN A 469 GLN B 387 GLN B 469 GLN C 387 GLN D 387 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.057932 restraints weight = 40610.385| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.24 r_work: 0.2577 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 18796 Z= 0.221 Angle : 0.534 4.666 25352 Z= 0.291 Chirality : 0.041 0.139 2732 Planarity : 0.004 0.036 3272 Dihedral : 4.084 40.664 2544 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.29 % Allowed : 21.43 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2268 helix: 1.78 (0.15), residues: 1156 sheet: 0.32 (0.39), residues: 196 loop : -0.63 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 374 TYR 0.012 0.001 TYR C 478 PHE 0.012 0.001 PHE B 510 TRP 0.011 0.001 TRP C 246 HIS 0.005 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 (18796) covalent geometry : angle 0.53425 / 0.29 (25352) hydrogen bonds : bond 0.06388 / 4.20 ( 924) hydrogen bonds : angle 4.36559 / 3.09 ( 2772) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 161 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.8045 (mmt) cc_final: 0.7782 (mmm) REVERT: A 470 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.9095 (mmm) REVERT: B 258 GLN cc_start: 0.7984 (pp30) cc_final: 0.7693 (pp30) REVERT: B 398 MET cc_start: 0.8102 (mmt) cc_final: 0.7891 (mmm) REVERT: B 470 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.9098 (mmm) REVERT: C 128 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8660 (pp20) REVERT: C 398 MET cc_start: 0.8049 (mmt) cc_final: 0.7792 (mmm) REVERT: C 470 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.9094 (mmm) REVERT: D 398 MET cc_start: 0.8082 (mmt) cc_final: 0.7873 (mmm) outliers start: 84 outliers final: 21 residues processed: 221 average time/residue: 0.5634 time to fit residues: 139.8843 Evaluate side-chains 172 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 589 MET Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 589 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [220, 172, 129, 143, 138, 31, 157, 185, 107, 162, 21] chunk 220 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 129 optimal weight: 0.1980 chunk 143 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 HIS A 469 GLN B 194 HIS B 469 GLN C 194 HIS C 469 GLN D 194 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.085000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.060740 restraints weight = 40710.318| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.29 r_work: 0.2651 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18796 Z= 0.100 Angle : 0.434 5.258 25352 Z= 0.232 Chirality : 0.038 0.133 2732 Planarity : 0.003 0.027 3272 Dihedral : 3.960 41.675 2544 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.60 % Allowed : 23.27 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.18), residues: 2268 helix: 2.30 (0.15), residues: 1180 sheet: 0.45 (0.38), residues: 196 loop : -0.60 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 374 TYR 0.008 0.001 TYR B 478 PHE 0.007 0.001 PHE D 510 TRP 0.008 0.001 TRP B 246 HIS 0.003 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (18796) covalent geometry : angle 0.43441 / 0.23 (25352) hydrogen bonds : bond 0.04672 / 3.09 ( 924) hydrogen bonds : angle 3.97334 / 2.82 ( 2772) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 GLN cc_start: 0.7880 (pp30) cc_final: 0.7528 (pp30) REVERT: A 381 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9118 (pp) REVERT: A 398 MET cc_start: 0.7999 (mmt) cc_final: 0.7735 (mmm) REVERT: A 470 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8974 (mmm) REVERT: B 258 GLN cc_start: 0.7862 (pp30) cc_final: 0.7595 (pp30) REVERT: B 381 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9177 (pp) REVERT: B 398 MET cc_start: 0.8027 (mmt) cc_final: 0.7766 (mmm) REVERT: B 470 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8980 (mmm) REVERT: C 128 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8760 (pp20) REVERT: C 381 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9180 (pp) REVERT: C 398 MET cc_start: 0.7999 (mmt) cc_final: 0.7736 (mmm) REVERT: C 470 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8988 (mmm) REVERT: D 381 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9180 (pp) REVERT: D 398 MET cc_start: 0.8004 (mmt) cc_final: 0.7750 (mmm) outliers start: 51 outliers final: 9 residues processed: 198 average time/residue: 0.5878 time to fit residues: 130.6267 Evaluate side-chains 168 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 589 MET Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 589 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [63, 52, 1, 32, 162, 73, 67, 66, 57, 181, 170] chunk 63 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.079613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.055119 restraints weight = 41224.100| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 3.24 r_work: 0.2521 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 18796 Z= 0.303 Angle : 0.561 7.271 25352 Z= 0.299 Chirality : 0.042 0.150 2732 Planarity : 0.003 0.028 3272 Dihedral : 4.265 40.554 2544 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.65 % Allowed : 22.24 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.17), residues: 2268 helix: 2.37 (0.15), residues: 1156 sheet: -0.15 (0.36), residues: 204 loop : -0.60 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.016 0.001 TYR A 478 PHE 0.015 0.002 PHE B 130 TRP 0.008 0.001 TRP A 246 HIS 0.007 0.002 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.30 (18796) covalent geometry : angle 0.56119 / 0.30 (25352) hydrogen bonds : bond 0.06821 / 4.49 ( 924) hydrogen bonds : angle 4.13703 / 2.93 ( 2772) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8594 (mm-30) REVERT: A 381 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9145 (pp) REVERT: A 533 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8832 (ttmm) REVERT: B 281 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8598 (mm-30) REVERT: B 381 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9143 (pp) REVERT: B 533 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8831 (ttmm) REVERT: C 128 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8684 (pp20) REVERT: C 281 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8601 (mm-30) REVERT: C 381 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.9145 (pp) REVERT: C 533 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8833 (ttmm) REVERT: D 281 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8586 (mm-30) REVERT: D 381 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9149 (pp) REVERT: D 533 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8829 (ttmm) outliers start: 52 outliers final: 21 residues processed: 187 average time/residue: 0.6160 time to fit residues: 128.6668 Evaluate side-chains 174 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 533 LYS Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain D residue 563 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [189, 155, 14, 112, 69, 134, 60, 119, 139, 63, 221] chunk 189 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 469 GLN B 469 GLN C 469 GLN D 469 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.083381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.059046 restraints weight = 40356.592| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.29 r_work: 0.2612 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18796 Z= 0.103 Angle : 0.437 6.088 25352 Z= 0.232 Chirality : 0.039 0.161 2732 Planarity : 0.003 0.028 3272 Dihedral : 4.071 41.034 2544 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.94 % Allowed : 22.14 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.18), residues: 2268 helix: 2.65 (0.15), residues: 1156 sheet: 0.32 (0.38), residues: 196 loop : -0.52 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 423 TYR 0.008 0.001 TYR C 478 PHE 0.007 0.001 PHE C 510 TRP 0.008 0.001 TRP C 246 HIS 0.004 0.001 HIS D 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (18796) covalent geometry : angle 0.43677 / 0.23 (25352) hydrogen bonds : bond 0.04556 / 3.01 ( 924) hydrogen bonds : angle 3.76265 / 2.68 ( 2772) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.577 Fit side-chains REVERT: A 258 GLN cc_start: 0.7936 (pp30) cc_final: 0.7520 (pp30) REVERT: A 381 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9045 (pp) REVERT: B 258 GLN cc_start: 0.7934 (pp30) cc_final: 0.7595 (pp30) REVERT: B 381 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9051 (pp) REVERT: C 128 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8666 (pp20) REVERT: C 381 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9047 (pp) REVERT: D 381 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9057 (pp) outliers start: 38 outliers final: 9 residues processed: 180 average time/residue: 0.6339 time to fit residues: 127.2773 Evaluate side-chains 153 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 383 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [204, 90, 217, 181, 140, 147, 98, 124, 145, 121, 101] chunk 204 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 140 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 124 optimal weight: 0.2980 chunk 145 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.083248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.058998 restraints weight = 40204.289| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.27 r_work: 0.2618 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18796 Z= 0.110 Angle : 0.453 7.762 25352 Z= 0.236 Chirality : 0.038 0.132 2732 Planarity : 0.003 0.025 3272 Dihedral : 4.005 41.005 2544 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.84 % Allowed : 22.81 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.18), residues: 2268 helix: 2.72 (0.15), residues: 1156 sheet: 0.41 (0.39), residues: 196 loop : -0.46 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 423 TYR 0.010 0.001 TYR A 478 PHE 0.007 0.001 PHE B 130 TRP 0.005 0.001 TRP A 246 HIS 0.003 0.001 HIS C 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (18796) covalent geometry : angle 0.45297 / 0.24 (25352) hydrogen bonds : bond 0.04522 / 2.99 ( 924) hydrogen bonds : angle 3.68757 / 2.63 ( 2772) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 GLN cc_start: 0.7929 (pp30) cc_final: 0.7534 (pp30) REVERT: A 381 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9101 (pp) REVERT: A 398 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7166 (mtp) REVERT: B 258 GLN cc_start: 0.7910 (pp30) cc_final: 0.7615 (pp30) REVERT: B 381 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9103 (pp) REVERT: B 398 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7320 (mtp) REVERT: C 128 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8662 (pp20) REVERT: C 381 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9100 (pp) REVERT: C 398 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7181 (mtp) REVERT: D 381 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9109 (pp) REVERT: D 398 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7306 (mtp) outliers start: 36 outliers final: 12 residues processed: 161 average time/residue: 0.6256 time to fit residues: 112.4150 Evaluate side-chains 160 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 398 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [155, 163, 142, 61, 34, 40, 200, 160, 63, 207, 100] chunk 155 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 200 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.082926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.058599 restraints weight = 40575.007| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.30 r_work: 0.2609 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18796 Z= 0.120 Angle : 0.462 8.380 25352 Z= 0.240 Chirality : 0.039 0.132 2732 Planarity : 0.003 0.024 3272 Dihedral : 3.988 40.852 2544 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.79 % Allowed : 23.16 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.18), residues: 2268 helix: 2.77 (0.15), residues: 1156 sheet: 0.34 (0.38), residues: 196 loop : -0.45 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 423 TYR 0.010 0.001 TYR D 478 PHE 0.007 0.001 PHE A 510 TRP 0.007 0.001 TRP C 246 HIS 0.003 0.001 HIS D 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (18796) covalent geometry : angle 0.46153 / 0.24 (25352) hydrogen bonds : bond 0.04577 / 3.02 ( 924) hydrogen bonds : angle 3.67040 / 2.62 ( 2772) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.625 Fit side-chains REVERT: A 191 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8198 (mp0) REVERT: A 258 GLN cc_start: 0.7941 (pp30) cc_final: 0.7513 (pp30) REVERT: A 381 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9014 (pp) REVERT: A 398 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7179 (mtp) REVERT: B 258 GLN cc_start: 0.7878 (pp30) cc_final: 0.7554 (pp30) REVERT: B 381 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9079 (pp) REVERT: B 398 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7330 (mtp) REVERT: B 444 MET cc_start: 0.7728 (ptp) cc_final: 0.7496 (ptt) REVERT: C 128 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8702 (pp20) REVERT: C 381 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9013 (pp) REVERT: C 398 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7176 (mtp) REVERT: C 533 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8868 (ttmm) REVERT: D 191 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8196 (mp0) REVERT: D 381 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9080 (pp) REVERT: D 398 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7321 (mtp) REVERT: D 444 MET cc_start: 0.7764 (ptp) cc_final: 0.7532 (ptt) outliers start: 35 outliers final: 21 residues processed: 167 average time/residue: 0.6235 time to fit residues: 116.1588 Evaluate side-chains 174 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 533 LYS Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 411 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [140, 219, 106, 123, 125, 36, 187, 84, 160, 137, 16] chunk 140 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 123 optimal weight: 0.0370 chunk 125 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 overall best weight: 1.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 HIS C 154 HIS C 418 GLN D 469 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.081474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.056982 restraints weight = 40667.753| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.30 r_work: 0.2570 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 18796 Z= 0.174 Angle : 0.508 9.326 25352 Z= 0.261 Chirality : 0.040 0.131 2732 Planarity : 0.003 0.024 3272 Dihedral : 4.102 40.658 2544 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.99 % Allowed : 23.16 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.18), residues: 2268 helix: 2.74 (0.15), residues: 1156 sheet: 0.19 (0.38), residues: 196 loop : -0.47 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 508 TYR 0.012 0.001 TYR D 478 PHE 0.011 0.001 PHE B 572 TRP 0.010 0.001 TRP C 246 HIS 0.004 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (18796) covalent geometry : angle 0.50816 / 0.26 (25352) hydrogen bonds : bond 0.05324 / 3.51 ( 924) hydrogen bonds : angle 3.76232 / 2.68 ( 2772) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.709 Fit side-chains REVERT: A 191 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8227 (mp0) REVERT: A 258 GLN cc_start: 0.7963 (pp30) cc_final: 0.7531 (pp30) REVERT: A 381 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9090 (pp) REVERT: A 398 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7219 (mtp) REVERT: A 533 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8861 (ttmm) REVERT: B 191 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8214 (mp0) REVERT: B 258 GLN cc_start: 0.7926 (pp30) cc_final: 0.7599 (pp30) REVERT: B 381 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9083 (pp) REVERT: B 398 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7308 (mtp) REVERT: B 533 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8863 (ttmm) REVERT: C 128 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8698 (pp20) REVERT: C 191 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8229 (mp0) REVERT: C 381 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9087 (pp) REVERT: C 398 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7232 (mtp) REVERT: C 533 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8863 (ttmm) REVERT: D 191 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8227 (mp0) REVERT: D 381 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9082 (pp) REVERT: D 398 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7292 (mtp) REVERT: D 533 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8857 (ttmm) outliers start: 39 outliers final: 16 residues processed: 167 average time/residue: 0.6559 time to fit residues: 121.6422 Evaluate side-chains 172 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 533 LYS Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 533 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [137, 142, 107, 7, 123, 116, 219, 8, 17, 154, 201] chunk 137 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 7 optimal weight: 0.0050 chunk 123 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 219 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 GLN B 154 HIS C 418 GLN D 154 HIS D 418 GLN D 469 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.083503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.059078 restraints weight = 40513.525| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.32 r_work: 0.2623 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18796 Z= 0.108 Angle : 0.486 11.469 25352 Z= 0.248 Chirality : 0.039 0.135 2732 Planarity : 0.003 0.023 3272 Dihedral : 4.048 41.110 2544 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.04 % Allowed : 22.91 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.18), residues: 2268 helix: 2.81 (0.15), residues: 1156 sheet: 0.22 (0.39), residues: 196 loop : -0.43 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 423 TYR 0.010 0.001 TYR D 478 PHE 0.007 0.001 PHE A 510 TRP 0.007 0.001 TRP A 246 HIS 0.003 0.001 HIS B 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (18796) covalent geometry : angle 0.48637 / 0.25 (25352) hydrogen bonds : bond 0.04400 / 2.90 ( 924) hydrogen bonds : angle 3.64527 / 2.60 ( 2772) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.595 Fit side-chains REVERT: A 191 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8184 (mp0) REVERT: A 258 GLN cc_start: 0.7890 (pp30) cc_final: 0.7568 (pp30) REVERT: A 381 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9019 (pp) REVERT: A 398 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7165 (mtp) REVERT: A 533 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8844 (ttmm) REVERT: B 191 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8166 (mp0) REVERT: B 258 GLN cc_start: 0.7858 (pp30) cc_final: 0.7522 (pp30) REVERT: B 381 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9013 (pp) REVERT: B 398 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7272 (mtp) REVERT: B 533 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8881 (ttmm) REVERT: C 128 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8708 (pp20) REVERT: C 191 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8177 (mp0) REVERT: C 381 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9017 (pp) REVERT: C 398 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7168 (mtp) REVERT: D 191 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8167 (mp0) REVERT: D 381 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9013 (pp) REVERT: D 398 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7250 (mtp) REVERT: D 533 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8851 (ttmm) outliers start: 40 outliers final: 11 residues processed: 169 average time/residue: 0.6631 time to fit residues: 124.7014 Evaluate side-chains 162 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 533 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [146, 130, 162, 102, 5, 191, 145, 218, 61, 157, 64] chunk 146 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 218 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 GLN B 418 GLN C 418 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.082006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.057536 restraints weight = 40618.882| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.29 r_work: 0.2584 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18796 Z= 0.166 Angle : 0.528 13.113 25352 Z= 0.265 Chirality : 0.040 0.132 2732 Planarity : 0.003 0.024 3272 Dihedral : 4.120 40.675 2544 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.63 % Allowed : 23.62 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.18), residues: 2268 helix: 2.76 (0.15), residues: 1152 sheet: 0.16 (0.38), residues: 196 loop : -0.43 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 267 TYR 0.012 0.001 TYR A 478 PHE 0.010 0.001 PHE C 130 TRP 0.010 0.001 TRP C 246 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (18796) covalent geometry : angle 0.52776 / 0.26 (25352) hydrogen bonds : bond 0.05243 / 3.45 ( 924) hydrogen bonds : angle 3.74186 / 2.67 ( 2772) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8206 (mp0) REVERT: A 258 GLN cc_start: 0.7960 (pp30) cc_final: 0.7527 (pp30) REVERT: A 381 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9067 (pp) REVERT: A 398 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7182 (mtp) REVERT: A 465 GLU cc_start: 0.8975 (tt0) cc_final: 0.8758 (tm-30) REVERT: A 533 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8880 (ttmm) REVERT: B 191 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8197 (mp0) REVERT: B 258 GLN cc_start: 0.7917 (pp30) cc_final: 0.7581 (pp30) REVERT: B 381 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9084 (pp) REVERT: B 398 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7303 (mtp) REVERT: B 465 GLU cc_start: 0.8993 (tt0) cc_final: 0.8780 (tm-30) REVERT: B 533 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8887 (ttmm) REVERT: C 128 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8707 (pp20) REVERT: C 191 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8208 (mp0) REVERT: C 381 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9064 (pp) REVERT: C 398 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7183 (mtp) REVERT: C 465 GLU cc_start: 0.8975 (tt0) cc_final: 0.8759 (tm-30) REVERT: C 533 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8876 (ttmm) REVERT: D 191 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8201 (mp0) REVERT: D 381 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9082 (pp) REVERT: D 398 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7277 (mtp) REVERT: D 465 GLU cc_start: 0.8996 (tt0) cc_final: 0.8772 (tm-30) REVERT: D 533 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8882 (ttmm) outliers start: 32 outliers final: 14 residues processed: 162 average time/residue: 0.6442 time to fit residues: 116.0984 Evaluate side-chains 169 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 533 LYS Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 394 MET Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 533 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [7, 213, 96, 226, 215, 214, 181, 163, 14, 114, 82] chunk 7 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 214 optimal weight: 0.5980 chunk 181 optimal weight: 0.0980 chunk 163 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 HIS B 154 HIS B 418 GLN C 154 HIS C 418 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.060162 restraints weight = 40417.711| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.32 r_work: 0.2641 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18796 Z= 0.097 Angle : 0.483 10.296 25352 Z= 0.242 Chirality : 0.039 0.130 2732 Planarity : 0.003 0.025 3272 Dihedral : 4.049 41.287 2544 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.48 % Allowed : 23.83 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.18), residues: 2268 helix: 2.81 (0.15), residues: 1152 sheet: 0.27 (0.39), residues: 196 loop : -0.36 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 100 TYR 0.009 0.001 TYR A 478 PHE 0.006 0.001 PHE D 510 TRP 0.007 0.001 TRP A 246 HIS 0.003 0.001 HIS C 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (18796) covalent geometry : angle 0.48323 / 0.24 (25352) hydrogen bonds : bond 0.04180 / 2.76 ( 924) hydrogen bonds : angle 3.61695 / 2.58 ( 2772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5124.54 seconds wall clock time: 88 minutes 11.80 seconds (5291.80 seconds total)