Starting phenix.real_space_refine on Sat Aug 23 22:01:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jd9_36077/08_2025/8jd9_36077_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jd9_36077/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jd9_36077/08_2025/8jd9_36077_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jd9_36077/08_2025/8jd9_36077_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jd9_36077/08_2025/8jd9_36077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jd9_36077/08_2025/8jd9_36077.map" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.28, per 1000 atoms: 0.22 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: 1.50 Conformation dependent library (CDL) restraints added in 491.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.54 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: 2.81 Time building geometry restraints manager: 1.93 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.470 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.780 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.000 ARG A 378 TYR 0.014 0.001 TYR B 590 PHE 0.012 0.001 PHE A 749 TRP 0.009 0.001 TRP B 393 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00248 (15031) covalent geometry : angle 0.55864 (20355) hydrogen bonds : bond 0.14964 ( 935) hydrogen bonds : angle 6.12477 ( 2715) 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 : 0.357 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: 0.5677 time to fit residues: 140.7100 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 : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 B 94 ASN B 323 ASN B 349 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.177200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.138232 restraints weight = 15813.190| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.64 r_work: 0.3517 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15033 Z= 0.169 Angle : 0.626 8.445 20355 Z= 0.318 Chirality : 0.041 0.154 2392 Planarity : 0.006 0.135 2494 Dihedral : 6.825 75.471 2063 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.62 % Favored : 94.05 % Rotamer: Outliers : 1.17 % Allowed : 10.51 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.20), residues: 1850 helix: 1.33 (0.15), residues: 1216 sheet: 2.49 (0.56), residues: 94 loop : -1.41 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 378 TYR 0.021 0.002 TYR B 812 PHE 0.014 0.001 PHE B 636 TRP 0.010 0.001 TRP A1013 HIS 0.009 0.001 HIS B 626 Details of bonding type rmsd covalent geometry : bond 0.00394 (15031) covalent geometry : angle 0.62595 (20355) hydrogen bonds : bond 0.04271 ( 935) hydrogen bonds : angle 4.77211 ( 2715) Misc. bond : bond 0.00122 ( 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 199 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 761 MET cc_start: 0.8351 (ttt) cc_final: 0.7850 (tmm) REVERT: B 187 LYS cc_start: 0.8437 (tptt) cc_final: 0.8228 (tptt) REVERT: B 349 ASN cc_start: 0.7460 (OUTLIER) cc_final: 0.7253 (m-40) REVERT: B 670 GLN cc_start: 0.8039 (pm20) cc_final: 0.7771 (pm20) REVERT: B 761 MET cc_start: 0.8310 (ttt) cc_final: 0.7798 (tmm) outliers start: 19 outliers final: 4 residues processed: 187 average time/residue: 0.4641 time to fit residues: 97.3513 Evaluate side-chains 157 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 152 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 349 ASN 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 20 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 172 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN 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 = 0.4139 r_free = 0.4139 target = 0.180302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.142498 restraints weight = 15928.956| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.66 r_work: 0.3536 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1421 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= 0.122 Angle : 0.574 10.274 20355 Z= 0.289 Chirality : 0.038 0.308 2392 Planarity : 0.005 0.134 2494 Dihedral : 6.496 59.693 2063 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.81 % Favored : 94.86 % Rotamer: Outliers : 2.04 % Allowed : 11.87 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.20), residues: 1850 helix: 1.46 (0.15), residues: 1230 sheet: 2.73 (0.60), residues: 82 loop : -1.34 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 378 TYR 0.019 0.001 TYR B 812 PHE 0.017 0.001 PHE B 636 TRP 0.015 0.001 TRP A 279 HIS 0.006 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00278 (15031) covalent geometry : angle 0.57370 (20355) hydrogen bonds : bond 0.03731 ( 935) hydrogen bonds : angle 4.47811 ( 2715) Misc. bond : bond 0.00102 ( 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 205 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.506 Fit side-chains REVERT: A 375 LEU cc_start: 0.8363 (tp) cc_final: 0.8149 (tt) REVERT: A 472 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8315 (tt) REVERT: A 636 PHE cc_start: 0.8461 (t80) cc_final: 0.8165 (t80) REVERT: A 735 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6520 (mtp) REVERT: A 761 MET cc_start: 0.8349 (ttt) cc_final: 0.7970 (tmm) REVERT: A 770 LYS cc_start: 0.7759 (mmmt) cc_final: 0.7559 (mmmt) REVERT: B 761 MET cc_start: 0.8329 (ttt) cc_final: 0.7943 (tmm) outliers start: 33 outliers final: 10 residues processed: 183 average time/residue: 0.5046 time to fit residues: 103.0744 Evaluate side-chains 160 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 735 MET 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 808 THR Chi-restraints excluded: chain B residue 825 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 137 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 89 optimal weight: 40.0000 chunk 64 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 0.0470 chunk 19 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.0880 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.180445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.141579 restraints weight = 15940.399| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.77 r_work: 0.3510 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1651 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= 0.148 Angle : 0.586 10.681 20355 Z= 0.295 Chirality : 0.040 0.273 2392 Planarity : 0.005 0.133 2494 Dihedral : 6.512 58.018 2063 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.19 % Favored : 94.49 % Rotamer: Outliers : 2.47 % Allowed : 12.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.20), residues: 1850 helix: 1.40 (0.15), residues: 1230 sheet: 2.64 (0.59), residues: 82 loop : -1.37 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 378 TYR 0.034 0.002 TYR A 606 PHE 0.018 0.001 PHE A 607 TRP 0.017 0.001 TRP B 279 HIS 0.008 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00349 (15031) covalent geometry : angle 0.58555 (20355) hydrogen bonds : bond 0.03803 ( 935) hydrogen bonds : angle 4.37902 ( 2715) Misc. bond : bond 0.00117 ( 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 204 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.620 Fit side-chains REVERT: A 472 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8326 (tt) REVERT: A 532 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.8045 (mtt90) REVERT: A 636 PHE cc_start: 0.8621 (t80) cc_final: 0.8409 (t80) REVERT: A 761 MET cc_start: 0.8336 (ttt) cc_final: 0.7933 (tmm) REVERT: A 770 LYS cc_start: 0.7621 (mmmt) cc_final: 0.7393 (mmmt) REVERT: B 472 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8355 (tt) REVERT: B 761 MET cc_start: 0.8323 (ttt) cc_final: 0.7939 (tmm) outliers start: 40 outliers final: 15 residues processed: 180 average time/residue: 0.4566 time to fit residues: 92.9125 Evaluate side-chains 166 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 735 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 808 THR Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 825 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 48 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 182 optimal weight: 30.0000 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** B 562 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.180369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.141089 restraints weight = 15815.755| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.91 r_work: 0.3524 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15033 Z= 0.144 Angle : 0.580 11.307 20355 Z= 0.292 Chirality : 0.039 0.275 2392 Planarity : 0.005 0.133 2494 Dihedral : 6.521 59.463 2063 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.81 % Favored : 94.86 % Rotamer: Outliers : 2.47 % Allowed : 14.46 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.20), residues: 1850 helix: 1.39 (0.15), residues: 1236 sheet: 2.59 (0.59), residues: 82 loop : -1.34 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 378 TYR 0.021 0.001 TYR A 812 PHE 0.014 0.001 PHE B 636 TRP 0.016 0.001 TRP B 279 HIS 0.007 0.001 HIS B 626 Details of bonding type rmsd covalent geometry : bond 0.00338 (15031) covalent geometry : angle 0.57978 (20355) hydrogen bonds : bond 0.03711 ( 935) hydrogen bonds : angle 4.33463 ( 2715) Misc. bond : bond 0.00108 ( 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 200 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 472 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8326 (tt) REVERT: A 735 MET cc_start: 0.6641 (OUTLIER) cc_final: 0.6395 (mtp) REVERT: A 761 MET cc_start: 0.8311 (ttt) cc_final: 0.7885 (tmm) REVERT: B 670 GLN cc_start: 0.7996 (pm20) cc_final: 0.7746 (pm20) REVERT: B 761 MET cc_start: 0.8280 (ttt) cc_final: 0.7854 (tmm) outliers start: 40 outliers final: 15 residues processed: 178 average time/residue: 0.4747 time to fit residues: 95.0839 Evaluate side-chains 169 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 568 LEU Chi-restraints excluded: chain A residue 720 LEU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 144 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** B 562 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.180552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141241 restraints weight = 15817.211| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.77 r_work: 0.3530 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1817 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= 0.136 Angle : 0.567 11.476 20355 Z= 0.286 Chirality : 0.039 0.282 2392 Planarity : 0.005 0.133 2494 Dihedral : 6.438 58.899 2063 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.92 % Favored : 94.76 % Rotamer: Outliers : 2.35 % Allowed : 15.33 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.20), residues: 1850 helix: 1.45 (0.15), residues: 1234 sheet: 2.39 (0.58), residues: 88 loop : -1.34 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 378 TYR 0.023 0.001 TYR A 812 PHE 0.018 0.001 PHE A 607 TRP 0.017 0.001 TRP B 279 HIS 0.007 0.001 HIS A 626 Details of bonding type rmsd covalent geometry : bond 0.00318 (15031) covalent geometry : angle 0.56652 (20355) hydrogen bonds : bond 0.03624 ( 935) hydrogen bonds : angle 4.29561 ( 2715) 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 200 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 472 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8325 (tt) REVERT: A 607 PHE cc_start: 0.7977 (m-80) cc_final: 0.7745 (m-80) REVERT: A 735 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6511 (mtp) REVERT: A 761 MET cc_start: 0.8277 (ttt) cc_final: 0.7846 (tmm) REVERT: B 472 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8335 (tt) REVERT: B 577 ASP cc_start: 0.7100 (p0) cc_final: 0.6689 (p0) REVERT: B 670 GLN cc_start: 0.8018 (pm20) cc_final: 0.7777 (pm20) REVERT: B 761 MET cc_start: 0.8249 (ttt) cc_final: 0.7801 (tmm) outliers start: 38 outliers final: 13 residues processed: 182 average time/residue: 0.4593 time to fit residues: 94.6486 Evaluate side-chains 170 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 735 MET 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 825 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 124 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 136 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.181562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.142174 restraints weight = 15734.552| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.98 r_work: 0.3532 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1875 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= 0.125 Angle : 0.576 13.003 20355 Z= 0.289 Chirality : 0.039 0.308 2392 Planarity : 0.005 0.139 2494 Dihedral : 6.372 59.764 2063 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.76 % Favored : 94.92 % Rotamer: Outliers : 1.98 % Allowed : 16.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.20), residues: 1850 helix: 1.56 (0.15), residues: 1224 sheet: 2.33 (0.58), residues: 88 loop : -1.36 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 378 TYR 0.022 0.001 TYR A 812 PHE 0.023 0.001 PHE A 870 TRP 0.019 0.001 TRP A 279 HIS 0.006 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00287 (15031) covalent geometry : angle 0.57636 (20355) hydrogen bonds : bond 0.03527 ( 935) hydrogen bonds : angle 4.29502 ( 2715) Misc. bond : bond 0.00100 ( 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 195 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 472 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8314 (tt) REVERT: A 735 MET cc_start: 0.6746 (OUTLIER) cc_final: 0.6528 (mtp) REVERT: A 761 MET cc_start: 0.8234 (ttt) cc_final: 0.7803 (tmm) REVERT: A 780 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7575 (mt) REVERT: B 472 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8324 (tt) REVERT: B 485 ASP cc_start: 0.6572 (t70) cc_final: 0.6300 (t70) REVERT: B 570 GLN cc_start: 0.5654 (pt0) cc_final: 0.5378 (pp30) REVERT: B 577 ASP cc_start: 0.7214 (p0) cc_final: 0.6765 (p0) REVERT: B 670 GLN cc_start: 0.8025 (pm20) cc_final: 0.7802 (pm20) REVERT: B 761 MET cc_start: 0.8194 (ttt) cc_final: 0.7748 (tmm) outliers start: 32 outliers final: 13 residues processed: 183 average time/residue: 0.4096 time to fit residues: 84.8229 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 : 0.356 ------------------------------------------------------------------------------- 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 735 MET Chi-restraints excluded: chain A residue 780 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 570 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.180049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.140452 restraints weight = 15797.205| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.94 r_work: 0.3513 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15033 Z= 0.153 Angle : 0.599 11.247 20355 Z= 0.301 Chirality : 0.040 0.326 2392 Planarity : 0.006 0.140 2494 Dihedral : 6.430 57.799 2063 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.86 % Favored : 94.81 % Rotamer: Outliers : 2.10 % Allowed : 16.32 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.20), residues: 1850 helix: 1.42 (0.15), residues: 1226 sheet: 2.27 (0.58), residues: 88 loop : -1.36 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 378 TYR 0.033 0.002 TYR A 606 PHE 0.015 0.001 PHE B 607 TRP 0.023 0.001 TRP A 279 HIS 0.007 0.001 HIS B 626 Details of bonding type rmsd covalent geometry : bond 0.00363 (15031) covalent geometry : angle 0.59918 (20355) hydrogen bonds : bond 0.03713 ( 935) hydrogen bonds : angle 4.34020 ( 2715) Misc. bond : bond 0.00102 ( 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 197 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.637 Fit side-chains REVERT: A 472 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8334 (tt) REVERT: A 780 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7576 (mt) REVERT: B 472 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8338 (tt) REVERT: B 570 GLN cc_start: 0.5769 (OUTLIER) cc_final: 0.5461 (pp30) REVERT: B 577 ASP cc_start: 0.7322 (p0) cc_final: 0.6843 (p0) REVERT: B 670 GLN cc_start: 0.8000 (pm20) cc_final: 0.7777 (pm20) REVERT: B 761 MET cc_start: 0.8174 (ttt) cc_final: 0.7724 (tmm) outliers start: 34 outliers final: 16 residues processed: 179 average time/residue: 0.4158 time to fit residues: 84.3382 Evaluate side-chains 170 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 568 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 780 LEU 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 260 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 570 GLN 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 856 GLU Chi-restraints excluded: chain B residue 1041 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 162 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 631 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.179944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140737 restraints weight = 15830.398| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.76 r_work: 0.3507 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15033 Z= 0.154 Angle : 0.609 12.397 20355 Z= 0.306 Chirality : 0.040 0.356 2392 Planarity : 0.006 0.140 2494 Dihedral : 6.430 58.018 2063 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.59 % Favored : 95.08 % Rotamer: Outliers : 1.55 % Allowed : 17.43 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.20), residues: 1850 helix: 1.40 (0.15), residues: 1226 sheet: 2.26 (0.58), residues: 88 loop : -1.38 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 378 TYR 0.026 0.002 TYR A 812 PHE 0.017 0.001 PHE A 607 TRP 0.033 0.001 TRP B 279 HIS 0.007 0.001 HIS B 626 Details of bonding type rmsd covalent geometry : bond 0.00365 (15031) covalent geometry : angle 0.60927 (20355) hydrogen bonds : bond 0.03719 ( 935) hydrogen bonds : angle 4.36653 ( 2715) Misc. bond : bond 0.00114 ( 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 178 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.406 Fit side-chains REVERT: A 472 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8337 (tt) REVERT: A 735 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6475 (mtp) REVERT: A 761 MET cc_start: 0.7958 (ttt) cc_final: 0.7459 (tmm) REVERT: B 472 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8331 (tt) REVERT: B 577 ASP cc_start: 0.7333 (p0) cc_final: 0.6840 (p0) REVERT: B 670 GLN cc_start: 0.8016 (pm20) cc_final: 0.7778 (pm20) outliers start: 25 outliers final: 16 residues processed: 166 average time/residue: 0.3624 time to fit residues: 68.1733 Evaluate side-chains 166 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 568 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 671 VAL 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 968 ILE 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 856 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 32 optimal weight: 0.0970 chunk 84 optimal weight: 0.9990 chunk 180 optimal weight: 0.0470 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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** A 739 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.180429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142277 restraints weight = 15740.994| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.92 r_work: 0.3569 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15033 Z= 0.117 Angle : 0.597 13.809 20355 Z= 0.298 Chirality : 0.039 0.362 2392 Planarity : 0.005 0.140 2494 Dihedral : 6.282 59.283 2063 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.70 % Favored : 94.97 % Rotamer: Outliers : 1.30 % Allowed : 18.05 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.20), residues: 1850 helix: 1.59 (0.15), residues: 1226 sheet: 2.21 (0.58), residues: 88 loop : -1.33 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 579 TYR 0.024 0.001 TYR A 812 PHE 0.016 0.001 PHE B 607 TRP 0.038 0.001 TRP B 279 HIS 0.006 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00261 (15031) covalent geometry : angle 0.59702 (20355) hydrogen bonds : bond 0.03475 ( 935) hydrogen bonds : angle 4.31306 ( 2715) Misc. bond : bond 0.00093 ( 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 179 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.626 Fit side-chains REVERT: A 472 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8274 (tt) REVERT: A 735 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6495 (mtp) REVERT: A 761 MET cc_start: 0.8018 (ttt) cc_final: 0.7518 (tmm) REVERT: A 1037 MET cc_start: 0.6742 (ttt) cc_final: 0.6340 (ttt) REVERT: B 472 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8285 (tt) REVERT: B 577 ASP cc_start: 0.7029 (p0) cc_final: 0.6601 (p0) REVERT: B 670 GLN cc_start: 0.7961 (pm20) cc_final: 0.7750 (pm20) REVERT: B 761 MET cc_start: 0.7721 (ttt) cc_final: 0.7450 (tmm) outliers start: 21 outliers final: 11 residues processed: 169 average time/residue: 0.5062 time to fit residues: 96.7515 Evaluate side-chains 163 residues out of total 1618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 671 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 155 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 107 optimal weight: 0.1980 chunk 146 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 180 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.180257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.142330 restraints weight = 15705.400| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.74 r_work: 0.3580 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 0.057 15033 Z= 0.124 Angle : 0.605 13.753 20355 Z= 0.303 Chirality : 0.039 0.352 2392 Planarity : 0.005 0.141 2494 Dihedral : 6.226 59.580 2063 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.43 % Favored : 95.24 % Rotamer: Outliers : 1.17 % Allowed : 18.36 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.20), residues: 1850 helix: 1.60 (0.15), residues: 1226 sheet: 2.24 (0.59), residues: 88 loop : -1.33 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 378 TYR 0.024 0.001 TYR A 812 PHE 0.012 0.001 PHE A 607 TRP 0.032 0.001 TRP B 279 HIS 0.006 0.001 HIS B 626 Details of bonding type rmsd covalent geometry : bond 0.00286 (15031) covalent geometry : angle 0.60465 (20355) hydrogen bonds : bond 0.03435 ( 935) hydrogen bonds : angle 4.28638 ( 2715) Misc. bond : bond 0.00091 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4359.34 seconds wall clock time: 75 minutes 18.29 seconds (4518.29 seconds total)