Starting phenix.real_space_refine on Mon Nov 18 00:09:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd9_36077/11_2024/8jd9_36077_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd9_36077/11_2024/8jd9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd9_36077/11_2024/8jd9_36077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd9_36077/11_2024/8jd9_36077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd9_36077/11_2024/8jd9_36077_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd9_36077/11_2024/8jd9_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.95, per 1000 atoms: 0.61 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: 4.06 Conformation dependent library (CDL) restraints added in 2.1 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: 1.65 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: 5.79 Time building geometry restraints manager: 4.53 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: 0.830 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: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.350 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.610 ------------------------------------------------------------------------------- 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 15031 Z= 0.161 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 *********************** 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 : 1.567 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: 1.2860 time to fit residues: 319.8883 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 : 1.624 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 15031 Z= 0.236 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 *********************** 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 : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 378 ARG cc_start: 0.7444 (mtt90) cc_final: 0.7082 (mtt90) outliers start: 17 outliers final: 4 residues processed: 180 average time/residue: 1.0920 time to fit residues: 222.5151 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 : 1.743 ------------------------------------------------------------------------------- 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 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 140 optimal weight: 0.3980 chunk 115 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15031 Z= 0.184 Angle : 0.570 10.204 20355 Z= 0.288 Chirality : 0.039 0.302 2392 Planarity : 0.005 0.134 2494 Dihedral : 6.476 59.586 2063 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.97 % Favored : 94.70 % Rotamer: Outliers : 2.22 % Allowed : 11.62 % Favored : 86.16 % 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: 1.14 (0.20), residues: 1850 helix: 1.50 (0.15), residues: 1230 sheet: 2.77 (0.61), residues: 82 loop : -1.34 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 279 HIS 0.007 0.001 HIS A 626 PHE 0.015 0.001 PHE A 636 TYR 0.020 0.001 TYR B 812 ARG 0.003 0.000 ARG A 378 *********************** 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 207 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 1.558 Fit side-chains REVERT: A 378 ARG cc_start: 0.7418 (mtt90) cc_final: 0.7216 (mtt90) REVERT: A 472 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8007 (tt) REVERT: A 579 ARG cc_start: 0.7199 (mtp-110) cc_final: 0.6991 (mtp180) REVERT: A 761 MET cc_start: 0.7560 (ttt) cc_final: 0.7142 (tmm) REVERT: B 378 ARG cc_start: 0.7479 (mtt90) cc_final: 0.7192 (mtt90) REVERT: B 761 MET cc_start: 0.7525 (ttt) cc_final: 0.7086 (tmm) outliers start: 36 outliers final: 12 residues processed: 184 average time/residue: 1.1711 time to fit residues: 241.3867 Evaluate side-chains 166 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 1.713 ------------------------------------------------------------------------------- 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 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 349 ASN 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 167 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 113 optimal weight: 0.2980 chunk 169 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 88 optimal weight: 20.0000 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 94 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN B 52 HIS B 94 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15031 Z= 0.419 Angle : 0.697 10.148 20355 Z= 0.350 Chirality : 0.044 0.291 2392 Planarity : 0.006 0.134 2494 Dihedral : 6.921 59.335 2063 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.68 % Favored : 94.00 % Rotamer: Outliers : 3.21 % Allowed : 12.86 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.11 % 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: 0.42 (0.20), residues: 1850 helix: 0.92 (0.15), residues: 1218 sheet: 2.37 (0.58), residues: 88 loop : -1.52 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 279 HIS 0.012 0.002 HIS A 626 PHE 0.017 0.002 PHE A 607 TYR 0.032 0.002 TYR B 274 ARG 0.004 0.001 ARG A 722 *********************** 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 220 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ARG cc_start: 0.7518 (mtt90) cc_final: 0.7307 (mtt90) REVERT: A 579 ARG cc_start: 0.7526 (mtp-110) cc_final: 0.7223 (mtp180) REVERT: A 720 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7680 (tt) REVERT: A 735 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6689 (mtp) REVERT: A 761 MET cc_start: 0.7596 (ttt) cc_final: 0.7169 (tmm) REVERT: B 378 ARG cc_start: 0.7609 (mtt90) cc_final: 0.7297 (mtt90) REVERT: B 761 MET cc_start: 0.7490 (ttt) cc_final: 0.7053 (tmm) outliers start: 52 outliers final: 21 residues processed: 192 average time/residue: 1.1490 time to fit residues: 247.1054 Evaluate side-chains 174 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 865 LEU 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 728 LYS Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 1041 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 0.0070 chunk 161 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 A 570 GLN B 94 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15031 Z= 0.177 Angle : 0.572 11.541 20355 Z= 0.289 Chirality : 0.038 0.278 2392 Planarity : 0.005 0.133 2494 Dihedral : 6.575 59.658 2063 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.70 % Favored : 94.97 % Rotamer: Outliers : 2.41 % Allowed : 15.02 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.06 % 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: 0.89 (0.20), residues: 1850 helix: 1.32 (0.15), residues: 1230 sheet: 2.32 (0.57), residues: 88 loop : -1.44 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 279 HIS 0.005 0.001 HIS B 626 PHE 0.015 0.001 PHE B 636 TYR 0.021 0.001 TYR A 812 ARG 0.004 0.000 ARG A 378 *********************** 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 203 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ARG cc_start: 0.7548 (mtt90) cc_final: 0.7315 (mtt90) REVERT: A 579 ARG cc_start: 0.7454 (mtp-110) cc_final: 0.7179 (mtp180) REVERT: A 606 TYR cc_start: 0.7624 (t80) cc_final: 0.7238 (t80) REVERT: A 761 MET cc_start: 0.7566 (ttt) cc_final: 0.7117 (tmm) REVERT: B 761 MET cc_start: 0.7520 (ttt) cc_final: 0.7095 (tmm) outliers start: 39 outliers final: 12 residues processed: 182 average time/residue: 1.1576 time to fit residues: 237.1137 Evaluate side-chains 172 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 532 ARG 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 728 LYS Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 105 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15031 Z= 0.182 Angle : 0.559 10.394 20355 Z= 0.283 Chirality : 0.038 0.275 2392 Planarity : 0.005 0.132 2494 Dihedral : 6.405 59.580 2063 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.86 % Favored : 94.81 % Rotamer: Outliers : 2.35 % Allowed : 15.88 % 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: 1.09 (0.20), residues: 1850 helix: 1.46 (0.15), residues: 1234 sheet: 2.26 (0.57), residues: 88 loop : -1.33 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 279 HIS 0.006 0.001 HIS A 626 PHE 0.017 0.001 PHE A 607 TYR 0.022 0.001 TYR A 812 ARG 0.002 0.000 ARG A 579 *********************** 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 207 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 472 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8041 (tt) REVERT: A 579 ARG cc_start: 0.7448 (mtp-110) cc_final: 0.7171 (mtp180) REVERT: A 761 MET cc_start: 0.7594 (ttt) cc_final: 0.7143 (tmm) REVERT: B 472 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8056 (tt) REVERT: B 577 ASP cc_start: 0.7019 (p0) cc_final: 0.6709 (p0) REVERT: B 761 MET cc_start: 0.7565 (ttt) cc_final: 0.7126 (tmm) outliers start: 38 outliers final: 14 residues processed: 189 average time/residue: 1.0568 time to fit residues: 225.9015 Evaluate side-chains 172 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 882 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.0770 chunk 20 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 B 570 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15031 Z= 0.181 Angle : 0.584 13.596 20355 Z= 0.293 Chirality : 0.039 0.310 2392 Planarity : 0.005 0.139 2494 Dihedral : 6.364 59.683 2063 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.43 % Favored : 95.24 % Rotamer: Outliers : 1.98 % Allowed : 16.87 % Favored : 81.15 % 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: 1.17 (0.20), residues: 1850 helix: 1.57 (0.15), residues: 1224 sheet: 2.20 (0.57), residues: 88 loop : -1.35 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 279 HIS 0.005 0.001 HIS A 626 PHE 0.022 0.001 PHE A 870 TYR 0.022 0.001 TYR A 812 ARG 0.007 0.000 ARG B 579 *********************** 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 195 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 1.598 Fit side-chains revert: symmetry clash REVERT: A 472 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8034 (tt) REVERT: A 579 ARG cc_start: 0.7450 (mtp-110) cc_final: 0.7168 (mtp180) REVERT: A 720 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7747 (tp) REVERT: A 761 MET cc_start: 0.7576 (ttt) cc_final: 0.7125 (tmm) REVERT: B 472 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8037 (tt) REVERT: B 577 ASP cc_start: 0.7164 (p0) cc_final: 0.6844 (p0) REVERT: B 761 MET cc_start: 0.7515 (ttt) cc_final: 0.7074 (tmm) outliers start: 32 outliers final: 14 residues processed: 178 average time/residue: 1.0068 time to fit residues: 203.4364 Evaluate side-chains 171 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 1.672 ------------------------------------------------------------------------------- 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 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 728 LYS Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 882 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 0.044 15031 Z= 0.185 Angle : 0.578 12.618 20355 Z= 0.290 Chirality : 0.039 0.301 2392 Planarity : 0.005 0.140 2494 Dihedral : 6.294 59.779 2063 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.59 % Favored : 95.08 % Rotamer: Outliers : 1.61 % Allowed : 17.55 % Favored : 80.84 % 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: 1.21 (0.20), residues: 1850 helix: 1.59 (0.15), residues: 1226 sheet: 2.17 (0.57), residues: 88 loop : -1.29 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 279 HIS 0.005 0.001 HIS B 626 PHE 0.018 0.001 PHE A 607 TYR 0.028 0.001 TYR A 606 ARG 0.006 0.000 ARG A 378 *********************** 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 192 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: A 472 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8023 (tt) REVERT: A 579 ARG cc_start: 0.7441 (mtp-110) cc_final: 0.7179 (mtp180) REVERT: A 720 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7683 (tp) REVERT: A 761 MET cc_start: 0.7595 (ttt) cc_final: 0.7106 (tmm) REVERT: A 907 LEU cc_start: 0.8717 (tt) cc_final: 0.8463 (tt) REVERT: B 472 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8035 (tt) REVERT: B 577 ASP cc_start: 0.6895 (p0) cc_final: 0.6527 (p0) REVERT: B 735 MET cc_start: 0.6398 (mtm) cc_final: 0.5996 (mtp) REVERT: B 761 MET cc_start: 0.7533 (ttt) cc_final: 0.7060 (tmm) outliers start: 26 outliers final: 14 residues processed: 179 average time/residue: 1.0272 time to fit residues: 207.7884 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 : 1.736 ------------------------------------------------------------------------------- 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 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 728 LYS Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 882 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 158 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15031 Z= 0.207 Angle : 0.600 13.378 20355 Z= 0.300 Chirality : 0.040 0.384 2392 Planarity : 0.005 0.140 2494 Dihedral : 6.315 59.607 2063 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.54 % Favored : 95.14 % Rotamer: Outliers : 1.42 % Allowed : 17.68 % Favored : 80.90 % 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: 1.54 (0.15), residues: 1226 sheet: 2.17 (0.57), residues: 88 loop : -1.30 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 279 HIS 0.006 0.001 HIS B 626 PHE 0.011 0.001 PHE A 607 TYR 0.023 0.001 TYR A 812 ARG 0.008 0.000 ARG A 378 *********************** 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 185 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: A 472 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8038 (tt) REVERT: A 579 ARG cc_start: 0.7485 (mtp-110) cc_final: 0.7203 (mtp180) REVERT: A 720 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7698 (tp) REVERT: A 761 MET cc_start: 0.7622 (ttt) cc_final: 0.7112 (tmm) REVERT: A 907 LEU cc_start: 0.8710 (tt) cc_final: 0.8447 (tt) REVERT: B 472 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8044 (tt) REVERT: B 577 ASP cc_start: 0.6958 (p0) cc_final: 0.6574 (p0) REVERT: B 735 MET cc_start: 0.6422 (mtm) cc_final: 0.6035 (mtp) REVERT: B 761 MET cc_start: 0.7558 (ttt) cc_final: 0.7074 (tmm) outliers start: 23 outliers final: 14 residues processed: 176 average time/residue: 0.9572 time to fit residues: 191.4501 Evaluate side-chains 171 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 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 728 LYS Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 862 LEU 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 109 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 185 optimal weight: 0.0030 chunk 170 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15031 Z= 0.191 Angle : 0.599 13.297 20355 Z= 0.300 Chirality : 0.039 0.353 2392 Planarity : 0.005 0.140 2494 Dihedral : 6.262 59.705 2063 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.54 % Favored : 95.14 % Rotamer: Outliers : 1.11 % Allowed : 18.05 % Favored : 80.84 % 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: 1.21 (0.20), residues: 1850 helix: 1.59 (0.15), residues: 1226 sheet: 2.12 (0.57), residues: 88 loop : -1.30 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 279 HIS 0.006 0.001 HIS B 626 PHE 0.020 0.001 PHE A 870 TYR 0.023 0.001 TYR A 812 ARG 0.006 0.000 ARG A 378 ********************** 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 174 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 472 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8028 (tt) REVERT: A 720 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7685 (tp) REVERT: A 761 MET cc_start: 0.7620 (ttt) cc_final: 0.7129 (tmm) REVERT: A 907 LEU cc_start: 0.8722 (tt) cc_final: 0.8453 (tt) REVERT: B 472 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8036 (tt) REVERT: B 577 ASP cc_start: 0.6962 (p0) cc_final: 0.6596 (p0) REVERT: B 735 MET cc_start: 0.6423 (mtm) cc_final: 0.6026 (mtp) REVERT: B 761 MET cc_start: 0.7544 (ttt) cc_final: 0.7064 (tmm) outliers start: 18 outliers final: 13 residues processed: 165 average time/residue: 1.0686 time to fit residues: 200.5043 Evaluate side-chains 169 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 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 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 117 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 147 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN B 94 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN ** B 570 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 = 0.4150 r_free = 0.4150 target = 0.181297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.138770 restraints weight = 15788.984| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.67 r_work: 0.3566 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15031 Z= 0.174 Angle : 0.585 13.289 20355 Z= 0.292 Chirality : 0.039 0.328 2392 Planarity : 0.005 0.140 2494 Dihedral : 6.138 58.611 2063 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.43 % Favored : 95.24 % Rotamer: Outliers : 1.30 % Allowed : 17.80 % Favored : 80.90 % 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: 1.33 (0.20), residues: 1850 helix: 1.70 (0.15), residues: 1226 sheet: 2.13 (0.58), residues: 88 loop : -1.30 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 279 HIS 0.005 0.001 HIS B 626 PHE 0.013 0.001 PHE A 870 TYR 0.020 0.001 TYR A 812 ARG 0.009 0.000 ARG B 449 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4550.81 seconds wall clock time: 84 minutes 12.24 seconds (5052.24 seconds total)