Starting phenix.real_space_refine on Sat Jul 4 05:06:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t7l_55638/07_2026/9t7l_55638.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t7l_55638/07_2026/9t7l_55638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t7l_55638/07_2026/9t7l_55638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t7l_55638/07_2026/9t7l_55638.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t7l_55638/07_2026/9t7l_55638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t7l_55638/07_2026/9t7l_55638.map" } resolution = 2.8 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= 0.008 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: 6 Type Number sf(0) Gaussians P 120 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 11142 2.51 5 N 3056 2.21 5 O 3562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17938 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4943 Classifications: {'peptide': 608} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 574} Chain breaks: 3 Chain: "B" Number of atoms: 4943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4943 Classifications: {'peptide': 608} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 574} Chain breaks: 3 Chain: "C" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2775 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 19, 'TRANS': 316} Chain breaks: 2 Chain: "D" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2775 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 19, 'TRANS': 316} Chain breaks: 2 Chain: "E" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 592 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 658 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 592 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "H" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 658 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.11, per 1000 atoms: 0.23 Number of scatterers: 17938 At special positions: 0 Unit cell: (152.75, 103.35, 117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 120 15.00 Mg 2 11.99 O 3562 8.00 N 3056 7.00 C 11142 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: 1.24 Conformation dependent library (CDL) restraints added in 517.9 milliseconds 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3620 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 18 sheets defined 47.5% alpha, 14.1% beta 56 base pairs and 98 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 31 through 43 removed outlier: 3.614A pdb=" N PHE A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.653A pdb=" N TYR A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 163 through 170 Processing helix chain 'A' and resid 173 through 187 Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.749A pdb=" N VAL A 262 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 278 through 299 Processing helix chain 'A' and resid 304 through 316 Proline residue: A 310 - end of helix Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 363 through 375 removed outlier: 3.717A pdb=" N LYS A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 399 removed outlier: 4.038A pdb=" N SER A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 420 removed outlier: 3.680A pdb=" N ILE A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 431 removed outlier: 3.553A pdb=" N VAL A 425 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 440 Processing helix chain 'A' and resid 502 through 515 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.814A pdb=" N ARG A 579 " --> pdb=" O PRO A 575 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 630 Processing helix chain 'A' and resid 642 through 654 removed outlier: 3.600A pdb=" N ALA A 653 " --> pdb=" O GLN A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'B' and resid 31 through 43 removed outlier: 3.614A pdb=" N PHE B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 43 " --> pdb=" O PHE B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 94 through 110 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 127 through 138 removed outlier: 3.653A pdb=" N TYR B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 159 Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 173 through 187 Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.749A pdb=" N VAL B 262 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 278 through 299 Processing helix chain 'B' and resid 304 through 316 Proline residue: B 310 - end of helix Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 342 through 347 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 363 through 375 removed outlier: 3.717A pdb=" N LYS B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 399 removed outlier: 4.038A pdb=" N SER B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 removed outlier: 3.681A pdb=" N ILE B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 431 removed outlier: 3.553A pdb=" N VAL B 425 " --> pdb=" O PRO B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 440 Processing helix chain 'B' and resid 502 through 515 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 572 through 584 removed outlier: 3.813A pdb=" N ARG B 579 " --> pdb=" O PRO B 575 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 630 Processing helix chain 'B' and resid 642 through 654 removed outlier: 3.600A pdb=" N ALA B 653 " --> pdb=" O GLN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'C' and resid 501 through 515 removed outlier: 3.851A pdb=" N SER C 505 " --> pdb=" O PRO C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 522 Processing helix chain 'C' and resid 549 through 559 removed outlier: 3.584A pdb=" N ALA C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 584 removed outlier: 3.572A pdb=" N GLU C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG C 579 " --> pdb=" O PRO C 575 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE C 580 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 588 Processing helix chain 'C' and resid 616 through 630 Processing helix chain 'C' and resid 642 through 654 Processing helix chain 'C' and resid 660 through 669 removed outlier: 3.603A pdb=" N ARG C 666 " --> pdb=" O GLU C 662 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 667 " --> pdb=" O GLU C 663 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 668 " --> pdb=" O GLU C 664 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET C 669 " --> pdb=" O THR C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 672 No H-bonds generated for 'chain 'C' and resid 670 through 672' Processing helix chain 'C' and resid 693 through 703 Processing helix chain 'C' and resid 750 through 769 Processing helix chain 'C' and resid 770 through 795 Processing helix chain 'D' and resid 501 through 515 removed outlier: 3.796A pdb=" N SER D 505 " --> pdb=" O PRO D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 522 Processing helix chain 'D' and resid 549 through 559 removed outlier: 3.575A pdb=" N ALA D 559 " --> pdb=" O ALA D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 583 removed outlier: 3.634A pdb=" N GLU D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG D 579 " --> pdb=" O PRO D 575 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE D 580 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 630 Processing helix chain 'D' and resid 642 through 652 Processing helix chain 'D' and resid 660 through 669 removed outlier: 3.683A pdb=" N ARG D 666 " --> pdb=" O GLU D 662 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 668 " --> pdb=" O GLU D 664 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET D 669 " --> pdb=" O THR D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 672 No H-bonds generated for 'chain 'D' and resid 670 through 672' Processing helix chain 'D' and resid 693 through 703 Processing helix chain 'D' and resid 750 through 769 Processing helix chain 'D' and resid 770 through 795 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 removed outlier: 3.989A pdb=" N VAL A 15 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 493 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP A 485 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 491 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.501A pdb=" N TYR A 83 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL A 118 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU A 85 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 61 Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 271 removed outlier: 7.061A pdb=" N LYS C 723 " --> pdb=" O ASP C 717 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP C 717 " --> pdb=" O LYS C 723 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU C 713 " --> pdb=" O TYR C 727 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 476 removed outlier: 7.065A pdb=" N LEU A 466 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 29 removed outlier: 3.988A pdb=" N VAL B 15 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 493 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP B 485 " --> pdb=" O VAL B 491 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 491 " --> pdb=" O ASP B 485 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.501A pdb=" N TYR B 83 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL B 118 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLU B 85 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 61 Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 162 Processing sheet with id=AB2, first strand: chain 'B' and resid 270 through 271 removed outlier: 7.063A pdb=" N LYS D 723 " --> pdb=" O ASP D 717 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP D 717 " --> pdb=" O LYS D 723 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU D 713 " --> pdb=" O TYR D 727 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 474 through 476 removed outlier: 7.064A pdb=" N LEU B 466 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 491 through 497 removed outlier: 6.342A pdb=" N VAL C 491 " --> pdb=" O ASP C 485 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP C 485 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY C 493 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL C 455 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ASP C 542 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N ILE C 457 " --> pdb=" O ASP C 542 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU C 539 " --> pdb=" O GLN C 564 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASN C 566 " --> pdb=" O LEU C 539 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 541 " --> pdb=" O ASN C 566 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 474 through 476 removed outlier: 6.946A pdb=" N LEU C 466 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 684 through 686 Processing sheet with id=AB7, first strand: chain 'D' and resid 491 through 497 removed outlier: 6.792A pdb=" N VAL D 491 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASP D 485 " --> pdb=" O VAL D 491 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY D 493 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASP D 542 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N HIS D 459 " --> pdb=" O ASP D 542 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU D 539 " --> pdb=" O GLN D 564 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN D 566 " --> pdb=" O LEU D 539 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 541 " --> pdb=" O ASN D 566 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 474 through 476 removed outlier: 6.913A pdb=" N LEU D 466 " --> pdb=" O ILE D 475 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 684 through 686 725 hydrogen bonds defined for protein. 2034 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 136 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 98 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2972 1.32 - 1.45: 5472 1.45 - 1.57: 9852 1.57 - 1.69: 240 1.69 - 1.82: 90 Bond restraints: 18626 Sorted by residual: bond pdb=" CA TYR A 289 " pdb=" C TYR A 289 " ideal model delta sigma weight residual 1.524 1.462 0.062 1.32e-02 5.74e+03 2.20e+01 bond pdb=" CA TYR B 289 " pdb=" C TYR B 289 " ideal model delta sigma weight residual 1.524 1.462 0.062 1.32e-02 5.74e+03 2.18e+01 bond pdb=" CA LEU B 291 " pdb=" C LEU B 291 " ideal model delta sigma weight residual 1.525 1.463 0.062 1.37e-02 5.33e+03 2.03e+01 bond pdb=" CA LEU A 291 " pdb=" C LEU A 291 " ideal model delta sigma weight residual 1.525 1.463 0.062 1.37e-02 5.33e+03 2.03e+01 bond pdb=" CA ASN A 543 " pdb=" C ASN A 543 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.30e-02 5.92e+03 1.73e+01 ... (remaining 18621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 25342 2.39 - 4.78: 342 4.78 - 7.17: 31 7.17 - 9.55: 15 9.55 - 11.94: 2 Bond angle restraints: 25732 Sorted by residual: angle pdb=" O4' DC G -2 " pdb=" C1' DC G -2 " pdb=" N1 DC G -2 " ideal model delta sigma weight residual 108.00 111.87 -3.87 7.00e-01 2.04e+00 3.06e+01 angle pdb=" N3 DT G -16 " pdb=" C4 DT G -16 " pdb=" O4 DT G -16 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT E -26 " pdb=" C4 DT E -26 " pdb=" O4 DT E -26 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT E -10 " pdb=" C4 DT E -10 " pdb=" O4 DT E -10 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT E -16 " pdb=" C4 DT E -16 " pdb=" O4 DT E -16 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 25727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 10106 35.40 - 70.80: 773 70.80 - 106.20: 27 106.20 - 141.60: 6 141.60 - 177.00: 2 Dihedral angle restraints: 10914 sinusoidal: 5338 harmonic: 5576 Sorted by residual: dihedral pdb=" C4' DT G -26 " pdb=" C3' DT G -26 " pdb=" O3' DT G -26 " pdb=" P DA G -25 " ideal model delta sinusoidal sigma weight residual 220.00 43.00 177.00 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT E -26 " pdb=" C3' DT E -26 " pdb=" O3' DT E -26 " pdb=" P DA E -25 " ideal model delta sinusoidal sigma weight residual 220.00 50.47 169.53 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC E -17 " pdb=" C3' DC E -17 " pdb=" O3' DC E -17 " pdb=" P DT E -16 " ideal model delta sinusoidal sigma weight residual 220.00 79.65 140.35 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 10911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2223 0.051 - 0.103: 477 0.103 - 0.154: 89 0.154 - 0.206: 9 0.206 - 0.257: 6 Chirality restraints: 2804 Sorted by residual: chirality pdb=" CA PHE A 547 " pdb=" N PHE A 547 " pdb=" C PHE A 547 " pdb=" CB PHE A 547 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA PHE B 547 " pdb=" N PHE B 547 " pdb=" C PHE B 547 " pdb=" CB PHE B 547 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA TRP B 572 " pdb=" N TRP B 572 " pdb=" C TRP B 572 " pdb=" CB TRP B 572 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2801 not shown) Planarity restraints: 2862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 566 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C ASN A 566 " 0.067 2.00e-02 2.50e+03 pdb=" O ASN A 566 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO A 567 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 566 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ASN B 566 " 0.067 2.00e-02 2.50e+03 pdb=" O ASN B 566 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO B 567 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 546 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C GLU A 546 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU A 546 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 547 " -0.012 2.00e-02 2.50e+03 ... (remaining 2859 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 48 2.60 - 3.18: 14977 3.18 - 3.75: 30052 3.75 - 4.33: 41980 4.33 - 4.90: 65625 Nonbonded interactions: 152682 Sorted by model distance: nonbonded pdb=" OD2 ASP A 71 " pdb="MG MG A1000 " model vdw 2.031 2.170 nonbonded pdb=" OD2 ASP B 71 " pdb="MG MG B1000 " model vdw 2.031 2.170 nonbonded pdb=" O TYR A 86 " pdb="MG MG A1000 " model vdw 2.074 2.170 nonbonded pdb=" O TYR B 86 " pdb="MG MG B1000 " model vdw 2.075 2.170 nonbonded pdb=" OP2 DT F -2 " pdb="MG MG A1000 " model vdw 2.154 2.170 ... (remaining 152677 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 6.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.890 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 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 : 0.005 0.062 18626 Z= 0.350 Angle : 0.678 11.942 25732 Z= 0.476 Chirality : 0.046 0.257 2804 Planarity : 0.004 0.039 2862 Dihedral : 20.797 177.002 7294 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.59 % Allowed : 18.67 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 1860 helix: 1.46 (0.18), residues: 806 sheet: 0.43 (0.30), residues: 286 loop : 0.09 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 379 TYR 0.019 0.001 TYR C 587 PHE 0.020 0.001 PHE D 588 TRP 0.014 0.001 TRP B 548 HIS 0.003 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.35 (18626) covalent geometry : angle 0.67797 / 0.48 (25732) hydrogen bonds : bond 0.13020 / 8.66 ( 861) hydrogen bonds : angle 5.75205 / 4.13 ( 2306) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8050 (tmt) REVERT: A 463 ASP cc_start: 0.7943 (p0) cc_final: 0.7548 (p0) REVERT: A 471 LEU cc_start: 0.9157 (mp) cc_final: 0.8850 (tt) REVERT: A 499 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8951 (ptmt) REVERT: B 463 ASP cc_start: 0.7956 (p0) cc_final: 0.7556 (p0) REVERT: B 471 LEU cc_start: 0.9150 (mp) cc_final: 0.8833 (tt) REVERT: B 499 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8908 (ptmt) REVERT: B 666 ARG cc_start: 0.9068 (ttp-110) cc_final: 0.8863 (mtp85) REVERT: C 454 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6458 (tpt-90) REVERT: C 543 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8686 (m-40) REVERT: C 649 GLN cc_start: 0.9222 (pt0) cc_final: 0.8750 (pp30) REVERT: C 705 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8650 (mp10) REVERT: D 536 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8883 (m-80) REVERT: D 543 ASN cc_start: 0.9179 (OUTLIER) cc_final: 0.8815 (m110) REVERT: D 607 LYS cc_start: 0.8682 (mtpm) cc_final: 0.8343 (ptpp) REVERT: D 610 LYS cc_start: 0.8791 (ptpp) cc_final: 0.8460 (pttp) REVERT: D 787 GLN cc_start: 0.7817 (mm110) cc_final: 0.7457 (tm-30) outliers start: 44 outliers final: 14 residues processed: 143 average time/residue: 0.7128 time to fit residues: 111.4797 Evaluate side-chains 122 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 536 PHE Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 705 GLN Chi-restraints excluded: chain D residue 536 PHE Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 568 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 459 HIS D 459 HIS D 557 GLN D 564 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.102282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.069246 restraints weight = 35910.659| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.67 r_work: 0.2825 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18626 Z= 0.207 Angle : 0.575 8.131 25732 Z= 0.315 Chirality : 0.042 0.272 2804 Planarity : 0.004 0.032 2862 Dihedral : 22.431 179.856 3458 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.24 % Allowed : 15.84 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.19), residues: 1860 helix: 1.64 (0.18), residues: 812 sheet: 0.32 (0.29), residues: 290 loop : 0.13 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 379 TYR 0.019 0.002 TYR A 289 PHE 0.013 0.001 PHE A 547 TRP 0.019 0.001 TRP A 548 HIS 0.004 0.001 HIS D 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (18626) covalent geometry : angle 0.57532 / 0.32 (25732) hydrogen bonds : bond 0.04592 / 3.06 ( 861) hydrogen bonds : angle 4.73037 / 3.37 ( 2306) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 113 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: A 463 ASP cc_start: 0.7975 (p0) cc_final: 0.7585 (p0) REVERT: A 471 LEU cc_start: 0.9166 (mp) cc_final: 0.8849 (tt) REVERT: B 62 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8014 (tmt) REVERT: B 364 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: B 463 ASP cc_start: 0.7975 (p0) cc_final: 0.7592 (p0) REVERT: B 471 LEU cc_start: 0.9154 (mp) cc_final: 0.8819 (tt) REVERT: B 503 TYR cc_start: 0.7079 (p90) cc_final: 0.6350 (p90) REVERT: B 666 ARG cc_start: 0.9088 (ttp-110) cc_final: 0.8868 (ttm-80) REVERT: C 468 ASP cc_start: 0.8632 (t0) cc_final: 0.8429 (t0) REVERT: C 552 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8318 (tt) REVERT: C 641 ARG cc_start: 0.6900 (mmm-85) cc_final: 0.6627 (mmm-85) REVERT: C 709 THR cc_start: 0.8842 (m) cc_final: 0.8635 (p) REVERT: D 536 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8942 (m-80) REVERT: D 543 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8729 (m-40) REVERT: D 607 LYS cc_start: 0.8709 (mtpm) cc_final: 0.8434 (ptpp) REVERT: D 649 GLN cc_start: 0.9279 (pt0) cc_final: 0.8898 (pp30) outliers start: 72 outliers final: 23 residues processed: 175 average time/residue: 0.6095 time to fit residues: 118.9513 Evaluate side-chains 133 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 536 PHE Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain D residue 536 PHE Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 669 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 84 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 67 optimal weight: 0.4980 chunk 160 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS A 495 HIS B 84 HIS B 495 HIS C 649 GLN D 632 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.102715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.069883 restraints weight = 36123.097| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.65 r_work: 0.2839 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18626 Z= 0.156 Angle : 0.537 7.779 25732 Z= 0.296 Chirality : 0.041 0.276 2804 Planarity : 0.004 0.032 2862 Dihedral : 22.371 178.603 3431 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.71 % Allowed : 15.67 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.19), residues: 1860 helix: 1.83 (0.18), residues: 812 sheet: 0.39 (0.30), residues: 268 loop : 0.15 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 379 TYR 0.018 0.001 TYR B 389 PHE 0.012 0.001 PHE A 547 TRP 0.013 0.001 TRP A 548 HIS 0.015 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (18626) covalent geometry : angle 0.53704 / 0.30 (25732) hydrogen bonds : bond 0.04142 / 2.75 ( 861) hydrogen bonds : angle 4.53854 / 3.20 ( 2306) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 105 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7834 (tt) REVERT: A 364 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: A 463 ASP cc_start: 0.7962 (p0) cc_final: 0.7572 (p0) REVERT: A 471 LEU cc_start: 0.9172 (mp) cc_final: 0.8848 (tt) REVERT: B 62 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7988 (tmt) REVERT: B 291 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7787 (tt) REVERT: B 364 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8073 (m-30) REVERT: B 463 ASP cc_start: 0.7960 (p0) cc_final: 0.7572 (p0) REVERT: B 471 LEU cc_start: 0.9163 (mp) cc_final: 0.8838 (tt) REVERT: B 566 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7293 (t0) REVERT: B 666 ARG cc_start: 0.9102 (ttp-110) cc_final: 0.8787 (ttm-80) REVERT: C 468 ASP cc_start: 0.8650 (t0) cc_final: 0.8445 (t0) REVERT: C 536 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8918 (m-80) REVERT: C 543 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8677 (m-40) REVERT: C 552 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8319 (tt) REVERT: C 793 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7766 (tp) REVERT: D 536 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8892 (m-80) REVERT: D 543 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8697 (m-40) REVERT: D 552 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8401 (tt) REVERT: D 607 LYS cc_start: 0.8696 (mtpm) cc_final: 0.8294 (ptpp) REVERT: D 610 LYS cc_start: 0.8782 (ptpp) cc_final: 0.8549 (pttp) REVERT: D 649 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.8931 (pp30) REVERT: D 752 TYR cc_start: 0.8750 (t80) cc_final: 0.8548 (t80) outliers start: 80 outliers final: 18 residues processed: 168 average time/residue: 0.6233 time to fit residues: 117.4891 Evaluate side-chains 135 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 536 PHE Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 536 PHE Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain D residue 536 PHE Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 649 GLN Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 716 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 66 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 85 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 564 GLN C 649 GLN D 632 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.102773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.069739 restraints weight = 35870.287| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.66 r_work: 0.2838 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18626 Z= 0.148 Angle : 0.536 8.415 25732 Z= 0.293 Chirality : 0.041 0.276 2804 Planarity : 0.003 0.032 2862 Dihedral : 22.349 178.135 3431 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.00 % Allowed : 16.37 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.19), residues: 1860 helix: 1.88 (0.18), residues: 812 sheet: 0.29 (0.31), residues: 258 loop : 0.17 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 641 TYR 0.018 0.001 TYR B 389 PHE 0.011 0.001 PHE A 547 TRP 0.010 0.001 TRP A 548 HIS 0.012 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (18626) covalent geometry : angle 0.53633 / 0.29 (25732) hydrogen bonds : bond 0.04007 / 2.66 ( 861) hydrogen bonds : angle 4.49637 / 3.17 ( 2306) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 105 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7822 (tt) REVERT: A 364 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: A 463 ASP cc_start: 0.7953 (p0) cc_final: 0.7567 (p0) REVERT: A 471 LEU cc_start: 0.9175 (mp) cc_final: 0.8849 (tt) REVERT: A 566 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.7340 (t0) REVERT: B 62 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7995 (tmt) REVERT: B 291 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7816 (tt) REVERT: B 364 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: B 463 ASP cc_start: 0.7960 (p0) cc_final: 0.7573 (p0) REVERT: B 471 LEU cc_start: 0.9177 (mp) cc_final: 0.8847 (tt) REVERT: B 566 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.7256 (t0) REVERT: B 666 ARG cc_start: 0.9108 (ttp-110) cc_final: 0.8869 (ttm-80) REVERT: C 468 ASP cc_start: 0.8645 (t0) cc_final: 0.8432 (t0) REVERT: C 536 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8936 (m-80) REVERT: C 543 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8678 (m-40) REVERT: C 552 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8327 (tt) REVERT: C 723 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8233 (ptpp) REVERT: D 536 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8881 (m-80) REVERT: D 543 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8692 (m-40) REVERT: D 552 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8389 (tt) REVERT: D 607 LYS cc_start: 0.8709 (mtpm) cc_final: 0.8313 (ptpp) REVERT: D 610 LYS cc_start: 0.8786 (ptpp) cc_final: 0.8564 (pttp) REVERT: D 649 GLN cc_start: 0.9289 (pt0) cc_final: 0.8907 (pp30) REVERT: D 709 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8623 (p) REVERT: D 723 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8245 (ptpp) REVERT: D 752 TYR cc_start: 0.8757 (t80) cc_final: 0.8551 (t80) outliers start: 68 outliers final: 22 residues processed: 159 average time/residue: 0.6113 time to fit residues: 108.5591 Evaluate side-chains 136 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 98 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 536 PHE Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain D residue 536 PHE Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 723 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 97 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 186 optimal weight: 20.0000 chunk 194 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 564 GLN C 649 GLN D 632 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.101917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.068837 restraints weight = 35947.249| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.65 r_work: 0.2821 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18626 Z= 0.201 Angle : 0.554 7.238 25732 Z= 0.302 Chirality : 0.042 0.281 2804 Planarity : 0.004 0.039 2862 Dihedral : 22.438 177.919 3431 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.42 % Allowed : 17.26 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 1860 helix: 1.89 (0.18), residues: 812 sheet: 0.34 (0.29), residues: 290 loop : 0.20 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 666 TYR 0.016 0.001 TYR B 389 PHE 0.013 0.001 PHE B 547 TRP 0.009 0.001 TRP A 548 HIS 0.012 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (18626) covalent geometry : angle 0.55449 / 0.30 (25732) hydrogen bonds : bond 0.04122 / 2.75 ( 861) hydrogen bonds : angle 4.46781 / 3.15 ( 2306) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 101 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7995 (tmm) REVERT: A 291 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7869 (tt) REVERT: A 364 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8055 (m-30) REVERT: A 463 ASP cc_start: 0.7980 (p0) cc_final: 0.7600 (p0) REVERT: A 500 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8209 (t) REVERT: A 566 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.7326 (t0) REVERT: B 62 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7981 (tmt) REVERT: B 291 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7842 (tt) REVERT: B 364 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8073 (m-30) REVERT: B 463 ASP cc_start: 0.7982 (p0) cc_final: 0.7604 (p0) REVERT: B 500 SER cc_start: 0.8650 (OUTLIER) cc_final: 0.8250 (t) REVERT: B 566 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.7275 (t0) REVERT: B 666 ARG cc_start: 0.9115 (ttp-110) cc_final: 0.8864 (ttm-80) REVERT: C 468 ASP cc_start: 0.8657 (t0) cc_final: 0.8410 (t0) REVERT: C 536 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8944 (m-80) REVERT: C 543 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8681 (m-40) REVERT: C 552 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8316 (tt) REVERT: C 723 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8206 (ptpp) REVERT: D 543 ASN cc_start: 0.9117 (OUTLIER) cc_final: 0.8676 (m-40) REVERT: D 552 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8390 (tt) REVERT: D 607 LYS cc_start: 0.8743 (mtpm) cc_final: 0.8323 (ptpp) REVERT: D 610 LYS cc_start: 0.8787 (ptpp) cc_final: 0.8565 (pttp) REVERT: D 613 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8153 (mp) REVERT: D 649 GLN cc_start: 0.9282 (pt0) cc_final: 0.8888 (pp30) REVERT: D 709 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8621 (p) REVERT: D 723 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8260 (ptpp) REVERT: D 752 TYR cc_start: 0.8808 (t80) cc_final: 0.8603 (t80) outliers start: 75 outliers final: 26 residues processed: 160 average time/residue: 0.6157 time to fit residues: 110.1656 Evaluate side-chains 143 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 98 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 536 PHE Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 584 MET Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 723 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 120 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 188 optimal weight: 10.9990 chunk 5 optimal weight: 0.0870 chunk 116 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 632 HIS C 649 GLN D 632 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.103322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.070815 restraints weight = 35629.278| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.68 r_work: 0.2867 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18626 Z= 0.174 Angle : 0.554 8.899 25732 Z= 0.300 Chirality : 0.042 0.279 2804 Planarity : 0.004 0.033 2862 Dihedral : 22.443 177.316 3429 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.36 % Allowed : 17.67 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.19), residues: 1860 helix: 1.93 (0.18), residues: 812 sheet: 0.34 (0.30), residues: 292 loop : 0.22 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 666 TYR 0.017 0.001 TYR B 389 PHE 0.015 0.001 PHE A 547 TRP 0.008 0.001 TRP A 548 HIS 0.012 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (18626) covalent geometry : angle 0.55450 / 0.30 (25732) hydrogen bonds : bond 0.04007 / 2.65 ( 861) hydrogen bonds : angle 4.41517 / 3.11 ( 2306) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 107 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7997 (tmm) REVERT: A 121 ARG cc_start: 0.8897 (mmm-85) cc_final: 0.8673 (mmm-85) REVERT: A 291 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7896 (tt) REVERT: A 364 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: A 463 ASP cc_start: 0.7986 (p0) cc_final: 0.7608 (p0) REVERT: A 471 LEU cc_start: 0.9362 (mm) cc_final: 0.8917 (tt) REVERT: A 500 SER cc_start: 0.8615 (OUTLIER) cc_final: 0.8213 (t) REVERT: B 62 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8006 (tmt) REVERT: B 291 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7878 (tt) REVERT: B 364 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: B 463 ASP cc_start: 0.7989 (p0) cc_final: 0.7623 (p0) REVERT: B 500 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8230 (t) REVERT: B 503 TYR cc_start: 0.7177 (p90) cc_final: 0.6427 (p90) REVERT: B 566 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.7251 (t0) REVERT: B 666 ARG cc_start: 0.9115 (ttp-110) cc_final: 0.8865 (ttm-80) REVERT: C 454 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6544 (tpt-90) REVERT: C 468 ASP cc_start: 0.8701 (t0) cc_final: 0.8443 (t0) REVERT: C 536 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8911 (m-80) REVERT: C 543 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8691 (m-40) REVERT: C 552 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8321 (tt) REVERT: C 723 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8256 (ptpp) REVERT: D 543 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8669 (m-40) REVERT: D 552 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8383 (tt) REVERT: D 607 LYS cc_start: 0.8748 (mtpm) cc_final: 0.8342 (ptpp) REVERT: D 610 LYS cc_start: 0.8777 (ptpp) cc_final: 0.8563 (pttp) REVERT: D 649 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8895 (pp30) REVERT: D 709 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8620 (p) REVERT: D 723 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8294 (ptpp) outliers start: 74 outliers final: 24 residues processed: 166 average time/residue: 0.6609 time to fit residues: 122.2631 Evaluate side-chains 143 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 100 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 536 PHE Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 649 GLN Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 723 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 147 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 187 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 0.0070 chunk 177 optimal weight: 0.0870 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS C 632 HIS C 649 GLN D 632 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.104577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.072299 restraints weight = 35824.036| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.69 r_work: 0.2905 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18626 Z= 0.119 Angle : 0.539 9.119 25732 Z= 0.293 Chirality : 0.040 0.272 2804 Planarity : 0.003 0.031 2862 Dihedral : 22.314 177.273 3429 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.53 % Allowed : 18.49 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.19), residues: 1860 helix: 1.99 (0.18), residues: 812 sheet: 0.48 (0.31), residues: 268 loop : 0.20 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 569 TYR 0.019 0.001 TYR B 389 PHE 0.014 0.001 PHE B 547 TRP 0.006 0.001 TRP D 530 HIS 0.011 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (18626) covalent geometry : angle 0.53866 / 0.29 (25732) hydrogen bonds : bond 0.03693 / 2.43 ( 861) hydrogen bonds : angle 4.34228 / 3.06 ( 2306) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 111 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7982 (tmm) REVERT: A 121 ARG cc_start: 0.8881 (mmm-85) cc_final: 0.8666 (mmm-85) REVERT: A 291 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7957 (tt) REVERT: A 364 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8038 (m-30) REVERT: A 463 ASP cc_start: 0.7947 (p0) cc_final: 0.7585 (p0) REVERT: A 471 LEU cc_start: 0.9341 (mm) cc_final: 0.8917 (tt) REVERT: A 500 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8208 (t) REVERT: B 62 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7996 (tmt) REVERT: B 291 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7931 (tt) REVERT: B 364 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8047 (m-30) REVERT: B 463 ASP cc_start: 0.7953 (p0) cc_final: 0.7596 (p0) REVERT: B 471 LEU cc_start: 0.9054 (mp) cc_final: 0.8837 (tt) REVERT: B 500 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8236 (t) REVERT: B 666 ARG cc_start: 0.9089 (ttp-110) cc_final: 0.8883 (mtp85) REVERT: C 454 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6473 (tpt-90) REVERT: C 468 ASP cc_start: 0.8669 (t0) cc_final: 0.8401 (t0) REVERT: C 543 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8669 (m-40) REVERT: C 723 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8266 (ptpp) REVERT: D 543 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8648 (m-40) REVERT: D 552 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8372 (tt) REVERT: D 607 LYS cc_start: 0.8741 (mtpm) cc_final: 0.8351 (ptpp) REVERT: D 649 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.8868 (pp30) REVERT: D 709 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8634 (p) REVERT: D 723 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8284 (ptpp) REVERT: D 787 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7383 (tm-30) outliers start: 60 outliers final: 11 residues processed: 159 average time/residue: 0.6706 time to fit residues: 118.5675 Evaluate side-chains 132 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 649 GLN Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 723 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 130 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 180 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 HIS C 632 HIS C 649 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.104540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.072255 restraints weight = 35940.665| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.69 r_work: 0.2903 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18626 Z= 0.132 Angle : 0.548 8.595 25732 Z= 0.296 Chirality : 0.041 0.271 2804 Planarity : 0.003 0.031 2862 Dihedral : 22.266 177.421 3427 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.12 % Allowed : 19.49 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.20), residues: 1860 helix: 2.03 (0.18), residues: 812 sheet: 0.51 (0.30), residues: 290 loop : 0.20 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 121 TYR 0.017 0.001 TYR B 389 PHE 0.015 0.001 PHE B 547 TRP 0.005 0.001 TRP B 572 HIS 0.011 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (18626) covalent geometry : angle 0.54771 / 0.30 (25732) hydrogen bonds : bond 0.03737 / 2.46 ( 861) hydrogen bonds : angle 4.30633 / 3.04 ( 2306) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 107 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7975 (tmm) REVERT: A 121 ARG cc_start: 0.8907 (mmm-85) cc_final: 0.8702 (mmm-85) REVERT: A 364 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: A 463 ASP cc_start: 0.7954 (p0) cc_final: 0.7588 (p0) REVERT: A 471 LEU cc_start: 0.9356 (mm) cc_final: 0.8903 (tt) REVERT: A 500 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8231 (t) REVERT: B 62 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8008 (tmt) REVERT: B 364 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: B 463 ASP cc_start: 0.7966 (p0) cc_final: 0.7608 (p0) REVERT: B 471 LEU cc_start: 0.9065 (mp) cc_final: 0.8837 (tt) REVERT: B 500 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8225 (t) REVERT: B 666 ARG cc_start: 0.9089 (ttp-110) cc_final: 0.8856 (ttm-80) REVERT: C 454 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6513 (tpt-90) REVERT: C 468 ASP cc_start: 0.8673 (t0) cc_final: 0.8403 (t0) REVERT: C 536 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8885 (m-80) REVERT: C 543 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8684 (m-40) REVERT: C 552 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8388 (tt) REVERT: C 649 GLN cc_start: 0.9032 (pt0) cc_final: 0.8697 (pp30) REVERT: C 723 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8289 (ptpp) REVERT: D 543 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.8643 (m-40) REVERT: D 552 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8388 (tt) REVERT: D 649 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8894 (pp30) REVERT: D 709 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8616 (p) REVERT: D 723 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8307 (ptpp) REVERT: D 787 GLN cc_start: 0.7766 (mm110) cc_final: 0.7398 (tm-30) outliers start: 53 outliers final: 16 residues processed: 148 average time/residue: 0.6712 time to fit residues: 109.9097 Evaluate side-chains 132 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 536 PHE Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 649 GLN Chi-restraints excluded: chain D residue 659 MET Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 723 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 192 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 632 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.103816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.071331 restraints weight = 35743.228| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.68 r_work: 0.2884 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18626 Z= 0.168 Angle : 0.573 10.536 25732 Z= 0.305 Chirality : 0.041 0.274 2804 Planarity : 0.003 0.031 2862 Dihedral : 22.331 177.562 3422 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.65 % Allowed : 19.91 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.20), residues: 1860 helix: 2.07 (0.18), residues: 810 sheet: 0.51 (0.30), residues: 290 loop : 0.13 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 569 TYR 0.016 0.001 TYR B 389 PHE 0.016 0.001 PHE B 547 TRP 0.005 0.001 TRP A 572 HIS 0.012 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (18626) covalent geometry : angle 0.57264 / 0.31 (25732) hydrogen bonds : bond 0.03873 / 2.56 ( 861) hydrogen bonds : angle 4.31580 / 3.05 ( 2306) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 103 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7981 (tmm) REVERT: A 121 ARG cc_start: 0.8868 (mmm-85) cc_final: 0.8648 (mmm-85) REVERT: A 364 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: A 463 ASP cc_start: 0.7946 (p0) cc_final: 0.7600 (p0) REVERT: A 471 LEU cc_start: 0.9365 (mm) cc_final: 0.8928 (tt) REVERT: A 500 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8223 (t) REVERT: B 62 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7992 (tmt) REVERT: B 364 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: B 463 ASP cc_start: 0.7989 (p0) cc_final: 0.7622 (p0) REVERT: B 471 LEU cc_start: 0.9073 (mp) cc_final: 0.8837 (tt) REVERT: B 500 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8245 (t) REVERT: C 454 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6473 (tpt-90) REVERT: C 468 ASP cc_start: 0.8689 (t0) cc_final: 0.8415 (t0) REVERT: C 536 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8882 (m-80) REVERT: C 543 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8675 (m-40) REVERT: C 552 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8338 (tt) REVERT: C 614 MET cc_start: 0.8177 (mtp) cc_final: 0.7930 (mtp) REVERT: C 649 GLN cc_start: 0.9088 (pt0) cc_final: 0.8845 (pp30) REVERT: C 723 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8265 (ptpp) REVERT: D 543 ASN cc_start: 0.9041 (OUTLIER) cc_final: 0.8640 (m-40) REVERT: D 610 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7744 (pptt) REVERT: D 649 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8880 (pp30) REVERT: D 709 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8553 (p) REVERT: D 723 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8279 (ptpp) outliers start: 45 outliers final: 19 residues processed: 137 average time/residue: 0.6893 time to fit residues: 104.0835 Evaluate side-chains 133 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 536 PHE Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 610 LYS Chi-restraints excluded: chain D residue 649 GLN Chi-restraints excluded: chain D residue 659 MET Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 723 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 23 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 180 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 632 HIS D 702 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.104757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.072491 restraints weight = 35518.868| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.68 r_work: 0.2909 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18626 Z= 0.126 Angle : 0.566 9.988 25732 Z= 0.303 Chirality : 0.041 0.270 2804 Planarity : 0.003 0.032 2862 Dihedral : 22.257 178.268 3422 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.06 % Allowed : 20.67 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.20), residues: 1860 helix: 2.08 (0.18), residues: 810 sheet: 0.55 (0.30), residues: 290 loop : 0.14 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 666 TYR 0.018 0.001 TYR B 389 PHE 0.016 0.001 PHE B 547 TRP 0.006 0.001 TRP A 572 HIS 0.012 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (18626) covalent geometry : angle 0.56572 / 0.30 (25732) hydrogen bonds : bond 0.03691 / 2.41 ( 861) hydrogen bonds : angle 4.27915 / 3.02 ( 2306) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8021 (tmt) REVERT: A 121 ARG cc_start: 0.8870 (mmm-85) cc_final: 0.8661 (mmm-85) REVERT: A 364 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: A 463 ASP cc_start: 0.7944 (p0) cc_final: 0.7599 (p0) REVERT: A 471 LEU cc_start: 0.9363 (mm) cc_final: 0.8912 (tt) REVERT: A 500 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8210 (t) REVERT: B 62 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7993 (tmt) REVERT: B 364 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: B 463 ASP cc_start: 0.7981 (p0) cc_final: 0.7634 (p0) REVERT: B 471 LEU cc_start: 0.9072 (mp) cc_final: 0.8822 (tt) REVERT: B 500 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8235 (t) REVERT: C 454 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6445 (tpt-90) REVERT: C 468 ASP cc_start: 0.8678 (t0) cc_final: 0.8406 (t0) REVERT: C 543 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8652 (m-40) REVERT: C 584 MET cc_start: 0.8163 (ttm) cc_final: 0.7839 (ttm) REVERT: C 614 MET cc_start: 0.8176 (mtp) cc_final: 0.7956 (mtp) REVERT: C 649 GLN cc_start: 0.9116 (pt0) cc_final: 0.8870 (pp30) REVERT: C 723 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8283 (ptpp) REVERT: D 543 ASN cc_start: 0.9024 (OUTLIER) cc_final: 0.8617 (m-40) REVERT: D 610 LYS cc_start: 0.8220 (pttp) cc_final: 0.7825 (pptt) REVERT: D 649 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8883 (pp30) REVERT: D 723 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8299 (ptpp) outliers start: 35 outliers final: 15 residues processed: 130 average time/residue: 0.6979 time to fit residues: 100.4477 Evaluate side-chains 127 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 649 GLN Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 723 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 0.0030 chunk 134 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 87 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 632 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.106486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.074818 restraints weight = 36157.738| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.70 r_work: 0.2991 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18626 Z= 0.123 Angle : 0.560 10.550 25732 Z= 0.301 Chirality : 0.040 0.268 2804 Planarity : 0.003 0.039 2862 Dihedral : 22.192 178.494 3420 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.83 % Allowed : 20.79 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 1860 helix: 2.12 (0.18), residues: 810 sheet: 0.56 (0.30), residues: 290 loop : 0.12 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 666 TYR 0.017 0.001 TYR B 389 PHE 0.016 0.001 PHE B 547 TRP 0.006 0.001 TRP A 572 HIS 0.012 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (18626) covalent geometry : angle 0.55982 / 0.30 (25732) hydrogen bonds : bond 0.03649 / 2.39 ( 861) hydrogen bonds : angle 4.25448 / 3.00 ( 2306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4927.55 seconds wall clock time: 85 minutes 2.98 seconds (5102.98 seconds total)