Starting phenix.real_space_refine on Fri Jun 13 11:47:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jd9_36077/06_2025/8jd9_36077_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jd9_36077/06_2025/8jd9_36077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jd9_36077/06_2025/8jd9_36077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jd9_36077/06_2025/8jd9_36077.map" model { file = "/net/cci-nas-00/data/ceres_data/8jd9_36077/06_2025/8jd9_36077_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jd9_36077/06_2025/8jd9_36077_neut.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.103 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 60 5.16 5 C 9609 2.51 5 N 2388 2.21 5 O 2666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14725 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 935, 7318 Classifications: {'peptide': 935} Link IDs: {'PTRANS': 33, 'TRANS': 901} Chain breaks: 4 Chain: "B" Number of atoms: 7318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 935, 7318 Classifications: {'peptide': 935} Link IDs: {'PTRANS': 33, 'TRANS': 901} Chain breaks: 4 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 8.80, per 1000 atoms: 0.60 Number of scatterers: 14725 At special positions: 0 Unit cell: (104.76, 105.84, 130.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 2 15.00 O 2666 8.00 N 2388 7.00 C 9609 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.84 Conformation dependent library (CDL) restraints added in 1.8 seconds 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 8 sheets defined 68.9% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 34 through 54 removed outlier: 3.593A pdb=" N LEU A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 removed outlier: 3.840A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.975A pdb=" N GLU A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 116 removed outlier: 3.508A pdb=" N LEU A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Proline residue: A 107 - end of helix removed outlier: 4.696A pdb=" N GLU A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 125 through 152 removed outlier: 3.579A pdb=" N MET A 129 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 132 " --> pdb=" O GLN A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 157 through 169 Processing helix chain 'A' and resid 172 through 183 removed outlier: 3.635A pdb=" N LEU A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 217 removed outlier: 3.739A pdb=" N VAL A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 252 removed outlier: 4.935A pdb=" N GLY A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 278 removed outlier: 3.591A pdb=" N THR A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR A 274 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 306 through 339 removed outlier: 4.329A pdb=" N SER A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 377 removed outlier: 4.019A pdb=" N TRP A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 398 through 411 Processing helix chain 'A' and resid 418 through 451 removed outlier: 4.471A pdb=" N GLY A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 482 removed outlier: 5.138A pdb=" N MET A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 498 Processing helix chain 'A' and resid 499 through 504 removed outlier: 5.440A pdb=" N SER A 502 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 549 Processing helix chain 'A' and resid 553 through 570 removed outlier: 3.726A pdb=" N ASP A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.617A pdb=" N PHE A 593 " --> pdb=" O TYR A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 removed outlier: 4.174A pdb=" N TYR A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 638 Processing helix chain 'A' and resid 640 through 654 Processing helix chain 'A' and resid 654 through 668 Processing helix chain 'A' and resid 668 through 698 removed outlier: 4.511A pdb=" N LEU A 672 " --> pdb=" O PHE A 668 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG A 673 " --> pdb=" O PRO A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 723 removed outlier: 3.704A pdb=" N ASN A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 750 through 754 Processing helix chain 'A' and resid 810 through 817 Processing helix chain 'A' and resid 837 through 844 Processing helix chain 'A' and resid 846 through 866 removed outlier: 4.197A pdb=" N PHE A 852 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 874 through 884 removed outlier: 3.717A pdb=" N ALA A 880 " --> pdb=" O GLN A 876 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 881 " --> pdb=" O GLU A 877 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1017 removed outlier: 3.884A pdb=" N ILE A1017 " --> pdb=" O TRP A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1043 removed outlier: 3.825A pdb=" N ILE A1041 " --> pdb=" O MET A1037 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A1042 " --> pdb=" O GLN A1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 54 removed outlier: 3.586A pdb=" N LEU B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.839A pdb=" N ALA B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.757A pdb=" N GLU B 95 " --> pdb=" O ARG B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 116 Proline residue: B 107 - end of helix removed outlier: 4.732A pdb=" N GLU B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N SER B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 125 through 152 removed outlier: 3.542A pdb=" N LEU B 132 " --> pdb=" O GLN B 128 " (cutoff:3.500A) Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 157 through 169 Processing helix chain 'B' and resid 172 through 183 removed outlier: 3.654A pdb=" N LEU B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 217 removed outlier: 3.699A pdb=" N VAL B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 252 removed outlier: 3.586A pdb=" N GLY B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.581A pdb=" N THR B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR B 274 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 299 Processing helix chain 'B' and resid 304 through 339 removed outlier: 4.113A pdb=" N LYS B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 377 removed outlier: 4.034A pdb=" N TRP B 351 " --> pdb=" O GLN B 347 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE B 355 " --> pdb=" O TRP B 351 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 384 through 392 Processing helix chain 'B' and resid 398 through 411 Processing helix chain 'B' and resid 418 through 451 removed outlier: 4.386A pdb=" N GLY B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 482 removed outlier: 5.123A pdb=" N MET B 471 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 499 removed outlier: 3.723A pdb=" N TYR B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 504 Processing helix chain 'B' and resid 529 through 549 Processing helix chain 'B' and resid 553 through 570 removed outlier: 3.640A pdb=" N ASP B 569 " --> pdb=" O ASP B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 596 removed outlier: 3.854A pdb=" N PHE B 593 " --> pdb=" O TYR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 638 removed outlier: 3.596A pdb=" N THR B 605 " --> pdb=" O ARG B 601 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N SER B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 654 Processing helix chain 'B' and resid 654 through 668 Processing helix chain 'B' and resid 669 through 698 removed outlier: 4.533A pdb=" N ARG B 673 " --> pdb=" O PRO B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 723 removed outlier: 3.848A pdb=" N ASN B 723 " --> pdb=" O LYS B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 750 through 754 Processing helix chain 'B' and resid 810 through 817 Processing helix chain 'B' and resid 837 through 844 Processing helix chain 'B' and resid 846 through 866 removed outlier: 4.320A pdb=" N PHE B 852 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 860 " --> pdb=" O GLU B 856 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS B 863 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 871 removed outlier: 3.712A pdb=" N GLU B 871 " --> pdb=" O PRO B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 884 removed outlier: 3.696A pdb=" N ALA B 880 " --> pdb=" O GLN B 876 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 881 " --> pdb=" O GLU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1017 removed outlier: 3.523A pdb=" N ASN B1016 " --> pdb=" O SER B1012 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE B1017 " --> pdb=" O TRP B1013 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1012 through 1017' Processing helix chain 'B' and resid 1032 through 1043 Processing sheet with id=AA1, first strand: chain 'A' and resid 761 through 762 removed outlier: 7.085A pdb=" N PHE A 833 " --> pdb=" O ILE A 781 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE A 781 " --> pdb=" O PHE A 833 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE A 835 " --> pdb=" O TRP A 779 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N TRP A 779 " --> pdb=" O ILE A 835 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 807 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 802 through 803 Processing sheet with id=AA3, first strand: chain 'A' and resid 890 through 892 removed outlier: 3.583A pdb=" N ALA A 967 " --> pdb=" O THR A 890 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG A 966 " --> pdb=" O LEU A 909 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 897 through 899 Processing sheet with id=AA5, first strand: chain 'B' and resid 761 through 762 removed outlier: 7.095A pdb=" N PHE B 833 " --> pdb=" O ILE B 781 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE B 781 " --> pdb=" O PHE B 833 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE B 835 " --> pdb=" O TRP B 779 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TRP B 779 " --> pdb=" O ILE B 835 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 802 through 803 Processing sheet with id=AA7, first strand: chain 'B' and resid 890 through 892 removed outlier: 6.131A pdb=" N ARG B 966 " --> pdb=" O LEU B 909 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 913 through 915 935 hydrogen bonds defined for protein. 2715 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2492 1.33 - 1.45: 3754 1.45 - 1.57: 8679 1.57 - 1.69: 4 1.69 - 1.81: 102 Bond restraints: 15031 Sorted by residual: bond pdb=" CB PRO B 926 " pdb=" CG PRO B 926 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.25e+00 bond pdb=" CG LEU A 720 " pdb=" CD1 LEU A 720 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 bond pdb=" CB PRO A 926 " pdb=" CG PRO A 926 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.24e+00 bond pdb=" CG LEU B 720 " pdb=" CD1 LEU B 720 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 bond pdb=" N TRP B 279 " pdb=" CA TRP B 279 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.11e+00 ... (remaining 15026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 20078 2.03 - 4.07: 220 4.07 - 6.10: 49 6.10 - 8.13: 6 8.13 - 10.17: 2 Bond angle restraints: 20355 Sorted by residual: angle pdb=" C GLU B 278 " pdb=" N TRP B 279 " pdb=" CA TRP B 279 " ideal model delta sigma weight residual 121.54 131.71 -10.17 1.91e+00 2.74e-01 2.83e+01 angle pdb=" C GLU A 278 " pdb=" N TRP A 279 " pdb=" CA TRP A 279 " ideal model delta sigma weight residual 121.54 131.68 -10.14 1.91e+00 2.74e-01 2.82e+01 angle pdb=" CA PRO B 926 " pdb=" N PRO B 926 " pdb=" CD PRO B 926 " ideal model delta sigma weight residual 112.00 107.67 4.33 1.40e+00 5.10e-01 9.56e+00 angle pdb=" CA PRO A 926 " pdb=" N PRO A 926 " pdb=" CD PRO A 926 " ideal model delta sigma weight residual 112.00 107.76 4.24 1.40e+00 5.10e-01 9.17e+00 angle pdb=" N TRP B 279 " pdb=" CA TRP B 279 " pdb=" CB TRP B 279 " ideal model delta sigma weight residual 110.49 115.44 -4.95 1.69e+00 3.50e-01 8.59e+00 ... (remaining 20350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 8090 17.17 - 34.34: 718 34.34 - 51.51: 117 51.51 - 68.68: 28 68.68 - 85.85: 22 Dihedral angle restraints: 8975 sinusoidal: 3573 harmonic: 5402 Sorted by residual: dihedral pdb=" CA SER A 925 " pdb=" C SER A 925 " pdb=" N PRO A 926 " pdb=" CA PRO A 926 " ideal model delta harmonic sigma weight residual -180.00 -140.81 -39.19 0 5.00e+00 4.00e-02 6.14e+01 dihedral pdb=" CA SER B 925 " pdb=" C SER B 925 " pdb=" N PRO B 926 " pdb=" CA PRO B 926 " ideal model delta harmonic sigma weight residual 180.00 -140.97 -39.03 0 5.00e+00 4.00e-02 6.09e+01 dihedral pdb=" CA SER A 341 " pdb=" C SER A 341 " pdb=" N ASP A 342 " pdb=" CA ASP A 342 " ideal model delta harmonic sigma weight residual -180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 8972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1487 0.028 - 0.055: 578 0.055 - 0.083: 218 0.083 - 0.110: 80 0.110 - 0.137: 29 Chirality restraints: 2392 Sorted by residual: chirality pdb=" CA PRO A 926 " pdb=" N PRO A 926 " pdb=" C PRO A 926 " pdb=" CB PRO A 926 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL B 392 " pdb=" N VAL B 392 " pdb=" C VAL B 392 " pdb=" CB VAL B 392 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA PRO B 926 " pdb=" N PRO B 926 " pdb=" C PRO B 926 " pdb=" CB PRO B 926 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 2389 not shown) Planarity restraints: 2494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 925 " -0.090 5.00e-02 4.00e+02 1.36e-01 2.98e+01 pdb=" N PRO B 926 " 0.236 5.00e-02 4.00e+02 pdb=" CA PRO B 926 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO B 926 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 925 " 0.089 5.00e-02 4.00e+02 1.35e-01 2.92e+01 pdb=" N PRO A 926 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO A 926 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO A 926 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 582 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO B 583 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 583 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 583 " -0.025 5.00e-02 4.00e+02 ... (remaining 2491 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 332 2.71 - 3.26: 15152 3.26 - 3.80: 24090 3.80 - 4.35: 31429 4.35 - 4.90: 53188 Nonbonded interactions: 124191 Sorted by model distance: nonbonded pdb=" O ARG A 551 " pdb=" NE2 GLN A 679 " model vdw 2.162 3.120 nonbonded pdb=" OD1 ASN A 795 " pdb=" OG SER A 798 " model vdw 2.189 3.040 nonbonded pdb=" OH TYR A 274 " pdb=" OD1 ASP B 35 " model vdw 2.196 3.040 nonbonded pdb=" OD1 ASP A 35 " pdb=" OH TYR B 274 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR B 617 " pdb=" O VAL B 675 " model vdw 2.253 3.040 ... (remaining 124186 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 28 through 1047) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 34.520 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 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:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 15033 Z= 0.111 Angle : 0.559 10.169 20355 Z= 0.285 Chirality : 0.037 0.137 2392 Planarity : 0.005 0.136 2494 Dihedral : 13.879 85.846 5491 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.24 % Favored : 94.43 % Rotamer: Outliers : 0.06 % Allowed : 0.25 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1850 helix: 1.46 (0.15), residues: 1204 sheet: 2.36 (0.57), residues: 94 loop : -1.38 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 393 HIS 0.004 0.001 HIS A 626 PHE 0.012 0.001 PHE A 749 TYR 0.014 0.001 TYR B 590 ARG 0.009 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.14964 ( 935) hydrogen bonds : angle 6.12477 ( 2715) covalent geometry : bond 0.00248 (15031) covalent geometry : angle 0.55864 (20355) Misc. bond : bond 0.00081 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 761 MET cc_start: 0.7584 (ttt) cc_final: 0.7097 (ttt) REVERT: B 670 GLN cc_start: 0.7519 (pm20) cc_final: 0.7278 (pm20) REVERT: B 761 MET cc_start: 0.7579 (ttt) cc_final: 0.7087 (ttt) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 1.2484 time to fit residues: 310.3071 Evaluate side-chains 154 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 40.0000 chunk 108 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN B 349 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.178352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.139130 restraints weight = 15749.303| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.68 r_work: 0.3531 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15033 Z= 0.157 Angle : 0.612 8.210 20355 Z= 0.312 Chirality : 0.040 0.152 2392 Planarity : 0.006 0.135 2494 Dihedral : 6.790 76.354 2063 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.57 % Favored : 94.11 % Rotamer: Outliers : 1.05 % Allowed : 10.20 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1850 helix: 1.43 (0.15), residues: 1214 sheet: 2.52 (0.56), residues: 94 loop : -1.39 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1013 HIS 0.008 0.001 HIS A 626 PHE 0.014 0.001 PHE A 870 TYR 0.022 0.002 TYR B 812 ARG 0.004 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 935) hydrogen bonds : angle 4.76715 ( 2715) covalent geometry : bond 0.00362 (15031) covalent geometry : angle 0.61153 (20355) Misc. bond : bond 0.00111 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 378 ARG cc_start: 0.7785 (mtt90) cc_final: 0.7326 (mtt90) REVERT: B 636 PHE cc_start: 0.8042 (t80) cc_final: 0.7785 (t80) REVERT: B 670 GLN cc_start: 0.8046 (pm20) cc_final: 0.7776 (pm20) outliers start: 17 outliers final: 4 residues processed: 180 average time/residue: 1.0237 time to fit residues: 208.3835 Evaluate side-chains 155 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 856 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 11 optimal weight: 6.9990 chunk 65 optimal weight: 0.0670 chunk 52 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 323 ASN A 570 GLN B 94 ASN B 323 ASN B 349 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.178869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.139953 restraints weight = 15880.333| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.66 r_work: 0.3531 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15033 Z= 0.129 Angle : 0.576 10.456 20355 Z= 0.290 Chirality : 0.039 0.322 2392 Planarity : 0.005 0.134 2494 Dihedral : 6.518 59.750 2063 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.97 % Favored : 94.70 % Rotamer: Outliers : 2.22 % Allowed : 11.56 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1850 helix: 1.47 (0.15), residues: 1230 sheet: 2.76 (0.61), residues: 82 loop : -1.35 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 279 HIS 0.007 0.001 HIS B 626 PHE 0.015 0.001 PHE A 636 TYR 0.022 0.001 TYR B 812 ARG 0.003 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 935) hydrogen bonds : angle 4.50412 ( 2715) covalent geometry : bond 0.00298 (15031) covalent geometry : angle 0.57603 (20355) Misc. bond : bond 0.00100 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 1.665 Fit side-chains REVERT: A 378 ARG cc_start: 0.7699 (mtt90) cc_final: 0.7457 (mtt90) REVERT: A 472 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8289 (tt) REVERT: A 579 ARG cc_start: 0.7870 (mtp-110) cc_final: 0.7663 (mtp180) REVERT: A 636 PHE cc_start: 0.8397 (t80) cc_final: 0.8112 (t80) REVERT: A 761 MET cc_start: 0.8153 (ttt) cc_final: 0.7627 (tmm) REVERT: B 187 LYS cc_start: 0.8426 (tptt) cc_final: 0.8221 (tptt) REVERT: B 378 ARG cc_start: 0.7870 (mtt90) cc_final: 0.7418 (mtt90) REVERT: B 761 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7519 (tmm) outliers start: 36 outliers final: 10 residues processed: 182 average time/residue: 1.1095 time to fit residues: 225.4036 Evaluate side-chains 167 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 882 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 165 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 80 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 184 optimal weight: 0.0770 overall best weight: 1.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN B 94 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.175845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.134898 restraints weight = 15870.856| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.73 r_work: 0.3492 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15033 Z= 0.161 Angle : 0.602 10.871 20355 Z= 0.301 Chirality : 0.040 0.271 2392 Planarity : 0.005 0.133 2494 Dihedral : 6.539 57.762 2063 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.08 % Favored : 94.59 % Rotamer: Outliers : 2.84 % Allowed : 12.55 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1850 helix: 1.38 (0.15), residues: 1232 sheet: 2.46 (0.58), residues: 88 loop : -1.39 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 279 HIS 0.009 0.001 HIS A 626 PHE 0.018 0.001 PHE B 636 TYR 0.021 0.002 TYR A 812 ARG 0.003 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 935) hydrogen bonds : angle 4.43610 ( 2715) covalent geometry : bond 0.00380 (15031) covalent geometry : angle 0.60196 (20355) Misc. bond : bond 0.00116 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 2.191 Fit side-chains REVERT: A 378 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7540 (mtt90) REVERT: A 472 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8327 (tt) REVERT: A 532 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7994 (mtt90) REVERT: A 562 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7502 (pt0) REVERT: A 579 ARG cc_start: 0.7994 (mtp-110) cc_final: 0.7775 (mtp180) REVERT: A 761 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7601 (tmm) REVERT: B 378 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7630 (mtt90) REVERT: B 472 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8346 (tt) REVERT: B 761 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7684 (tmm) outliers start: 46 outliers final: 15 residues processed: 185 average time/residue: 1.3054 time to fit residues: 272.3272 Evaluate side-chains 171 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 882 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 38 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN B 94 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.178233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.139730 restraints weight = 15872.346| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.66 r_work: 0.3505 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15033 Z= 0.126 Angle : 0.567 11.257 20355 Z= 0.286 Chirality : 0.039 0.268 2392 Planarity : 0.005 0.132 2494 Dihedral : 6.482 59.549 2063 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.81 % Favored : 94.86 % Rotamer: Outliers : 2.53 % Allowed : 14.15 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.20), residues: 1850 helix: 1.49 (0.15), residues: 1234 sheet: 2.43 (0.57), residues: 88 loop : -1.35 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 279 HIS 0.006 0.001 HIS B 626 PHE 0.018 0.001 PHE B 636 TYR 0.020 0.001 TYR A 812 ARG 0.003 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 935) hydrogen bonds : angle 4.31537 ( 2715) covalent geometry : bond 0.00292 (15031) covalent geometry : angle 0.56697 (20355) Misc. bond : bond 0.00099 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7515 (mtt90) REVERT: A 472 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8308 (tt) REVERT: A 562 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7429 (pt0) REVERT: A 579 ARG cc_start: 0.8031 (mtp-110) cc_final: 0.7803 (mtp180) REVERT: A 761 MET cc_start: 0.8073 (ttt) cc_final: 0.7541 (tmm) REVERT: B 378 ARG cc_start: 0.7972 (mtt90) cc_final: 0.7765 (mtt-85) REVERT: B 761 MET cc_start: 0.8121 (ttt) cc_final: 0.7602 (tmm) outliers start: 41 outliers final: 17 residues processed: 179 average time/residue: 1.1754 time to fit residues: 237.1167 Evaluate side-chains 173 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 968 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 175 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN B 94 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.179522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140757 restraints weight = 15939.956| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.73 r_work: 0.3523 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15033 Z= 0.126 Angle : 0.563 11.513 20355 Z= 0.284 Chirality : 0.039 0.280 2392 Planarity : 0.005 0.132 2494 Dihedral : 6.382 59.714 2063 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.86 % Favored : 94.81 % Rotamer: Outliers : 2.41 % Allowed : 15.14 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 1850 helix: 1.52 (0.15), residues: 1234 sheet: 2.40 (0.57), residues: 88 loop : -1.32 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 279 HIS 0.006 0.001 HIS A 626 PHE 0.017 0.001 PHE A 607 TYR 0.021 0.001 TYR A 812 ARG 0.003 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 935) hydrogen bonds : angle 4.27051 ( 2715) covalent geometry : bond 0.00294 (15031) covalent geometry : angle 0.56302 (20355) Misc. bond : bond 0.00106 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ARG cc_start: 0.7867 (mtt90) cc_final: 0.7592 (mtt90) REVERT: A 472 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8297 (tt) REVERT: A 562 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7347 (pt0) REVERT: A 579 ARG cc_start: 0.8066 (mtp-110) cc_final: 0.7812 (mtp180) REVERT: A 761 MET cc_start: 0.8020 (ttt) cc_final: 0.7498 (tmm) REVERT: A 870 PHE cc_start: 0.8275 (m-80) cc_final: 0.7993 (m-80) REVERT: B 472 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8311 (tt) REVERT: B 486 GLU cc_start: 0.7132 (pt0) cc_final: 0.6921 (pt0) REVERT: B 761 MET cc_start: 0.8032 (ttt) cc_final: 0.7529 (tmm) outliers start: 39 outliers final: 16 residues processed: 184 average time/residue: 1.0262 time to fit residues: 213.4791 Evaluate side-chains 173 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 107 optimal weight: 0.0170 chunk 57 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.182274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.142646 restraints weight = 15958.094| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.76 r_work: 0.3568 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15033 Z= 0.122 Angle : 0.578 16.438 20355 Z= 0.287 Chirality : 0.038 0.284 2392 Planarity : 0.005 0.139 2494 Dihedral : 6.335 59.894 2063 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.70 % Favored : 94.97 % Rotamer: Outliers : 2.10 % Allowed : 15.88 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1850 helix: 1.57 (0.15), residues: 1234 sheet: 2.29 (0.58), residues: 88 loop : -1.30 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 279 HIS 0.006 0.001 HIS A 626 PHE 0.012 0.001 PHE B 636 TYR 0.021 0.001 TYR A 812 ARG 0.003 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 935) hydrogen bonds : angle 4.24410 ( 2715) covalent geometry : bond 0.00279 (15031) covalent geometry : angle 0.57847 (20355) Misc. bond : bond 0.00095 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7609 (mtt90) REVERT: A 472 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8285 (tt) REVERT: A 562 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7240 (pt0) REVERT: A 579 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7820 (mtp180) REVERT: A 761 MET cc_start: 0.8093 (ttt) cc_final: 0.7582 (tmm) REVERT: B 472 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8321 (tt) REVERT: B 485 ASP cc_start: 0.6545 (t70) cc_final: 0.6198 (t70) REVERT: B 486 GLU cc_start: 0.7153 (pt0) cc_final: 0.6930 (pt0) REVERT: B 570 GLN cc_start: 0.5515 (pt0) cc_final: 0.5072 (pp30) REVERT: B 577 ASP cc_start: 0.7219 (p0) cc_final: 0.6801 (p0) REVERT: B 721 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8309 (mt) REVERT: B 761 MET cc_start: 0.8117 (ttt) cc_final: 0.7626 (tmm) outliers start: 34 outliers final: 15 residues processed: 186 average time/residue: 1.0460 time to fit residues: 218.5596 Evaluate side-chains 175 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 127 optimal weight: 0.0010 chunk 133 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 152 optimal weight: 0.1980 chunk 86 optimal weight: 0.6980 chunk 88 optimal weight: 0.0770 chunk 171 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.182325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.143787 restraints weight = 15819.695| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.64 r_work: 0.3591 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15033 Z= 0.108 Angle : 0.558 11.597 20355 Z= 0.279 Chirality : 0.038 0.264 2392 Planarity : 0.005 0.140 2494 Dihedral : 6.118 58.768 2063 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.59 % Favored : 95.08 % Rotamer: Outliers : 1.73 % Allowed : 16.38 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 1850 helix: 1.71 (0.15), residues: 1236 sheet: 2.21 (0.58), residues: 88 loop : -1.22 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 279 HIS 0.004 0.001 HIS B 626 PHE 0.018 0.001 PHE A 607 TYR 0.017 0.001 TYR B 590 ARG 0.008 0.000 ARG B 579 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 935) hydrogen bonds : angle 4.16803 ( 2715) covalent geometry : bond 0.00242 (15031) covalent geometry : angle 0.55809 (20355) Misc. bond : bond 0.00088 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: A 378 ARG cc_start: 0.7841 (mtt90) cc_final: 0.7578 (mtt90) REVERT: A 472 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8244 (tt) REVERT: A 562 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7052 (pt0) REVERT: A 579 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7730 (mtp180) REVERT: A 761 MET cc_start: 0.8018 (ttt) cc_final: 0.7508 (tmm) REVERT: A 907 LEU cc_start: 0.8715 (tt) cc_final: 0.8331 (tt) REVERT: B 472 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8278 (tt) REVERT: B 485 ASP cc_start: 0.6591 (t70) cc_final: 0.6282 (t70) REVERT: B 570 GLN cc_start: 0.5508 (pt0) cc_final: 0.5143 (pp30) REVERT: B 577 ASP cc_start: 0.7228 (p0) cc_final: 0.6785 (p0) REVERT: B 761 MET cc_start: 0.7988 (ttt) cc_final: 0.7471 (tmm) outliers start: 28 outliers final: 13 residues processed: 186 average time/residue: 1.0135 time to fit residues: 212.3435 Evaluate side-chains 175 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 124 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 78 optimal weight: 0.0030 chunk 33 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.180779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.142051 restraints weight = 15764.894| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.74 r_work: 0.3572 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15033 Z= 0.126 Angle : 0.588 14.176 20355 Z= 0.292 Chirality : 0.039 0.361 2392 Planarity : 0.005 0.140 2494 Dihedral : 6.163 59.564 2063 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.38 % Favored : 95.30 % Rotamer: Outliers : 1.61 % Allowed : 16.63 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1850 helix: 1.66 (0.15), residues: 1236 sheet: 2.24 (0.58), residues: 88 loop : -1.24 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 279 HIS 0.006 0.001 HIS B 626 PHE 0.011 0.001 PHE A 870 TYR 0.020 0.001 TYR B 812 ARG 0.007 0.000 ARG B 449 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 935) hydrogen bonds : angle 4.22504 ( 2715) covalent geometry : bond 0.00293 (15031) covalent geometry : angle 0.58839 (20355) Misc. bond : bond 0.00089 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ARG cc_start: 0.7832 (mtt90) cc_final: 0.7551 (mtt90) REVERT: A 472 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8285 (tt) REVERT: A 562 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: A 579 ARG cc_start: 0.8024 (mtp-110) cc_final: 0.7764 (mtp180) REVERT: A 636 PHE cc_start: 0.8549 (t80) cc_final: 0.8269 (t80) REVERT: A 761 MET cc_start: 0.8005 (ttt) cc_final: 0.7485 (tmm) REVERT: A 907 LEU cc_start: 0.8719 (tt) cc_final: 0.8333 (tt) REVERT: B 472 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8295 (tt) REVERT: B 485 ASP cc_start: 0.6541 (t70) cc_final: 0.6290 (t70) REVERT: B 570 GLN cc_start: 0.5623 (pt0) cc_final: 0.5338 (pp30) REVERT: B 577 ASP cc_start: 0.7245 (p0) cc_final: 0.6790 (p0) REVERT: B 721 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8320 (mt) REVERT: B 761 MET cc_start: 0.8014 (ttt) cc_final: 0.7499 (tmm) outliers start: 26 outliers final: 14 residues processed: 181 average time/residue: 1.0779 time to fit residues: 222.6260 Evaluate side-chains 176 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 103 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.180457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142178 restraints weight = 15789.461| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.77 r_work: 0.3562 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15033 Z= 0.128 Angle : 0.594 14.325 20355 Z= 0.295 Chirality : 0.039 0.347 2392 Planarity : 0.005 0.141 2494 Dihedral : 6.173 59.867 2063 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.65 % Favored : 95.03 % Rotamer: Outliers : 1.36 % Allowed : 17.31 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1850 helix: 1.63 (0.15), residues: 1236 sheet: 2.23 (0.59), residues: 88 loop : -1.24 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 279 HIS 0.006 0.001 HIS A 626 PHE 0.013 0.001 PHE B 607 TYR 0.027 0.001 TYR A 606 ARG 0.007 0.000 ARG B 449 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 935) hydrogen bonds : angle 4.23613 ( 2715) covalent geometry : bond 0.00298 (15031) covalent geometry : angle 0.59397 (20355) Misc. bond : bond 0.00100 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ARG cc_start: 0.7855 (mtt90) cc_final: 0.7552 (mtt90) REVERT: A 472 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8292 (tt) REVERT: A 562 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: A 579 ARG cc_start: 0.8032 (mtp-110) cc_final: 0.7778 (mtp180) REVERT: A 761 MET cc_start: 0.8034 (ttt) cc_final: 0.7500 (tmm) REVERT: A 907 LEU cc_start: 0.8675 (tt) cc_final: 0.8272 (tt) REVERT: B 472 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8299 (tt) REVERT: B 485 ASP cc_start: 0.6475 (t70) cc_final: 0.6207 (t70) REVERT: B 570 GLN cc_start: 0.5686 (pt0) cc_final: 0.5305 (pp30) REVERT: B 577 ASP cc_start: 0.7264 (p0) cc_final: 0.6831 (p0) REVERT: B 721 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8301 (mt) REVERT: B 761 MET cc_start: 0.8053 (ttt) cc_final: 0.7554 (tmm) outliers start: 22 outliers final: 13 residues processed: 170 average time/residue: 1.0406 time to fit residues: 199.5030 Evaluate side-chains 173 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 22 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 101 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 138 optimal weight: 0.0170 chunk 113 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.184076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143964 restraints weight = 15872.660| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.90 r_work: 0.3575 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15033 Z= 0.112 Angle : 0.579 14.141 20355 Z= 0.287 Chirality : 0.038 0.344 2392 Planarity : 0.005 0.141 2494 Dihedral : 6.074 58.798 2063 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.54 % Favored : 95.14 % Rotamer: Outliers : 1.24 % Allowed : 17.31 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 1850 helix: 1.70 (0.15), residues: 1238 sheet: 2.24 (0.59), residues: 88 loop : -1.21 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 279 HIS 0.005 0.001 HIS B 626 PHE 0.011 0.001 PHE A 749 TYR 0.018 0.001 TYR A 812 ARG 0.008 0.000 ARG B 449 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 935) hydrogen bonds : angle 4.19081 ( 2715) covalent geometry : bond 0.00255 (15031) covalent geometry : angle 0.57863 (20355) Misc. bond : bond 0.00087 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10260.81 seconds wall clock time: 179 minutes 24.98 seconds (10764.98 seconds total)