Starting phenix.real_space_refine on Thu Aug 6 13:04:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11wq_76139/08_2026/11wq_76139.cif Found real_map, /net/cci-nas-00/data/ceres_data/11wq_76139/08_2026/11wq_76139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11wq_76139/08_2026/11wq_76139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11wq_76139/08_2026/11wq_76139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11wq_76139/08_2026/11wq_76139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11wq_76139/08_2026/11wq_76139.map" } resolution = 3.2 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= 0.011 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 75 5.16 5 C 9549 2.51 5 N 2568 2.21 5 O 2715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14907 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4969 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 41, 'TRANS': 596} Chain breaks: 2 Restraints were copied for chains: B, C Time building chain proxies: 3.67, per 1000 atoms: 0.25 Number of scatterers: 14907 At special positions: 0 Unit cell: (79.2, 141.9, 139.425, 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 75 16.00 O 2715 8.00 N 2568 7.00 C 9549 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: 1.01 Conformation dependent library (CDL) restraints added in 654.4 milliseconds 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 27 sheets defined 38.2% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.842A pdb=" N ASP A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 45 Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.642A pdb=" N PHE A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 120 through 138 Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.744A pdb=" N ILE A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.864A pdb=" N THR A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 288 through 301 Processing helix chain 'A' and resid 318 through 325 Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.632A pdb=" N LEU A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N MET A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 359 Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 378 through 382 removed outlier: 3.676A pdb=" N VAL A 381 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS A 382 " --> pdb=" O GLU A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 378 through 382' Processing helix chain 'A' and resid 399 through 410 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 538 through 548 removed outlier: 3.598A pdb=" N ILE A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 597 removed outlier: 3.536A pdb=" N ILE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 removed outlier: 3.583A pdb=" N ILE A 627 " --> pdb=" O ILE A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 661 Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.842A pdb=" N ASP B 21 " --> pdb=" O ARG B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 45 Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.642A pdb=" N PHE B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 92 through 99 Processing helix chain 'B' and resid 120 through 138 Processing helix chain 'B' and resid 152 through 165 removed outlier: 3.744A pdb=" N ILE B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.863A pdb=" N THR B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 288 through 301 Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.632A pdb=" N LEU B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N MET B 331 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 359 Processing helix chain 'B' and resid 366 through 377 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.676A pdb=" N VAL B 381 " --> pdb=" O ASN B 378 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 382 " --> pdb=" O GLU B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 382' Processing helix chain 'B' and resid 399 through 410 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.598A pdb=" N ILE B 542 " --> pdb=" O SER B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 597 removed outlier: 3.536A pdb=" N ILE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 630 removed outlier: 3.583A pdb=" N ILE B 627 " --> pdb=" O ILE B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 661 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.842A pdb=" N ASP C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 45 Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.642A pdb=" N PHE C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 120 through 138 Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.744A pdb=" N ILE C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 208 through 217 removed outlier: 3.864A pdb=" N THR C 217 " --> pdb=" O ASN C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 253 Processing helix chain 'C' and resid 288 through 301 Processing helix chain 'C' and resid 318 through 325 Processing helix chain 'C' and resid 326 through 333 removed outlier: 3.633A pdb=" N LEU C 330 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 359 Processing helix chain 'C' and resid 366 through 377 Processing helix chain 'C' and resid 378 through 382 removed outlier: 3.677A pdb=" N VAL C 381 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS C 382 " --> pdb=" O GLU C 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 378 through 382' Processing helix chain 'C' and resid 399 through 410 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 538 through 548 removed outlier: 3.598A pdb=" N ILE C 542 " --> pdb=" O SER C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 597 removed outlier: 3.535A pdb=" N ILE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 630 removed outlier: 3.583A pdb=" N ILE C 627 " --> pdb=" O ILE C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 661 Processing sheet with id=1, first strand: chain 'A' and resid 68 through 71 removed outlier: 3.627A pdb=" N ASP A 76 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 115 through 119 removed outlier: 6.737A pdb=" N ARG A 116 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE A 106 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 118 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N CYS A 312 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE A 339 " --> pdb=" O CYS A 312 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 362 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 168 through 171 removed outlier: 4.233A pdb=" N VAL A 192 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 196 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 225 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 198 through 201 Processing sheet with id=5, first strand: chain 'A' and resid 270 through 272 removed outlier: 3.998A pdb=" N THR A 486 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 390 through 393 removed outlier: 6.579A pdb=" N LEU A 391 " --> pdb=" O ALA A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=6 Processing sheet with id=7, first strand: chain 'A' and resid 454 through 457 removed outlier: 7.084A pdb=" N VAL A 470 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA A 512 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLY A 472 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASP A 510 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU A 474 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 508 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N GLY A 509 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG A 525 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLY A 511 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 530 through 532 Processing sheet with id=9, first strand: chain 'A' and resid 552 through 561 removed outlier: 4.145A pdb=" N GLU A 554 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 605 " --> pdb=" O VAL A 569 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 68 through 71 removed outlier: 3.627A pdb=" N ASP B 76 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 115 through 119 removed outlier: 6.737A pdb=" N ARG B 116 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE B 106 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE B 118 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N CYS B 312 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE B 339 " --> pdb=" O CYS B 312 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 362 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'B' and resid 168 through 171 removed outlier: 4.233A pdb=" N VAL B 192 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 196 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL B 225 " --> pdb=" O VAL B 244 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'B' and resid 198 through 201 Processing sheet with id=14, first strand: chain 'B' and resid 270 through 272 removed outlier: 3.999A pdb=" N THR B 486 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'B' and resid 390 through 393 removed outlier: 6.579A pdb=" N LEU B 391 " --> pdb=" O ALA B 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=15 Processing sheet with id=16, first strand: chain 'B' and resid 454 through 457 removed outlier: 7.084A pdb=" N VAL B 470 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA B 512 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLY B 472 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASP B 510 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU B 474 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 508 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N GLY B 509 " --> pdb=" O ARG B 525 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG B 525 " --> pdb=" O GLY B 509 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLY B 511 " --> pdb=" O ARG B 523 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'B' and resid 530 through 532 Processing sheet with id=18, first strand: chain 'B' and resid 552 through 561 removed outlier: 4.145A pdb=" N GLU B 554 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 605 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 68 through 71 removed outlier: 3.627A pdb=" N ASP C 76 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.737A pdb=" N ARG C 116 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE C 106 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE C 118 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N CYS C 312 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE C 339 " --> pdb=" O CYS C 312 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN C 362 " --> pdb=" O ARG C 309 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'C' and resid 168 through 171 removed outlier: 4.234A pdb=" N VAL C 192 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 196 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL C 225 " --> pdb=" O VAL C 244 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'C' and resid 198 through 201 Processing sheet with id=23, first strand: chain 'C' and resid 270 through 272 removed outlier: 3.998A pdb=" N THR C 486 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'C' and resid 390 through 393 removed outlier: 6.579A pdb=" N LEU C 391 " --> pdb=" O ALA C 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=24 Processing sheet with id=25, first strand: chain 'C' and resid 454 through 457 removed outlier: 7.084A pdb=" N VAL C 470 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA C 512 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLY C 472 " --> pdb=" O ASP C 510 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASP C 510 " --> pdb=" O GLY C 472 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU C 474 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 508 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N GLY C 509 " --> pdb=" O ARG C 525 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG C 525 " --> pdb=" O GLY C 509 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLY C 511 " --> pdb=" O ARG C 523 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'C' and resid 530 through 532 Processing sheet with id=27, first strand: chain 'C' and resid 552 through 561 removed outlier: 4.144A pdb=" N GLU C 554 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS C 605 " --> pdb=" O VAL C 569 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.47 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: 4837 1.34 - 1.46: 3518 1.46 - 1.58: 6822 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 15300 Sorted by residual: bond pdb=" N VAL C 646 " pdb=" CA VAL C 646 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.41e-02 5.03e+03 6.72e+00 bond pdb=" N VAL A 646 " pdb=" CA VAL A 646 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.41e-02 5.03e+03 6.50e+00 bond pdb=" N VAL B 646 " pdb=" CA VAL B 646 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.41e-02 5.03e+03 6.50e+00 bond pdb=" N VAL B 647 " pdb=" CA VAL B 647 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.14e-02 7.69e+03 6.37e+00 bond pdb=" N VAL A 647 " pdb=" CA VAL A 647 " ideal model delta sigma weight residual 1.462 1.490 -0.028 1.14e-02 7.69e+03 6.20e+00 ... (remaining 15295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 20277 1.68 - 3.36: 454 3.36 - 5.04: 80 5.04 - 6.71: 15 6.71 - 8.39: 6 Bond angle restraints: 20832 Sorted by residual: angle pdb=" N GLY C 395 " pdb=" CA GLY C 395 " pdb=" C GLY C 395 " ideal model delta sigma weight residual 111.35 115.87 -4.52 1.20e+00 6.94e-01 1.42e+01 angle pdb=" N GLY A 395 " pdb=" CA GLY A 395 " pdb=" C GLY A 395 " ideal model delta sigma weight residual 111.35 115.87 -4.52 1.20e+00 6.94e-01 1.42e+01 angle pdb=" N GLY B 395 " pdb=" CA GLY B 395 " pdb=" C GLY B 395 " ideal model delta sigma weight residual 111.35 115.86 -4.51 1.20e+00 6.94e-01 1.41e+01 angle pdb=" CA MET C 591 " pdb=" CB MET C 591 " pdb=" CG MET C 591 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA MET A 591 " pdb=" CB MET A 591 " pdb=" CG MET A 591 " ideal model delta sigma weight residual 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 ... (remaining 20827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 7776 16.73 - 33.45: 1028 33.45 - 50.18: 217 50.18 - 66.90: 39 66.90 - 83.63: 21 Dihedral angle restraints: 9081 sinusoidal: 3567 harmonic: 5514 Sorted by residual: dihedral pdb=" CA VAL C 92 " pdb=" C VAL C 92 " pdb=" N ASP C 93 " pdb=" CA ASP C 93 " ideal model delta harmonic sigma weight residual -180.00 -163.99 -16.01 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA VAL A 92 " pdb=" C VAL A 92 " pdb=" N ASP A 93 " pdb=" CA ASP A 93 " ideal model delta harmonic sigma weight residual -180.00 -164.00 -16.00 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA VAL B 92 " pdb=" C VAL B 92 " pdb=" N ASP B 93 " pdb=" CA ASP B 93 " ideal model delta harmonic sigma weight residual -180.00 -164.01 -15.99 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 9078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1523 0.037 - 0.075: 513 0.075 - 0.112: 216 0.112 - 0.149: 64 0.149 - 0.187: 3 Chirality restraints: 2319 Sorted by residual: chirality pdb=" CA VAL B 647 " pdb=" N VAL B 647 " pdb=" C VAL B 647 " pdb=" CB VAL B 647 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA VAL A 647 " pdb=" N VAL A 647 " pdb=" C VAL A 647 " pdb=" CB VAL A 647 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA VAL C 647 " pdb=" N VAL C 647 " pdb=" C VAL C 647 " pdb=" CB VAL C 647 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 2316 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 500 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B 501 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 500 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 501 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 501 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 501 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 500 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO C 501 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 501 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 501 " 0.026 5.00e-02 4.00e+02 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 24 2.04 - 2.75: 1673 2.75 - 3.47: 21343 3.47 - 4.18: 35562 4.18 - 4.90: 62340 Nonbonded interactions: 120942 Sorted by model distance: nonbonded pdb=" NZ LYS B 62 " pdb=" OD1 ASP C 61 " model vdw 1.321 3.120 nonbonded pdb=" NZ LYS A 62 " pdb=" OD1 ASP B 61 " model vdw 1.322 3.120 nonbonded pdb=" OD1 ASP A 61 " pdb=" NZ LYS C 62 " model vdw 1.322 3.120 nonbonded pdb=" CE LYS B 62 " pdb=" OD1 ASP C 61 " model vdw 1.341 3.440 nonbonded pdb=" CE LYS A 62 " pdb=" OD1 ASP B 61 " model vdw 1.342 3.440 ... (remaining 120937 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.550 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 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 : 0.003 0.037 15300 Z= 0.141 Angle : 0.610 8.392 20832 Z= 0.318 Chirality : 0.046 0.187 2319 Planarity : 0.004 0.047 2661 Dihedral : 15.639 83.629 5553 Min Nonbonded Distance : 1.321 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.43 % Favored : 96.41 % Rotamer: Outliers : 1.95 % Allowed : 18.40 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.20), residues: 1896 helix: 1.51 (0.21), residues: 633 sheet: -0.42 (0.42), residues: 177 loop : -0.13 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 625 TYR 0.013 0.001 TYR A 519 PHE 0.009 0.001 PHE B 269 TRP 0.009 0.001 TRP C 246 HIS 0.004 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15300) covalent geometry : angle 0.60970 / 0.32 (20832) hydrogen bonds : bond 0.17687 / 11.92 ( 594) hydrogen bonds : angle 6.95966 / 5.01 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.8508 (mmm) cc_final: 0.8178 (mmt) REVERT: A 375 ARG cc_start: 0.7875 (mmt-90) cc_final: 0.7600 (mmt-90) REVERT: A 645 LYS cc_start: 0.6397 (OUTLIER) cc_final: 0.6122 (ptpt) REVERT: C 591 MET cc_start: 0.3525 (mmt) cc_final: 0.2775 (ppp) REVERT: C 647 VAL cc_start: -0.3698 (OUTLIER) cc_final: -0.3913 (p) outliers start: 31 outliers final: 12 residues processed: 146 average time/residue: 0.1028 time to fit residues: 22.7326 Evaluate side-chains 93 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 647 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 GLN B 113 ASN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.158107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.080147 restraints weight = 30708.626| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 5.36 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 15300 Z= 0.265 Angle : 0.680 13.953 20832 Z= 0.337 Chirality : 0.048 0.206 2319 Planarity : 0.005 0.043 2661 Dihedral : 4.788 53.591 2117 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.06 % Favored : 96.78 % Rotamer: Outliers : 3.59 % Allowed : 17.77 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1896 helix: 1.53 (0.21), residues: 642 sheet: -0.66 (0.36), residues: 246 loop : -0.12 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 525 TYR 0.020 0.002 TYR A 406 PHE 0.017 0.002 PHE C 64 TRP 0.014 0.001 TRP A 246 HIS 0.005 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.26 (15300) covalent geometry : angle 0.68004 / 0.34 (20832) hydrogen bonds : bond 0.03650 / 2.47 ( 594) hydrogen bonds : angle 5.34583 / 3.87 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 81 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 ARG cc_start: 0.8642 (mmt-90) cc_final: 0.8276 (mmt-90) REVERT: B 404 MET cc_start: 0.9461 (mmm) cc_final: 0.9253 (mmm) REVERT: C 143 ASP cc_start: 0.7974 (m-30) cc_final: 0.7366 (m-30) REVERT: C 591 MET cc_start: 0.3902 (mmt) cc_final: 0.3679 (ppp) outliers start: 57 outliers final: 31 residues processed: 129 average time/residue: 0.0889 time to fit residues: 18.3939 Evaluate side-chains 108 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 547 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 10 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 178 optimal weight: 40.0000 chunk 167 optimal weight: 30.0000 chunk 131 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN B 113 ASN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.158265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.082358 restraints weight = 30378.790| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.83 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 15300 Z= 0.210 Angle : 0.605 9.644 20832 Z= 0.301 Chirality : 0.046 0.169 2319 Planarity : 0.004 0.043 2661 Dihedral : 4.351 34.070 2108 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.48 % Favored : 96.36 % Rotamer: Outliers : 2.65 % Allowed : 18.65 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.20), residues: 1896 helix: 1.62 (0.21), residues: 642 sheet: -0.64 (0.38), residues: 207 loop : -0.19 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 525 TYR 0.021 0.001 TYR C 406 PHE 0.014 0.001 PHE C 253 TRP 0.014 0.001 TRP A 246 HIS 0.005 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (15300) covalent geometry : angle 0.60541 / 0.30 (20832) hydrogen bonds : bond 0.03270 / 2.20 ( 594) hydrogen bonds : angle 5.02643 / 3.64 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 80 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.9042 (ttm) cc_final: 0.8756 (mtp) REVERT: A 137 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8074 (mpp) REVERT: A 375 ARG cc_start: 0.8636 (mmt-90) cc_final: 0.8260 (mmt-90) REVERT: B 113 ASN cc_start: 0.9641 (t0) cc_final: 0.9396 (t0) REVERT: B 151 MET cc_start: 0.8410 (mmm) cc_final: 0.8046 (mmt) REVERT: B 404 MET cc_start: 0.9504 (mmm) cc_final: 0.9209 (mmm) REVERT: C 57 MET cc_start: 0.8116 (ttm) cc_final: 0.7826 (mtp) REVERT: C 143 ASP cc_start: 0.7978 (m-30) cc_final: 0.7334 (m-30) REVERT: C 591 MET cc_start: 0.4017 (mmt) cc_final: 0.3731 (ppp) outliers start: 42 outliers final: 21 residues processed: 116 average time/residue: 0.0930 time to fit residues: 17.2258 Evaluate side-chains 97 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 286 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 83 optimal weight: 0.0060 chunk 42 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 chunk 184 optimal weight: 30.0000 chunk 10 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 GLN A 658 HIS ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.159779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.077895 restraints weight = 30232.211| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 5.47 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15300 Z= 0.121 Angle : 0.552 9.136 20832 Z= 0.275 Chirality : 0.045 0.252 2319 Planarity : 0.004 0.041 2661 Dihedral : 4.169 34.010 2106 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.89 % Rotamer: Outliers : 2.52 % Allowed : 19.41 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1896 helix: 1.73 (0.21), residues: 642 sheet: -0.84 (0.35), residues: 237 loop : -0.11 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 525 TYR 0.015 0.001 TYR C 406 PHE 0.019 0.001 PHE C 49 TRP 0.011 0.001 TRP A 246 HIS 0.004 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.12 (15300) covalent geometry : angle 0.55199 / 0.27 (20832) hydrogen bonds : bond 0.02771 / 1.85 ( 594) hydrogen bonds : angle 4.80246 / 3.47 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 78 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8943 (ttm) cc_final: 0.8537 (mtp) REVERT: A 137 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.7915 (mpp) REVERT: A 375 ARG cc_start: 0.8607 (mmt-90) cc_final: 0.8187 (mmt-90) REVERT: B 58 MET cc_start: 0.8570 (mtt) cc_final: 0.8337 (mtm) REVERT: B 61 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8117 (t0) REVERT: B 113 ASN cc_start: 0.9648 (t0) cc_final: 0.9398 (t0) REVERT: B 238 MET cc_start: 0.8424 (mmm) cc_final: 0.8208 (mmm) REVERT: B 382 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9210 (pptt) REVERT: B 404 MET cc_start: 0.9518 (mmm) cc_final: 0.9150 (mmm) REVERT: C 57 MET cc_start: 0.8144 (ttm) cc_final: 0.7817 (mtp) outliers start: 40 outliers final: 27 residues processed: 111 average time/residue: 0.1013 time to fit residues: 17.8012 Evaluate side-chains 102 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 460 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 182 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 131 optimal weight: 3.9990 chunk 163 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 147 optimal weight: 0.0040 chunk 15 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 GLN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.159407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.083933 restraints weight = 30383.062| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 4.85 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15300 Z= 0.121 Angle : 0.546 6.820 20832 Z= 0.270 Chirality : 0.045 0.206 2319 Planarity : 0.004 0.041 2661 Dihedral : 4.094 33.429 2106 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.22 % Favored : 96.62 % Rotamer: Outliers : 2.77 % Allowed : 19.79 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1896 helix: 1.73 (0.21), residues: 642 sheet: -0.82 (0.35), residues: 237 loop : -0.07 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 525 TYR 0.013 0.001 TYR C 406 PHE 0.019 0.001 PHE C 49 TRP 0.010 0.001 TRP A 246 HIS 0.004 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 (15300) covalent geometry : angle 0.54585 / 0.27 (20832) hydrogen bonds : bond 0.02681 / 1.78 ( 594) hydrogen bonds : angle 4.70272 / 3.40 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 77 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.7819 (mpp) REVERT: A 375 ARG cc_start: 0.8604 (mmt-90) cc_final: 0.8176 (mmt-90) REVERT: B 61 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8375 (t0) REVERT: B 298 CYS cc_start: 0.9127 (m) cc_final: 0.8923 (m) REVERT: B 404 MET cc_start: 0.9568 (mmm) cc_final: 0.9255 (mmm) outliers start: 44 outliers final: 29 residues processed: 114 average time/residue: 0.0988 time to fit residues: 17.6750 Evaluate side-chains 104 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 537 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 139 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 188 optimal weight: 40.0000 chunk 170 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 84 optimal weight: 0.0370 overall best weight: 2.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.156123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.078490 restraints weight = 30585.010| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 5.35 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 15300 Z= 0.271 Angle : 0.622 10.414 20832 Z= 0.309 Chirality : 0.047 0.225 2319 Planarity : 0.004 0.042 2661 Dihedral : 4.208 34.736 2106 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.38 % Favored : 96.41 % Rotamer: Outliers : 3.02 % Allowed : 19.91 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1896 helix: 1.69 (0.21), residues: 642 sheet: -0.72 (0.37), residues: 207 loop : -0.13 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 525 TYR 0.018 0.001 TYR A 406 PHE 0.019 0.001 PHE C 49 TRP 0.015 0.001 TRP A 246 HIS 0.006 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 (15300) covalent geometry : angle 0.62217 / 0.31 (20832) hydrogen bonds : bond 0.03044 / 2.04 ( 594) hydrogen bonds : angle 4.75675 / 3.46 ( 1728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 72 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8044 (mpp) REVERT: A 310 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8430 (tpp) REVERT: A 375 ARG cc_start: 0.8634 (mmt-90) cc_final: 0.8188 (mmt-90) REVERT: A 508 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8677 (t) REVERT: B 61 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8366 (t0) REVERT: B 404 MET cc_start: 0.9621 (mmm) cc_final: 0.9350 (mmm) REVERT: C 57 MET cc_start: 0.8193 (ttm) cc_final: 0.7897 (mtp) outliers start: 48 outliers final: 30 residues processed: 114 average time/residue: 0.0910 time to fit residues: 16.3759 Evaluate side-chains 106 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 460 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 101 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 21 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.158862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083443 restraints weight = 30165.366| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 4.88 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15300 Z= 0.111 Angle : 0.550 9.981 20832 Z= 0.273 Chirality : 0.045 0.267 2319 Planarity : 0.004 0.041 2661 Dihedral : 4.080 34.207 2106 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.27 % Favored : 96.52 % Rotamer: Outliers : 2.77 % Allowed : 19.97 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.20), residues: 1896 helix: 1.75 (0.21), residues: 642 sheet: -0.82 (0.34), residues: 240 loop : -0.06 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 525 TYR 0.011 0.001 TYR C 406 PHE 0.020 0.001 PHE C 49 TRP 0.011 0.001 TRP A 246 HIS 0.004 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.11 (15300) covalent geometry : angle 0.54953 / 0.27 (20832) hydrogen bonds : bond 0.02669 / 1.78 ( 594) hydrogen bonds : angle 4.61377 / 3.34 ( 1728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 76 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.7994 (mpp) REVERT: A 375 ARG cc_start: 0.8559 (mmt-90) cc_final: 0.8117 (mmt-90) REVERT: A 508 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8719 (t) REVERT: B 404 MET cc_start: 0.9608 (mmm) cc_final: 0.9270 (mmm) outliers start: 44 outliers final: 29 residues processed: 113 average time/residue: 0.0981 time to fit residues: 17.8839 Evaluate side-chains 105 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 460 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 93 optimal weight: 10.0000 chunk 167 optimal weight: 30.0000 chunk 65 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 182 optimal weight: 40.0000 chunk 183 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 135 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.156598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.080915 restraints weight = 30244.324| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.76 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 15300 Z= 0.222 Angle : 0.597 8.491 20832 Z= 0.294 Chirality : 0.046 0.243 2319 Planarity : 0.004 0.041 2661 Dihedral : 4.131 37.377 2104 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.48 % Favored : 96.31 % Rotamer: Outliers : 2.77 % Allowed : 19.47 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.20), residues: 1896 helix: 1.73 (0.21), residues: 642 sheet: -0.70 (0.36), residues: 210 loop : -0.09 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 525 TYR 0.018 0.001 TYR C 406 PHE 0.019 0.001 PHE C 49 TRP 0.014 0.001 TRP A 246 HIS 0.014 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (15300) covalent geometry : angle 0.59735 / 0.29 (20832) hydrogen bonds : bond 0.02882 / 1.92 ( 594) hydrogen bonds : angle 4.65246 / 3.38 ( 1728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 78 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8062 (mpp) REVERT: A 310 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8402 (tpp) REVERT: A 508 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8853 (t) REVERT: A 567 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8785 (pm20) REVERT: B 404 MET cc_start: 0.9639 (mmm) cc_final: 0.9304 (mmm) REVERT: C 44 ASN cc_start: 0.9298 (m-40) cc_final: 0.8988 (p0) REVERT: C 57 MET cc_start: 0.8357 (ttm) cc_final: 0.8048 (mtp) outliers start: 44 outliers final: 32 residues processed: 115 average time/residue: 0.1018 time to fit residues: 18.4247 Evaluate side-chains 113 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 77 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 460 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 154 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 169 optimal weight: 50.0000 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.156126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.079942 restraints weight = 30384.269| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 4.78 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 15300 Z= 0.240 Angle : 0.614 9.362 20832 Z= 0.304 Chirality : 0.046 0.215 2319 Planarity : 0.004 0.042 2661 Dihedral : 4.184 38.674 2104 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.85 % Favored : 95.94 % Rotamer: Outliers : 2.96 % Allowed : 19.72 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1896 helix: 1.67 (0.21), residues: 642 sheet: -0.75 (0.36), residues: 210 loop : -0.14 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 525 TYR 0.017 0.001 TYR C 406 PHE 0.020 0.001 PHE C 49 TRP 0.015 0.001 TRP A 246 HIS 0.008 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 (15300) covalent geometry : angle 0.61399 / 0.30 (20832) hydrogen bonds : bond 0.02967 / 1.99 ( 594) hydrogen bonds : angle 4.66683 / 3.39 ( 1728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 75 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8107 (mpp) REVERT: A 310 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8433 (tpp) REVERT: A 508 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8900 (t) REVERT: A 567 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8724 (pm20) REVERT: B 57 MET cc_start: 0.8796 (mtm) cc_final: 0.8108 (mtp) REVERT: B 159 MET cc_start: 0.9034 (mtm) cc_final: 0.8818 (ttm) REVERT: B 404 MET cc_start: 0.9655 (mmm) cc_final: 0.9344 (mmm) REVERT: C 57 MET cc_start: 0.8340 (ttm) cc_final: 0.8072 (mtp) outliers start: 47 outliers final: 34 residues processed: 114 average time/residue: 0.1021 time to fit residues: 18.2332 Evaluate side-chains 112 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 183 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 174 optimal weight: 0.9990 chunk 79 optimal weight: 0.0970 chunk 182 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 184 optimal weight: 40.0000 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.159011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.083988 restraints weight = 30283.028| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.81 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15300 Z= 0.106 Angle : 0.566 8.471 20832 Z= 0.280 Chirality : 0.045 0.226 2319 Planarity : 0.004 0.042 2661 Dihedral : 4.026 34.551 2104 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.38 % Favored : 96.41 % Rotamer: Outliers : 2.27 % Allowed : 20.54 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1896 helix: 1.73 (0.21), residues: 642 sheet: -0.95 (0.33), residues: 240 loop : -0.03 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 525 TYR 0.015 0.001 TYR C 406 PHE 0.021 0.001 PHE C 49 TRP 0.010 0.001 TRP B 480 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (15300) covalent geometry : angle 0.56560 / 0.28 (20832) hydrogen bonds : bond 0.02592 / 1.72 ( 594) hydrogen bonds : angle 4.54329 / 3.29 ( 1728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.9034 (mmm) cc_final: 0.8805 (mmt) REVERT: A 310 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8253 (tpp) REVERT: A 519 TYR cc_start: 0.8924 (m-10) cc_final: 0.8648 (m-10) REVERT: B 53 MET cc_start: 0.9064 (tpt) cc_final: 0.8333 (tpp) REVERT: B 57 MET cc_start: 0.8689 (mtm) cc_final: 0.7578 (mtp) REVERT: B 404 MET cc_start: 0.9646 (mmm) cc_final: 0.9314 (mmm) REVERT: C 57 MET cc_start: 0.8366 (ttm) cc_final: 0.8090 (mtp) outliers start: 36 outliers final: 30 residues processed: 109 average time/residue: 0.1022 time to fit residues: 17.4922 Evaluate side-chains 107 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 591 MET Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 28 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 9 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 GLN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.157979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.082411 restraints weight = 30257.478| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.89 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15300 Z= 0.155 Angle : 0.594 10.654 20832 Z= 0.291 Chirality : 0.045 0.206 2319 Planarity : 0.004 0.040 2661 Dihedral : 4.025 35.705 2104 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.38 % Favored : 96.41 % Rotamer: Outliers : 2.21 % Allowed : 20.48 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1896 helix: 1.74 (0.21), residues: 642 sheet: -1.01 (0.33), residues: 240 loop : -0.04 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 525 TYR 0.015 0.001 TYR C 406 PHE 0.021 0.001 PHE C 49 TRP 0.011 0.001 TRP A 246 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (15300) covalent geometry : angle 0.59435 / 0.29 (20832) hydrogen bonds : bond 0.02682 / 1.78 ( 594) hydrogen bonds : angle 4.52138 / 3.29 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3111.46 seconds wall clock time: 54 minutes 16.07 seconds (3256.07 seconds total)