Starting phenix.real_space_refine on Thu Aug 6 10:51:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh9_37535/08_2026/8wh9_37535.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh9_37535/08_2026/8wh9_37535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wh9_37535/08_2026/8wh9_37535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh9_37535/08_2026/8wh9_37535.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wh9_37535/08_2026/8wh9_37535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh9_37535/08_2026/8wh9_37535.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 286 5.49 5 S 30 5.16 5 Be 1 3.05 5 C 8799 2.51 5 N 2822 2.21 5 O 3387 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15328 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 755 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "B" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 768 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "D" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 799 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 688 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 750 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "H" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "I" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2893 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "J" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2929 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "K" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3669 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 16, 'TRANS': 435} Chain breaks: 1 Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.56, per 1000 atoms: 0.17 Number of scatterers: 15328 At special positions: 0 Unit cell: (131.67, 136.8, 122.265, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 30 16.00 P 286 15.00 F 3 9.00 O 3387 8.00 N 2822 7.00 C 8799 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 349.0 milliseconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2222 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 64.6% alpha, 5.6% beta 102 base pairs and 238 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.182A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.639A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.746A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.696A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.908A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 80 through 109 removed outlier: 3.535A pdb=" N GLY D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 removed outlier: 3.732A pdb=" N ILE D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 149 removed outlier: 3.743A pdb=" N SER D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.606A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.586A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.792A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 130 removed outlier: 3.804A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.844A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.869A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.689A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.453A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU G 59 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.602A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 62 through 74 Processing helix chain 'H' and resid 80 through 109 removed outlier: 3.785A pdb=" N ASN H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 127 removed outlier: 3.878A pdb=" N THR H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 148 removed outlier: 3.668A pdb=" N ALA H 132 " --> pdb=" O PRO H 128 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER H 137 " --> pdb=" O LYS H 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 220 Processing helix chain 'K' and resid 233 through 246 removed outlier: 5.860A pdb=" N GLY K 239 " --> pdb=" O ILE K 235 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 273 removed outlier: 3.913A pdb=" N SER K 263 " --> pdb=" O LEU K 259 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN K 264 " --> pdb=" O SER K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 291 removed outlier: 3.956A pdb=" N GLU K 290 " --> pdb=" O ASN K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 317 Processing helix chain 'K' and resid 317 through 323 removed outlier: 4.068A pdb=" N ILE K 321 " --> pdb=" O ASP K 317 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG K 323 " --> pdb=" O LYS K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 339 Processing helix chain 'K' and resid 343 through 352 removed outlier: 3.874A pdb=" N HIS K 351 " --> pdb=" O ARG K 347 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 380 Processing helix chain 'K' and resid 381 through 384 Processing helix chain 'K' and resid 416 through 425 removed outlier: 3.650A pdb=" N ILE K 423 " --> pdb=" O LYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 465 Processing helix chain 'K' and resid 467 through 472 Processing helix chain 'K' and resid 473 through 475 No H-bonds generated for 'chain 'K' and resid 473 through 475' Processing helix chain 'K' and resid 488 through 499 removed outlier: 3.846A pdb=" N ASN K 496 " --> pdb=" O GLN K 492 " (cutoff:3.500A) Processing helix chain 'K' and resid 500 through 508 removed outlier: 3.797A pdb=" N GLN K 506 " --> pdb=" O LEU K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 519 through 522 Processing helix chain 'K' and resid 523 through 536 Processing helix chain 'K' and resid 550 through 564 removed outlier: 3.565A pdb=" N LYS K 563 " --> pdb=" O TYR K 559 " (cutoff:3.500A) Processing helix chain 'K' and resid 575 through 587 Processing helix chain 'K' and resid 599 through 604 Processing helix chain 'K' and resid 623 through 635 removed outlier: 4.111A pdb=" N ASP K 627 " --> pdb=" O ASN K 623 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN K 629 " --> pdb=" O GLN K 625 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA K 630 " --> pdb=" O MET K 626 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG K 633 " --> pdb=" O GLN K 629 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS K 634 " --> pdb=" O ALA K 630 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 676 removed outlier: 3.558A pdb=" N ARG K 657 " --> pdb=" O SER K 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.396A pdb=" N ARG A 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.266A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.467A pdb=" N ARG C 43 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 78 through 79 removed outlier: 3.595A pdb=" N ILE C 79 " --> pdb=" O GLY D 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98 removed outlier: 7.491A pdb=" N THR F 96 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.544A pdb=" N ARG G 43 " --> pdb=" O ILE H 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'K' and resid 223 through 225 removed outlier: 4.246A pdb=" N GLY K 223 " --> pdb=" O LYS K 357 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL K 330 " --> pdb=" O LEU K 358 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU K 360 " --> pdb=" O VAL K 330 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE K 332 " --> pdb=" O LEU K 360 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU K 254 " --> pdb=" O TYR K 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 444 through 450 removed outlier: 6.325A pdb=" N LYS K 444 " --> pdb=" O VAL K 645 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG K 647 " --> pdb=" O LYS K 444 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE K 446 " --> pdb=" O ARG K 647 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER K 649 " --> pdb=" O ILE K 446 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET K 448 " --> pdb=" O SER K 649 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N CYS K 615 " --> pdb=" O TYR K 646 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU K 648 " --> pdb=" O CYS K 615 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU K 617 " --> pdb=" O LEU K 648 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N THR K 650 " --> pdb=" O LEU K 617 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU K 544 " --> pdb=" O ILE K 616 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 567 through 570 removed outlier: 6.351A pdb=" N CYS K 568 " --> pdb=" O LEU K 597 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 500 hydrogen bonds defined for protein. 1479 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 255 hydrogen bonds 510 hydrogen bond angles 0 basepair planarities 102 basepair parallelities 238 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1939 1.31 - 1.44: 5445 1.44 - 1.56: 8183 1.56 - 1.69: 576 1.69 - 1.82: 50 Bond restraints: 16193 Sorted by residual: bond pdb=" C1' DT I 134 " pdb=" N1 DT I 134 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.42e+01 bond pdb=" C4 ADP K 802 " pdb=" C5 ADP K 802 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C1' DC I 125 " pdb=" N1 DC I 125 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.93e+01 bond pdb=" C1' DC J 34 " pdb=" N1 DC J 34 " ideal model delta sigma weight residual 1.468 1.541 -0.073 1.40e-02 5.10e+03 2.75e+01 bond pdb=" F1 BEF K 801 " pdb="BE BEF K 801 " ideal model delta sigma weight residual 1.476 1.574 -0.098 2.00e-02 2.50e+03 2.38e+01 ... (remaining 16188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 22436 3.22 - 6.43: 589 6.43 - 9.65: 40 9.65 - 12.87: 11 12.87 - 16.08: 4 Bond angle restraints: 23080 Sorted by residual: angle pdb=" N THR E 107 " pdb=" CA THR E 107 " pdb=" C THR E 107 " ideal model delta sigma weight residual 113.18 102.22 10.96 1.21e+00 6.83e-01 8.21e+01 angle pdb=" N ARG K 293 " pdb=" CA ARG K 293 " pdb=" C ARG K 293 " ideal model delta sigma weight residual 113.19 102.98 10.21 1.19e+00 7.06e-01 7.36e+01 angle pdb=" N LYS K 667 " pdb=" CA LYS K 667 " pdb=" C LYS K 667 " ideal model delta sigma weight residual 111.11 102.42 8.69 1.20e+00 6.94e-01 5.24e+01 angle pdb=" N GLY K 674 " pdb=" CA GLY K 674 " pdb=" C GLY K 674 " ideal model delta sigma weight residual 112.73 104.91 7.82 1.20e+00 6.94e-01 4.25e+01 angle pdb=" O3' DT J 9 " pdb=" C3' DT J 9 " pdb=" C2' DT J 9 " ideal model delta sigma weight residual 109.40 125.48 -16.08 2.50e+00 1.60e-01 4.14e+01 ... (remaining 23075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 7685 35.86 - 71.71: 1276 71.71 - 107.57: 31 107.57 - 143.42: 3 143.42 - 179.28: 5 Dihedral angle restraints: 9000 sinusoidal: 5562 harmonic: 3438 Sorted by residual: dihedral pdb=" CA GLU H 118 " pdb=" C GLU H 118 " pdb=" N ILE H 119 " pdb=" CA ILE H 119 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" C5' ADP K 802 " pdb=" O5' ADP K 802 " pdb=" PA ADP K 802 " pdb=" O2A ADP K 802 " ideal model delta sinusoidal sigma weight residual -60.00 25.83 -85.82 1 2.00e+01 2.50e-03 2.23e+01 dihedral pdb=" CA LEU E 60 " pdb=" C LEU E 60 " pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta harmonic sigma weight residual -180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 8997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 2568 0.179 - 0.358: 42 0.358 - 0.537: 0 0.537 - 0.716: 3 0.716 - 0.895: 2 Chirality restraints: 2615 Sorted by residual: chirality pdb=" C3' DG I 126 " pdb=" C4' DG I 126 " pdb=" O3' DG I 126 " pdb=" C2' DG I 126 " both_signs ideal model delta sigma weight residual False -2.73 -1.84 -0.89 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" C3' DG J 138 " pdb=" C4' DG J 138 " pdb=" O3' DG J 138 " pdb=" C2' DG J 138 " both_signs ideal model delta sigma weight residual False -2.73 -1.90 -0.83 2.00e-01 2.50e+01 1.72e+01 chirality pdb=" C3' DT J 9 " pdb=" C4' DT J 9 " pdb=" O3' DT J 9 " pdb=" C2' DT J 9 " both_signs ideal model delta sigma weight residual False -2.73 -2.05 -0.68 2.00e-01 2.50e+01 1.15e+01 ... (remaining 2612 not shown) Planarity restraints: 1927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR K 550 " 0.020 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C THR K 550 " -0.066 2.00e-02 2.50e+03 pdb=" O THR K 550 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS K 551 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 536 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LEU K 536 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU K 536 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE K 537 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG K 293 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.26e+01 pdb=" C ARG K 293 " -0.061 2.00e-02 2.50e+03 pdb=" O ARG K 293 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS K 294 " 0.020 2.00e-02 2.50e+03 ... (remaining 1924 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2173 2.75 - 3.29: 13988 3.29 - 3.83: 27592 3.83 - 4.36: 34317 4.36 - 4.90: 49664 Nonbonded interactions: 127734 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.216 3.040 nonbonded pdb=" O ASP C 91 " pdb=" OG SER C 95 " model vdw 2.272 3.040 nonbonded pdb=" OD1 ASP K 227 " pdb=" NH1 ARG K 431 " model vdw 2.311 3.120 nonbonded pdb=" NH1 ARG G 30 " pdb=" O THR H 61 " model vdw 2.319 3.120 nonbonded pdb=" OD1 ASN K 368 " pdb=" N SER K 370 " model vdw 2.320 3.120 ... (remaining 127729 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' selection = (chain 'E' and resid 41 through 133) } ncs_group { reference = (chain 'B' and resid 23 through 100) selection = (chain 'F' and resid 23 through 100) } ncs_group { reference = (chain 'C' and resid 18 through 116) selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 61 through 149) } 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: 0.890 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.370 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 14.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 0.009 0.110 16193 Z= 0.652 Angle : 1.204 16.083 23080 Z= 0.854 Chirality : 0.071 0.895 2615 Planarity : 0.007 0.057 1927 Dihedral : 25.841 179.280 6778 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.86 % Allowed : 7.45 % Favored : 91.70 % Rotamer: Outliers : 1.08 % Allowed : 4.63 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.22), residues: 1168 helix: -1.19 (0.18), residues: 698 sheet: -2.75 (0.59), residues: 60 loop : -2.67 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 89 TYR 0.040 0.003 TYR K 329 PHE 0.048 0.003 PHE C 26 TRP 0.038 0.002 TRP K 217 HIS 0.014 0.001 HIS K 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00920 / 0.65 (16193) covalent geometry : angle 1.20448 / 0.85 (23080) hydrogen bonds : bond 0.22158 / 14.71 ( 755) hydrogen bonds : angle 8.38174 / 5.81 ( 1989) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 343 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.6689 (p0) cc_final: 0.6361 (p0) REVERT: C 44 VAL cc_start: 0.8384 (t) cc_final: 0.8107 (t) REVERT: C 96 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8289 (mmtm) REVERT: G 89 ARG cc_start: 0.8384 (mmt-90) cc_final: 0.8148 (mmt180) REVERT: H 62 TYR cc_start: 0.7682 (m-80) cc_final: 0.7482 (m-10) REVERT: H 101 GLU cc_start: 0.6909 (tp30) cc_final: 0.6245 (tp30) REVERT: K 213 LEU cc_start: 0.8634 (tp) cc_final: 0.8412 (mt) REVERT: K 304 PHE cc_start: 0.5218 (t80) cc_final: 0.4917 (t80) REVERT: K 367 ASN cc_start: 0.8641 (t0) cc_final: 0.8282 (m-40) REVERT: K 371 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7025 (mt-10) REVERT: K 463 LEU cc_start: 0.8292 (tp) cc_final: 0.7723 (tp) REVERT: K 468 LEU cc_start: 0.5944 (tp) cc_final: 0.5738 (tt) REVERT: K 553 LEU cc_start: 0.6646 (mt) cc_final: 0.6382 (mt) outliers start: 11 outliers final: 0 residues processed: 350 average time/residue: 0.1478 time to fit residues: 70.0129 Evaluate side-chains 197 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN E 68 GLN G 85 GLN K 286 ASN ** K 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.138700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.103394 restraints weight = 42507.689| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.66 r_work: 0.3476 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 16193 Z= 0.200 Angle : 0.801 10.112 23080 Z= 0.451 Chirality : 0.051 0.380 2615 Planarity : 0.006 0.082 1927 Dihedral : 29.655 178.806 4404 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.48 % Favored : 94.35 % Rotamer: Outliers : 2.86 % Allowed : 15.27 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.24), residues: 1168 helix: 0.41 (0.19), residues: 723 sheet: -2.36 (0.62), residues: 60 loop : -2.37 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 293 TYR 0.015 0.002 TYR F 88 PHE 0.022 0.002 PHE B 100 TRP 0.010 0.002 TRP K 212 HIS 0.006 0.001 HIS K 635 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.20 (16193) covalent geometry : angle 0.80116 / 0.45 (23080) hydrogen bonds : bond 0.07392 / 5.04 ( 755) hydrogen bonds : angle 3.97696 / 2.78 ( 1989) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.6797 (p0) cc_final: 0.6439 (p0) REVERT: C 93 GLU cc_start: 0.7725 (pm20) cc_final: 0.7509 (pm20) REVERT: C 96 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8425 (mmtm) REVERT: D 134 HIS cc_start: 0.8391 (m170) cc_final: 0.8065 (m170) REVERT: E 73 GLU cc_start: 0.7419 (tt0) cc_final: 0.7166 (tt0) REVERT: E 133 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6966 (mt-10) REVERT: G 92 GLU cc_start: 0.8264 (tp30) cc_final: 0.8058 (tp30) REVERT: G 109 MET cc_start: 0.7547 (mmp) cc_final: 0.7094 (mpp) REVERT: H 71 LYS cc_start: 0.9203 (tppt) cc_final: 0.8948 (mttp) REVERT: H 87 MET cc_start: 0.7801 (mmm) cc_final: 0.7600 (mmm) REVERT: H 101 GLU cc_start: 0.7535 (tp30) cc_final: 0.6809 (tp30) REVERT: H 111 LYS cc_start: 0.7862 (ttmm) cc_final: 0.7635 (ttmt) REVERT: K 253 TYR cc_start: 0.5751 (t80) cc_final: 0.5483 (t80) REVERT: K 306 ILE cc_start: 0.8187 (mm) cc_final: 0.7587 (mm) REVERT: K 367 ASN cc_start: 0.8715 (t0) cc_final: 0.8407 (m-40) REVERT: K 468 LEU cc_start: 0.6448 (tp) cc_final: 0.6146 (tt) REVERT: K 494 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8068 (mtp180) REVERT: K 621 ASP cc_start: 0.6585 (p0) cc_final: 0.6265 (p0) outliers start: 29 outliers final: 18 residues processed: 238 average time/residue: 0.1248 time to fit residues: 41.3103 Evaluate side-chains 209 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain K residue 276 ILE Chi-restraints excluded: chain K residue 346 LEU Chi-restraints excluded: chain K residue 448 MET Chi-restraints excluded: chain K residue 494 ARG Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 601 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 133 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 84 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 50.0000 chunk 124 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN H 74 HIS K 282 HIS K 336 HIS K 608 ASN ** K 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.121086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.081744 restraints weight = 40293.053| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.52 r_work: 0.3073 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.146 16193 Z= 0.301 Angle : 0.952 15.303 23080 Z= 0.515 Chirality : 0.058 0.363 2615 Planarity : 0.008 0.157 1927 Dihedral : 29.893 178.084 4404 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.59 % Favored : 93.24 % Rotamer: Outliers : 5.02 % Allowed : 15.17 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.24), residues: 1168 helix: 0.37 (0.19), residues: 717 sheet: -2.04 (0.62), residues: 66 loop : -2.18 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 30 TYR 0.077 0.004 TYR K 329 PHE 0.037 0.003 PHE K 266 TRP 0.015 0.002 TRP K 327 HIS 0.008 0.002 HIS K 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.30 (16193) covalent geometry : angle 0.95198 / 0.52 (23080) hydrogen bonds : bond 0.08759 / 5.83 ( 755) hydrogen bonds : angle 4.11299 / 2.89 ( 1989) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8663 (pp20) cc_final: 0.8158 (pm20) REVERT: B 24 ASP cc_start: 0.7127 (p0) cc_final: 0.6559 (p0) REVERT: C 91 ASP cc_start: 0.8275 (t70) cc_final: 0.8002 (t0) REVERT: C 93 GLU cc_start: 0.7934 (pm20) cc_final: 0.7670 (pm20) REVERT: C 96 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8798 (mmtm) REVERT: D 130 GLU cc_start: 0.8015 (tp30) cc_final: 0.7700 (tp30) REVERT: E 53 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8151 (tttt) REVERT: F 84 MET cc_start: 0.8791 (mmm) cc_final: 0.8307 (tmm) REVERT: G 85 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8397 (mm-40) REVERT: H 130 GLU cc_start: 0.8200 (tp30) cc_final: 0.7974 (tp30) REVERT: H 141 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9029 (ttmt) REVERT: K 306 ILE cc_start: 0.8549 (mm) cc_final: 0.7317 (mm) REVERT: K 448 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8128 (mpp) REVERT: K 570 ILE cc_start: 0.7994 (mt) cc_final: 0.7739 (mp) REVERT: K 631 MET cc_start: 0.8593 (mtp) cc_final: 0.8286 (mtm) outliers start: 51 outliers final: 23 residues processed: 249 average time/residue: 0.1229 time to fit residues: 43.1096 Evaluate side-chains 192 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 346 LEU Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 448 MET Chi-restraints excluded: chain K residue 490 VAL Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain K residue 601 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 56 optimal weight: 10.0000 chunk 96 optimal weight: 50.0000 chunk 34 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 118 optimal weight: 0.0570 chunk 90 optimal weight: 20.0000 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 55 GLN K 367 ASN ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 635 HIS ** 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 = 0.3999 r_free = 0.3999 target = 0.122024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.082902 restraints weight = 39829.002| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.54 r_work: 0.3089 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16193 Z= 0.158 Angle : 0.707 9.023 23080 Z= 0.397 Chirality : 0.048 0.558 2615 Planarity : 0.005 0.046 1927 Dihedral : 29.667 178.659 4404 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 2.46 % Allowed : 19.31 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.25), residues: 1168 helix: 1.14 (0.20), residues: 725 sheet: -2.04 (0.60), residues: 67 loop : -1.94 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 292 TYR 0.012 0.001 TYR K 281 PHE 0.015 0.002 PHE K 384 TRP 0.008 0.001 TRP K 622 HIS 0.006 0.001 HIS K 635 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (16193) covalent geometry : angle 0.70721 / 0.40 (23080) hydrogen bonds : bond 0.05908 / 4.04 ( 755) hydrogen bonds : angle 3.53216 / 2.47 ( 1989) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8676 (pp20) cc_final: 0.8170 (pm20) REVERT: B 24 ASP cc_start: 0.7133 (p0) cc_final: 0.6583 (p0) REVERT: C 91 ASP cc_start: 0.8224 (t70) cc_final: 0.7904 (t0) REVERT: C 93 GLU cc_start: 0.7918 (pm20) cc_final: 0.7664 (pm20) REVERT: C 96 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8762 (mmtm) REVERT: E 94 GLU cc_start: 0.8338 (tp30) cc_final: 0.8098 (tp30) REVERT: F 84 MET cc_start: 0.8636 (mmm) cc_final: 0.7873 (mmm) REVERT: F 88 TYR cc_start: 0.9108 (m-10) cc_final: 0.8813 (m-10) REVERT: H 141 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.9036 (ttmt) REVERT: K 448 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7872 (mpp) REVERT: K 466 ASN cc_start: 0.8778 (m-40) cc_final: 0.8421 (p0) REVERT: K 494 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8396 (mtp180) REVERT: K 601 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8295 (mtt180) REVERT: K 621 ASP cc_start: 0.6653 (p0) cc_final: 0.6279 (p0) REVERT: K 631 MET cc_start: 0.8551 (mtp) cc_final: 0.8233 (mtm) outliers start: 25 outliers final: 9 residues processed: 203 average time/residue: 0.1271 time to fit residues: 36.0452 Evaluate side-chains 181 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 448 MET Chi-restraints excluded: chain K residue 494 ARG Chi-restraints excluded: chain K residue 529 LEU Chi-restraints excluded: chain K residue 601 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 9 optimal weight: 0.0470 chunk 57 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 overall best weight: 3.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN E 39 HIS H 134 HIS K 267 ASN K 367 ASN ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.118162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.078501 restraints weight = 39447.295| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.51 r_work: 0.2994 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 16193 Z= 0.213 Angle : 0.733 9.673 23080 Z= 0.407 Chirality : 0.049 0.437 2615 Planarity : 0.005 0.068 1927 Dihedral : 29.564 178.100 4404 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.82 % Favored : 94.09 % Rotamer: Outliers : 2.66 % Allowed : 19.31 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1168 helix: 1.43 (0.20), residues: 723 sheet: -2.33 (0.60), residues: 61 loop : -1.82 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 72 TYR 0.012 0.002 TYR A 99 PHE 0.016 0.002 PHE K 384 TRP 0.011 0.002 TRP K 622 HIS 0.006 0.002 HIS K 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (16193) covalent geometry : angle 0.73275 / 0.41 (23080) hydrogen bonds : bond 0.06593 / 4.44 ( 755) hydrogen bonds : angle 3.54028 / 2.47 ( 1989) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9218 (tttt) cc_final: 0.8933 (tttp) REVERT: A 59 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: B 24 ASP cc_start: 0.7318 (p0) cc_final: 0.6778 (p0) REVERT: C 91 ASP cc_start: 0.8205 (t70) cc_final: 0.7855 (t0) REVERT: C 93 GLU cc_start: 0.7953 (pm20) cc_final: 0.7716 (pm20) REVERT: C 96 LYS cc_start: 0.9122 (mtmt) cc_final: 0.8821 (mmtm) REVERT: D 101 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8516 (mm-30) REVERT: D 130 GLU cc_start: 0.7618 (tp30) cc_final: 0.7326 (tp30) REVERT: D 145 LYS cc_start: 0.8846 (tttm) cc_final: 0.8371 (ttpp) REVERT: E 53 LYS cc_start: 0.8644 (tmtt) cc_final: 0.8382 (tttt) REVERT: E 94 GLU cc_start: 0.8524 (tp30) cc_final: 0.8171 (tp30) REVERT: F 84 MET cc_start: 0.8823 (mmm) cc_final: 0.8191 (mmm) REVERT: K 448 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7837 (mpp) REVERT: K 494 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8347 (mtp180) REVERT: K 601 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8242 (mtt180) REVERT: K 621 ASP cc_start: 0.6755 (p0) cc_final: 0.6479 (p0) REVERT: K 631 MET cc_start: 0.8576 (mtp) cc_final: 0.8261 (mtm) outliers start: 27 outliers final: 16 residues processed: 205 average time/residue: 0.1400 time to fit residues: 39.4528 Evaluate side-chains 192 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain K residue 448 MET Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 494 ARG Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 601 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 11 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 81 optimal weight: 40.0000 chunk 17 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 ASN K 367 ASN ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 504 GLN K 635 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.118936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.080036 restraints weight = 39468.837| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.63 r_work: 0.3008 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.7338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16193 Z= 0.144 Angle : 0.652 8.493 23080 Z= 0.370 Chirality : 0.045 0.304 2615 Planarity : 0.004 0.048 1927 Dihedral : 29.428 178.122 4404 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 2.07 % Allowed : 21.87 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.26), residues: 1168 helix: 1.79 (0.20), residues: 724 sheet: -1.84 (0.61), residues: 66 loop : -1.72 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG K 320 TYR 0.018 0.001 TYR F 98 PHE 0.016 0.001 PHE D 90 TRP 0.009 0.001 TRP K 622 HIS 0.007 0.001 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (16193) covalent geometry : angle 0.65212 / 0.37 (23080) hydrogen bonds : bond 0.05304 / 3.65 ( 755) hydrogen bonds : angle 3.26665 / 2.30 ( 1989) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: B 24 ASP cc_start: 0.7342 (p0) cc_final: 0.6775 (p0) REVERT: C 93 GLU cc_start: 0.8029 (pm20) cc_final: 0.7664 (pm20) REVERT: C 96 LYS cc_start: 0.9117 (mtmt) cc_final: 0.8812 (mmtm) REVERT: D 101 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8502 (mm-30) REVERT: D 130 GLU cc_start: 0.7332 (tp30) cc_final: 0.6963 (tp30) REVERT: D 145 LYS cc_start: 0.8848 (tttm) cc_final: 0.8563 (ttpp) REVERT: E 53 LYS cc_start: 0.8592 (tmtt) cc_final: 0.8338 (tttt) REVERT: F 84 MET cc_start: 0.8761 (mmm) cc_final: 0.8200 (mmm) REVERT: K 448 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7839 (mpp) REVERT: K 466 ASN cc_start: 0.8782 (m-40) cc_final: 0.8531 (p0) REVERT: K 494 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8407 (mtp180) REVERT: K 601 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8179 (mtt180) outliers start: 21 outliers final: 15 residues processed: 190 average time/residue: 0.1472 time to fit residues: 38.3764 Evaluate side-chains 184 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 448 MET Chi-restraints excluded: chain K residue 494 ARG Chi-restraints excluded: chain K residue 529 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 601 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 67 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 133 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 71 optimal weight: 30.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 ASN ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.116798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.077361 restraints weight = 38973.043| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.48 r_work: 0.2974 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.7776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 16193 Z= 0.183 Angle : 0.688 9.117 23080 Z= 0.384 Chirality : 0.046 0.287 2615 Planarity : 0.005 0.065 1927 Dihedral : 29.386 178.086 4404 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.35 % Rotamer: Outliers : 2.36 % Allowed : 21.38 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1168 helix: 1.81 (0.20), residues: 727 sheet: -1.93 (0.64), residues: 61 loop : -1.66 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 72 TYR 0.033 0.002 TYR H 108 PHE 0.019 0.002 PHE H 90 TRP 0.011 0.001 TRP K 622 HIS 0.005 0.001 HIS K 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (16193) covalent geometry : angle 0.68787 / 0.38 (23080) hydrogen bonds : bond 0.06007 / 4.06 ( 755) hydrogen bonds : angle 3.34552 / 2.34 ( 1989) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: C 25 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8391 (mp10) REVERT: C 91 ASP cc_start: 0.7883 (t0) cc_final: 0.7393 (t0) REVERT: C 93 GLU cc_start: 0.7883 (pm20) cc_final: 0.7604 (pm20) REVERT: C 96 LYS cc_start: 0.9140 (mtmt) cc_final: 0.8883 (mttm) REVERT: D 101 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8442 (mm-30) REVERT: D 130 GLU cc_start: 0.7500 (tp30) cc_final: 0.7109 (tp30) REVERT: D 145 LYS cc_start: 0.8851 (tttm) cc_final: 0.8575 (ttpp) REVERT: E 53 LYS cc_start: 0.8628 (tmtt) cc_final: 0.8343 (tttt) REVERT: F 84 MET cc_start: 0.8844 (mmm) cc_final: 0.8285 (mmm) REVERT: G 39 LYS cc_start: 0.9409 (mmmm) cc_final: 0.9160 (mtmt) REVERT: K 466 ASN cc_start: 0.8665 (m-40) cc_final: 0.8428 (p0) REVERT: K 601 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8196 (mtt180) outliers start: 24 outliers final: 19 residues processed: 184 average time/residue: 0.1475 time to fit residues: 37.0640 Evaluate side-chains 180 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 529 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 601 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 67 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 113 optimal weight: 0.0570 chunk 112 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 ASN K 377 ASN ** K 456 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 = 0.3921 r_free = 0.3921 target = 0.116900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.077640 restraints weight = 39457.677| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.49 r_work: 0.2987 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.7993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16193 Z= 0.151 Angle : 0.653 9.509 23080 Z= 0.368 Chirality : 0.044 0.331 2615 Planarity : 0.004 0.042 1927 Dihedral : 29.311 177.993 4404 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.22 % Favored : 94.69 % Rotamer: Outliers : 2.17 % Allowed : 22.17 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.26), residues: 1168 helix: 1.97 (0.20), residues: 727 sheet: -1.58 (0.62), residues: 66 loop : -1.62 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 72 TYR 0.020 0.002 TYR H 108 PHE 0.015 0.001 PHE D 90 TRP 0.010 0.001 TRP K 622 HIS 0.005 0.001 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (16193) covalent geometry : angle 0.65271 / 0.37 (23080) hydrogen bonds : bond 0.05236 / 3.60 ( 755) hydrogen bonds : angle 3.22568 / 2.27 ( 1989) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8100 (pm20) REVERT: B 24 ASP cc_start: 0.7242 (p0) cc_final: 0.6713 (p0) REVERT: B 88 TYR cc_start: 0.9276 (m-10) cc_final: 0.9067 (m-10) REVERT: C 25 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8416 (mp10) REVERT: C 91 ASP cc_start: 0.7899 (t0) cc_final: 0.7397 (t0) REVERT: C 96 LYS cc_start: 0.9143 (mtmt) cc_final: 0.8893 (mttm) REVERT: D 101 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8449 (mm-30) REVERT: D 145 LYS cc_start: 0.8853 (tttm) cc_final: 0.8604 (ttpp) REVERT: E 53 LYS cc_start: 0.8705 (tmtt) cc_final: 0.8479 (tttt) REVERT: F 84 MET cc_start: 0.8745 (mmm) cc_final: 0.8249 (mmm) REVERT: G 39 LYS cc_start: 0.9427 (mmmm) cc_final: 0.9136 (mtmt) REVERT: H 141 LYS cc_start: 0.9312 (tttp) cc_final: 0.9083 (ttmt) REVERT: K 601 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8228 (mtt180) outliers start: 22 outliers final: 19 residues processed: 179 average time/residue: 0.1396 time to fit residues: 34.5023 Evaluate side-chains 177 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 529 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 601 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 130 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 70 optimal weight: 40.0000 chunk 136 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 324 HIS K 351 HIS ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 548 GLN K 644 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.113596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.074059 restraints weight = 39051.119| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.45 r_work: 0.2911 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.8415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 16193 Z= 0.259 Angle : 0.749 10.786 23080 Z= 0.411 Chirality : 0.049 0.351 2615 Planarity : 0.005 0.045 1927 Dihedral : 29.367 177.038 4404 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.75 % Rotamer: Outliers : 2.17 % Allowed : 22.66 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.26), residues: 1168 helix: 1.71 (0.20), residues: 726 sheet: -1.67 (0.64), residues: 66 loop : -1.62 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 52 TYR 0.031 0.002 TYR H 108 PHE 0.037 0.002 PHE C 34 TRP 0.013 0.002 TRP K 373 HIS 0.006 0.002 HIS K 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.26 (16193) covalent geometry : angle 0.74856 / 0.41 (23080) hydrogen bonds : bond 0.06787 / 4.55 ( 755) hydrogen bonds : angle 3.48663 / 2.45 ( 1989) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8083 (pm20) REVERT: B 88 TYR cc_start: 0.9303 (m-10) cc_final: 0.8951 (m-10) REVERT: C 25 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8436 (mp10) REVERT: C 96 LYS cc_start: 0.9192 (mtmt) cc_final: 0.8952 (mttm) REVERT: D 111 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7585 (mtpt) REVERT: D 145 LYS cc_start: 0.8930 (tttm) cc_final: 0.8687 (ttpp) REVERT: E 53 LYS cc_start: 0.8751 (tmtt) cc_final: 0.8518 (tttt) REVERT: E 94 GLU cc_start: 0.8632 (tp30) cc_final: 0.8147 (tp30) REVERT: F 84 MET cc_start: 0.8937 (mmm) cc_final: 0.8345 (mmm) REVERT: G 39 LYS cc_start: 0.9453 (mmmm) cc_final: 0.9177 (mtmt) REVERT: H 141 LYS cc_start: 0.9320 (tttp) cc_final: 0.9081 (ttmt) REVERT: K 601 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8265 (mtt180) outliers start: 22 outliers final: 16 residues processed: 183 average time/residue: 0.1419 time to fit residues: 35.5647 Evaluate side-chains 175 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain K residue 529 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 601 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 3 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 135 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 351 HIS ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 462 HIS K 471 HIS ** K 492 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 = 0.3837 r_free = 0.3837 target = 0.111582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.072006 restraints weight = 39540.731| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.50 r_work: 0.2867 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.9173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16193 Z= 0.279 Angle : 0.804 12.055 23080 Z= 0.438 Chirality : 0.050 0.315 2615 Planarity : 0.006 0.066 1927 Dihedral : 29.459 176.196 4404 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 2.27 % Allowed : 22.66 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.25), residues: 1168 helix: 1.38 (0.20), residues: 724 sheet: -1.84 (0.66), residues: 68 loop : -1.75 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 107 TYR 0.030 0.003 TYR B 88 PHE 0.024 0.002 PHE D 90 TRP 0.017 0.003 TRP K 549 HIS 0.007 0.002 HIS K 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.28 (16193) covalent geometry : angle 0.80378 / 0.44 (23080) hydrogen bonds : bond 0.06874 / 4.65 ( 755) hydrogen bonds : angle 3.63316 / 2.57 ( 1989) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: C 91 ASP cc_start: 0.7543 (t0) cc_final: 0.7309 (t70) REVERT: C 96 LYS cc_start: 0.9250 (mtmt) cc_final: 0.8991 (mttm) REVERT: D 104 LYS cc_start: 0.8985 (tttt) cc_final: 0.8676 (tttm) REVERT: D 111 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7814 (mtpt) REVERT: D 145 LYS cc_start: 0.8969 (tttm) cc_final: 0.8645 (ttpp) REVERT: E 53 LYS cc_start: 0.8741 (tmtt) cc_final: 0.8523 (tttt) REVERT: E 94 GLU cc_start: 0.8690 (tp30) cc_final: 0.8182 (tp30) REVERT: F 84 MET cc_start: 0.8860 (mmm) cc_final: 0.8333 (mmm) REVERT: G 39 LYS cc_start: 0.9466 (mmmm) cc_final: 0.9192 (mtmt) REVERT: H 104 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8241 (ttpt) REVERT: H 111 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8385 (mtpt) REVERT: H 141 LYS cc_start: 0.9279 (tttp) cc_final: 0.9057 (ttmt) outliers start: 23 outliers final: 17 residues processed: 180 average time/residue: 0.1303 time to fit residues: 32.1137 Evaluate side-chains 171 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain K residue 529 LEU Chi-restraints excluded: chain K residue 570 ILE Chi-restraints excluded: chain K residue 601 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 77 optimal weight: 10.9990 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 122 optimal weight: 0.0570 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 HIS ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 644 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.113855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.074828 restraints weight = 39408.297| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.52 r_work: 0.2925 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.9219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16193 Z= 0.148 Angle : 0.678 10.466 23080 Z= 0.380 Chirality : 0.044 0.284 2615 Planarity : 0.004 0.048 1927 Dihedral : 29.259 178.526 4404 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.48 % Favored : 94.43 % Rotamer: Outliers : 1.67 % Allowed : 23.94 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1168 helix: 1.77 (0.20), residues: 724 sheet: -1.53 (0.67), residues: 67 loop : -1.60 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 72 TYR 0.029 0.002 TYR B 88 PHE 0.016 0.001 PHE C 34 TRP 0.010 0.001 TRP K 373 HIS 0.004 0.001 HIS K 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (16193) covalent geometry : angle 0.67822 / 0.38 (23080) hydrogen bonds : bond 0.05374 / 3.72 ( 755) hydrogen bonds : angle 3.28111 / 2.32 ( 1989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3262.52 seconds wall clock time: 56 minutes 23.59 seconds (3383.59 seconds total)