Starting phenix.real_space_refine on Sat Aug 23 21:46:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh9_37535/08_2025/8wh9_37535.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh9_37535/08_2025/8wh9_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_2025/8wh9_37535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh9_37535/08_2025/8wh9_37535.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wh9_37535/08_2025/8wh9_37535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh9_37535/08_2025/8wh9_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-2.0-5787/lib/python3.9/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: 4.12, per 1000 atoms: 0.27 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: 1.45 Conformation dependent library (CDL) restraints added in 523.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 2.26 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: 3.61 Time building geometry restraints manager: 1.90 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=" 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=" 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 bond pdb=" C ASP K 454 " pdb=" O ASP K 454 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.16e-02 7.43e+03 1.87e+01 bond pdb=" N LEU K 536 " pdb=" CA LEU K 536 " ideal model delta sigma weight residual 1.456 1.511 -0.055 1.33e-02 5.65e+03 1.73e+01 bond pdb=" C5 ADP K 802 " pdb=" C6 ADP K 802 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 16188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 22183 2.80 - 5.59: 804 5.59 - 8.39: 71 8.39 - 11.19: 15 11.19 - 13.98: 7 Bond angle restraints: 23080 Sorted by residual: angle pdb=" O3' DT J 9 " pdb=" C3' DT J 9 " pdb=" C2' DT J 9 " ideal model delta sigma weight residual 111.50 125.48 -13.98 1.50e+00 4.44e-01 8.69e+01 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=" O3' DG I 126 " pdb=" C3' DG I 126 " pdb=" C2' DG I 126 " ideal model delta sigma weight residual 111.50 124.52 -13.02 1.50e+00 4.44e-01 7.54e+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=" O3' DG J 97 " pdb=" C3' DG J 97 " pdb=" C2' DG J 97 " ideal model delta sigma weight residual 111.50 124.29 -12.79 1.50e+00 4.44e-01 7.27e+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 - 0.165: 2555 0.165 - 0.330: 55 0.330 - 0.495: 0 0.495 - 0.660: 3 0.660 - 0.825: 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 -2.66 -1.84 -0.82 2.00e-01 2.50e+01 1.70e+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 -2.66 -1.90 -0.76 2.00e-01 2.50e+01 1.44e+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 -2.66 -2.05 -0.61 2.00e-01 2.50e+01 9.27e+00 ... (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: 1.100 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.420 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 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= 0.532 Angle : 1.185 13.983 23080 Z= 0.787 Chirality : 0.066 0.825 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 aren 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 covalent geometry : bond 0.00897 (16193) covalent geometry : angle 1.18513 (23080) hydrogen bonds : bond 0.22158 ( 755) hydrogen bonds : angle 8.38174 ( 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 : 0.468 Fit side-chains revert: symmetry clash 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: 0.8149 (mmt180) REVERT: H 101 GLU cc_start: 0.6909 (tp30) cc_final: 0.6246 (tp30) REVERT: K 213 LEU cc_start: 0.8634 (tp) cc_final: 0.8413 (mt) REVERT: K 304 PHE cc_start: 0.5218 (t80) cc_final: 0.4918 (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: 0.7024 (mt-10) REVERT: K 463 LEU cc_start: 0.8292 (tp) cc_final: 0.7725 (tp) REVERT: K 468 LEU cc_start: 0.5944 (tp) cc_final: 0.5740 (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: 0.1889 time to fit residues: 87.8435 Evaluate side-chains 198 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 68 GLN K 267 ASN K 286 ASN K 336 HIS ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 548 GLN ** K 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.131731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.095096 restraints weight = 41452.580| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.59 r_work: 0.3324 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16193 Z= 0.191 Angle : 0.705 8.300 23080 Z= 0.397 Chirality : 0.041 0.202 2615 Planarity : 0.005 0.057 1927 Dihedral : 29.501 179.667 4404 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.97 % Favored : 94.86 % Rotamer: Outliers : 2.66 % Allowed : 13.89 % Favored : 83.45 % 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 aren not related in a simple way. whole: -0.72 (0.24), residues: 1168 helix: 0.61 (0.19), residues: 724 sheet: -2.46 (0.59), residues: 60 loop : -2.23 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 129 TYR 0.009 0.002 TYR K 281 PHE 0.028 0.002 PHE K 240 TRP 0.010 0.002 TRP K 212 HIS 0.004 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00414 (16193) covalent geometry : angle 0.70509 (23080) hydrogen bonds : bond 0.05699 ( 755) hydrogen bonds : angle 3.55190 ( 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 256 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8129 (tt0) cc_final: 0.7405 (tt0) REVERT: A 123 ASP cc_start: 0.8567 (m-30) cc_final: 0.8244 (m-30) REVERT: B 24 ASP cc_start: 0.6925 (p0) cc_final: 0.6521 (p0) REVERT: B 74 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8249 (tt0) REVERT: C 34 PHE cc_start: 0.8414 (m-10) cc_final: 0.8074 (m-10) REVERT: C 96 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8623 (mmtm) REVERT: F 24 ASP cc_start: 0.7223 (p0) cc_final: 0.6819 (p0) REVERT: F 53 GLU cc_start: 0.8840 (tp30) cc_final: 0.8515 (tp30) REVERT: F 84 MET cc_start: 0.7655 (mmm) cc_final: 0.7406 (mmm) REVERT: G 33 ARG cc_start: 0.8648 (ttp-170) cc_final: 0.8433 (ttm170) REVERT: G 93 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8237 (mm-30) REVERT: G 96 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8826 (ttpt) REVERT: H 100 SER cc_start: 0.8514 (m) cc_final: 0.8293 (m) REVERT: H 101 GLU cc_start: 0.7673 (tp30) cc_final: 0.7205 (tp30) REVERT: K 229 MET cc_start: 0.7839 (ptm) cc_final: 0.7456 (ptm) REVERT: K 299 THR cc_start: 0.7231 (m) cc_final: 0.6882 (m) REVERT: K 346 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7893 (mt) REVERT: K 466 ASN cc_start: 0.8786 (m-40) cc_final: 0.8454 (p0) REVERT: K 494 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8113 (mtp180) REVERT: K 621 ASP cc_start: 0.6299 (p0) cc_final: 0.6093 (p0) REVERT: K 623 ASN cc_start: 0.8642 (t0) cc_final: 0.7854 (t0) REVERT: K 631 MET cc_start: 0.8535 (mtp) cc_final: 0.8236 (mtm) outliers start: 27 outliers final: 13 residues processed: 246 average time/residue: 0.1560 time to fit residues: 52.8783 Evaluate side-chains 199 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 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 137 SER Chi-restraints excluded: chain H residue 143 VAL 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 494 ARG Chi-restraints excluded: chain K residue 599 SER 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: 20.0000 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 124 optimal weight: 0.0770 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 55 GLN G 85 GLN H 74 HIS H 134 HIS K 277 ASN ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 496 ASN K 629 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.125352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.087116 restraints weight = 41025.900| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.59 r_work: 0.3182 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16193 Z= 0.170 Angle : 0.621 7.640 23080 Z= 0.354 Chirality : 0.037 0.143 2615 Planarity : 0.004 0.048 1927 Dihedral : 29.166 178.214 4404 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 2.86 % Allowed : 15.96 % Favored : 81.18 % 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 aren not related in a simple way. whole: 0.35 (0.26), residues: 1168 helix: 1.35 (0.20), residues: 730 sheet: -1.44 (0.69), residues: 54 loop : -1.72 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 72 TYR 0.024 0.001 TYR K 253 PHE 0.015 0.001 PHE K 384 TRP 0.007 0.001 TRP K 212 HIS 0.005 0.001 HIS K 462 Details of bonding type rmsd covalent geometry : bond 0.00368 (16193) covalent geometry : angle 0.62061 (23080) hydrogen bonds : bond 0.05082 ( 755) hydrogen bonds : angle 3.16778 ( 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 234 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8493 (pp20) cc_final: 0.8061 (pm20) REVERT: A 123 ASP cc_start: 0.8653 (m-30) cc_final: 0.8443 (m-30) REVERT: B 24 ASP cc_start: 0.7151 (p0) cc_final: 0.6631 (p0) REVERT: C 93 GLU cc_start: 0.7753 (pm20) cc_final: 0.7523 (pm20) REVERT: C 96 LYS cc_start: 0.9033 (mtmt) cc_final: 0.8683 (mmtm) REVERT: E 73 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8455 (tm-30) REVERT: F 84 MET cc_start: 0.8292 (mmm) cc_final: 0.7703 (mmm) REVERT: G 93 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8312 (mm-30) REVERT: G 109 MET cc_start: 0.7184 (mmp) cc_final: 0.6918 (mmm) REVERT: H 111 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7727 (tttt) REVERT: H 130 GLU cc_start: 0.8310 (tp30) cc_final: 0.8003 (tp30) REVERT: H 141 LYS cc_start: 0.9268 (tttp) cc_final: 0.9022 (ttmt) REVERT: K 329 TYR cc_start: 0.6734 (OUTLIER) cc_final: 0.6486 (m-10) REVERT: K 359 LEU cc_start: 0.7598 (mt) cc_final: 0.7371 (mp) REVERT: K 448 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7963 (mpp) REVERT: K 466 ASN cc_start: 0.8606 (m-40) cc_final: 0.8333 (p0) REVERT: K 570 ILE cc_start: 0.7494 (mt) cc_final: 0.7138 (mp) REVERT: K 631 MET cc_start: 0.8398 (mtp) cc_final: 0.8059 (mtm) outliers start: 29 outliers final: 18 residues processed: 219 average time/residue: 0.1564 time to fit residues: 47.2532 Evaluate side-chains 187 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain F residue 73 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 137 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 354 MET Chi-restraints excluded: chain K residue 448 MET Chi-restraints excluded: chain K residue 490 VAL Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 617 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 56 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 GLN G 85 GLN K 236 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.122980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084756 restraints weight = 41060.941| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.62 r_work: 0.3125 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.6927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16193 Z= 0.155 Angle : 0.599 7.115 23080 Z= 0.340 Chirality : 0.036 0.151 2615 Planarity : 0.004 0.056 1927 Dihedral : 28.964 177.130 4404 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.03 % Rotamer: Outliers : 2.27 % Allowed : 17.24 % Favored : 80.49 % 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 aren not related in a simple way. whole: 0.75 (0.26), residues: 1168 helix: 1.72 (0.20), residues: 728 sheet: -1.53 (0.66), residues: 54 loop : -1.62 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 89 TYR 0.017 0.001 TYR K 281 PHE 0.018 0.001 PHE K 384 TRP 0.009 0.001 TRP K 373 HIS 0.004 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00335 (16193) covalent geometry : angle 0.59890 (23080) hydrogen bonds : bond 0.04573 ( 755) hydrogen bonds : angle 2.99113 ( 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 210 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8467 (pp20) cc_final: 0.8128 (pm20) REVERT: A 120 MET cc_start: 0.8648 (mtm) cc_final: 0.8325 (mtt) REVERT: B 24 ASP cc_start: 0.7315 (p0) cc_final: 0.6820 (p0) REVERT: C 25 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8772 (mm-40) REVERT: C 33 ARG cc_start: 0.8294 (ttp-170) cc_final: 0.7739 (ttm170) REVERT: C 93 GLU cc_start: 0.7595 (pm20) cc_final: 0.7386 (pm20) REVERT: C 96 LYS cc_start: 0.9041 (mtmt) cc_final: 0.8759 (mttm) REVERT: D 130 GLU cc_start: 0.7251 (tp30) cc_final: 0.6944 (tp30) REVERT: E 73 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8831 (tm-30) REVERT: F 84 MET cc_start: 0.8411 (mmm) cc_final: 0.7878 (mmm) REVERT: G 89 ARG cc_start: 0.8825 (mmp80) cc_final: 0.8482 (mmt180) REVERT: G 91 ASP cc_start: 0.8460 (t0) cc_final: 0.8255 (t0) REVERT: H 60 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7702 (mm-30) REVERT: H 111 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7994 (tptt) REVERT: H 130 GLU cc_start: 0.8141 (tp30) cc_final: 0.7893 (tp30) REVERT: K 217 TRP cc_start: 0.7625 (OUTLIER) cc_final: 0.6227 (t-100) REVERT: K 229 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7187 (ptm) REVERT: K 329 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.4952 (m-10) REVERT: K 359 LEU cc_start: 0.7657 (mt) cc_final: 0.7409 (mp) outliers start: 23 outliers final: 9 residues processed: 199 average time/residue: 0.1662 time to fit residues: 45.5752 Evaluate side-chains 174 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain K residue 217 TRP Chi-restraints excluded: chain K residue 229 MET Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 669 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 9 optimal weight: 0.0670 chunk 57 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 122 optimal weight: 0.0470 chunk 99 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.9618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.121164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.082835 restraints weight = 40800.487| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.59 r_work: 0.3096 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.7710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16193 Z= 0.147 Angle : 0.588 8.159 23080 Z= 0.331 Chirality : 0.036 0.175 2615 Planarity : 0.004 0.045 1927 Dihedral : 28.917 178.457 4404 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 2.07 % Allowed : 17.44 % Favored : 80.49 % 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 aren not related in a simple way. whole: 1.08 (0.26), residues: 1168 helix: 1.92 (0.20), residues: 739 sheet: -1.49 (0.64), residues: 54 loop : -1.47 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 494 TYR 0.012 0.001 TYR D 65 PHE 0.011 0.001 PHE K 384 TRP 0.011 0.001 TRP K 622 HIS 0.004 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00318 (16193) covalent geometry : angle 0.58759 (23080) hydrogen bonds : bond 0.04371 ( 755) hydrogen bonds : angle 2.94008 ( 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 190 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7197 (p0) cc_final: 0.6654 (p0) REVERT: C 25 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8885 (mm-40) REVERT: C 91 ASP cc_start: 0.7912 (t0) cc_final: 0.7396 (t0) REVERT: C 93 GLU cc_start: 0.7755 (pm20) cc_final: 0.7531 (pm20) REVERT: C 96 LYS cc_start: 0.9062 (mtmt) cc_final: 0.8774 (mttm) REVERT: E 52 ARG cc_start: 0.8675 (ttm110) cc_final: 0.8108 (ptp90) REVERT: E 73 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8793 (tm-30) REVERT: F 84 MET cc_start: 0.8574 (mmm) cc_final: 0.8057 (mmm) REVERT: H 130 GLU cc_start: 0.8114 (tp30) cc_final: 0.7843 (tp30) REVERT: K 217 TRP cc_start: 0.7686 (OUTLIER) cc_final: 0.6175 (t-100) REVERT: K 229 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7189 (ptm) REVERT: K 329 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.4868 (m-10) REVERT: K 445 GLU cc_start: 0.4917 (pm20) cc_final: 0.4673 (pm20) outliers start: 21 outliers final: 15 residues processed: 184 average time/residue: 0.1801 time to fit residues: 45.3015 Evaluate side-chains 169 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 80 VAL 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 H residue 144 THR Chi-restraints excluded: chain K residue 217 TRP Chi-restraints excluded: chain K residue 229 MET Chi-restraints excluded: chain K residue 306 ILE Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 354 MET Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 570 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 11 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 124 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS K 548 GLN K 629 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.115681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.077168 restraints weight = 39941.645| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.61 r_work: 0.2955 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.8651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16193 Z= 0.198 Angle : 0.632 9.257 23080 Z= 0.354 Chirality : 0.037 0.193 2615 Planarity : 0.004 0.045 1927 Dihedral : 28.894 177.499 4404 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 2.66 % Allowed : 18.52 % Favored : 78.82 % 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 aren not related in a simple way. whole: 1.11 (0.26), residues: 1168 helix: 1.99 (0.20), residues: 734 sheet: -1.29 (0.62), residues: 64 loop : -1.51 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 494 TYR 0.029 0.002 TYR H 108 PHE 0.011 0.001 PHE K 384 TRP 0.012 0.001 TRP K 622 HIS 0.004 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00445 (16193) covalent geometry : angle 0.63157 (23080) hydrogen bonds : bond 0.05475 ( 755) hydrogen bonds : angle 3.09937 ( 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 192 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.4765 (mpt180) cc_final: 0.4553 (mpt180) REVERT: C 25 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8923 (mm-40) REVERT: C 96 LYS cc_start: 0.9159 (mtmt) cc_final: 0.8893 (mttm) REVERT: D 130 GLU cc_start: 0.7612 (tp30) cc_final: 0.7365 (tp30) REVERT: E 52 ARG cc_start: 0.8665 (ttm110) cc_final: 0.8128 (ptp90) REVERT: E 73 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8897 (tm-30) REVERT: E 105 GLU cc_start: 0.8999 (tt0) cc_final: 0.8782 (mt-10) REVERT: F 84 MET cc_start: 0.8852 (mmm) cc_final: 0.8563 (mmm) REVERT: G 39 LYS cc_start: 0.9442 (mmmm) cc_final: 0.9153 (mtmt) REVERT: G 85 GLN cc_start: 0.9149 (tp40) cc_final: 0.8850 (tm-30) REVERT: K 217 TRP cc_start: 0.7718 (OUTLIER) cc_final: 0.6162 (t-100) REVERT: K 329 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.5385 (m-10) REVERT: K 448 MET cc_start: 0.8115 (mpp) cc_final: 0.7822 (mpp) REVERT: K 631 MET cc_start: 0.8535 (mtp) cc_final: 0.8148 (mtm) outliers start: 27 outliers final: 14 residues processed: 185 average time/residue: 0.1772 time to fit residues: 44.7039 Evaluate side-chains 167 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 80 VAL 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 H residue 144 THR Chi-restraints excluded: chain K residue 217 TRP Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 570 ILE 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: 10.0000 chunk 113 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN ** K 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.114562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.075707 restraints weight = 39841.927| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.51 r_work: 0.2959 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.9132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16193 Z= 0.196 Angle : 0.618 9.523 23080 Z= 0.349 Chirality : 0.037 0.169 2615 Planarity : 0.004 0.060 1927 Dihedral : 28.902 178.525 4404 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.74 % Favored : 94.18 % Rotamer: Outliers : 2.56 % Allowed : 19.21 % 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 aren not related in a simple way. whole: 1.18 (0.26), residues: 1168 helix: 2.00 (0.20), residues: 737 sheet: -1.21 (0.64), residues: 66 loop : -1.43 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 320 TYR 0.024 0.002 TYR H 108 PHE 0.011 0.001 PHE K 384 TRP 0.010 0.002 TRP K 622 HIS 0.004 0.001 HIS K 541 Details of bonding type rmsd covalent geometry : bond 0.00441 (16193) covalent geometry : angle 0.61813 (23080) hydrogen bonds : bond 0.05151 ( 755) hydrogen bonds : angle 3.03931 ( 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 177 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.4885 (mpt180) cc_final: 0.4641 (mpt180) REVERT: B 88 TYR cc_start: 0.9158 (m-10) cc_final: 0.8843 (m-10) REVERT: C 96 LYS cc_start: 0.9164 (mtmt) cc_final: 0.8915 (mttm) REVERT: E 52 ARG cc_start: 0.8625 (ttm110) cc_final: 0.8376 (ptp-110) REVERT: E 73 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8872 (tm-30) REVERT: F 84 MET cc_start: 0.8854 (mmm) cc_final: 0.8581 (mmm) REVERT: G 39 LYS cc_start: 0.9458 (mmmm) cc_final: 0.9185 (mtmt) REVERT: K 217 TRP cc_start: 0.7534 (OUTLIER) cc_final: 0.6427 (t-100) REVERT: K 448 MET cc_start: 0.8236 (mpp) cc_final: 0.7937 (mpp) REVERT: K 631 MET cc_start: 0.8566 (mtp) cc_final: 0.8176 (mtm) outliers start: 26 outliers final: 19 residues processed: 172 average time/residue: 0.1745 time to fit residues: 41.1997 Evaluate side-chains 156 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 70 VAL 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 115 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain K residue 217 TRP Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 570 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 67 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 66 optimal weight: 0.0060 chunk 52 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN ** K 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.117195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.079031 restraints weight = 40601.186| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.55 r_work: 0.3028 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.9368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16193 Z= 0.141 Angle : 0.582 7.257 23080 Z= 0.328 Chirality : 0.035 0.157 2615 Planarity : 0.004 0.048 1927 Dihedral : 28.696 179.631 4404 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 1.77 % Allowed : 19.90 % Favored : 78.33 % 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 aren not related in a simple way. whole: 1.44 (0.26), residues: 1168 helix: 2.22 (0.20), residues: 738 sheet: -1.01 (0.64), residues: 64 loop : -1.41 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 320 TYR 0.024 0.001 TYR H 108 PHE 0.023 0.001 PHE K 384 TRP 0.009 0.001 TRP K 212 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00305 (16193) covalent geometry : angle 0.58241 (23080) hydrogen bonds : bond 0.04188 ( 755) hydrogen bonds : angle 2.79990 ( 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 181 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.4754 (mpt180) cc_final: 0.4522 (mpt180) REVERT: C 25 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8507 (mp10) REVERT: C 91 ASP cc_start: 0.7635 (t0) cc_final: 0.7382 (t0) REVERT: C 96 LYS cc_start: 0.9144 (mtmt) cc_final: 0.8867 (mttm) REVERT: D 87 MET cc_start: 0.8927 (mmm) cc_final: 0.8716 (mmm) REVERT: E 52 ARG cc_start: 0.8622 (ttm110) cc_final: 0.8386 (ptp-110) REVERT: E 53 LYS cc_start: 0.8619 (tttt) cc_final: 0.8369 (tttm) REVERT: E 73 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8882 (tm-30) REVERT: F 84 MET cc_start: 0.8791 (mmm) cc_final: 0.8541 (mmm) REVERT: G 39 LYS cc_start: 0.9431 (mmmm) cc_final: 0.9175 (mtmt) REVERT: K 217 TRP cc_start: 0.7427 (OUTLIER) cc_final: 0.6331 (t-100) REVERT: K 448 MET cc_start: 0.8325 (mpp) cc_final: 0.8015 (mpp) REVERT: K 512 LEU cc_start: 0.8866 (pt) cc_final: 0.8497 (tp) REVERT: K 554 ASP cc_start: 0.8501 (t0) cc_final: 0.8249 (t0) REVERT: K 632 ASP cc_start: 0.8408 (m-30) cc_final: 0.8011 (m-30) outliers start: 18 outliers final: 13 residues processed: 176 average time/residue: 0.1651 time to fit residues: 40.2188 Evaluate side-chains 157 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain K residue 217 TRP Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 570 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 130 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 141 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** K 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 HIS ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 471 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.112562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.073442 restraints weight = 40011.962| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.53 r_work: 0.2913 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.9686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16193 Z= 0.248 Angle : 0.660 9.789 23080 Z= 0.370 Chirality : 0.039 0.164 2615 Planarity : 0.005 0.061 1927 Dihedral : 28.884 177.827 4404 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.31 % Favored : 94.61 % Rotamer: Outliers : 1.97 % Allowed : 20.99 % Favored : 77.04 % 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 aren not related in a simple way. whole: 1.23 (0.25), residues: 1168 helix: 2.03 (0.20), residues: 736 sheet: -1.10 (0.66), residues: 64 loop : -1.40 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 72 TYR 0.051 0.003 TYR H 108 PHE 0.024 0.002 PHE K 384 TRP 0.013 0.002 TRP K 622 HIS 0.006 0.001 HIS K 541 Details of bonding type rmsd covalent geometry : bond 0.00572 (16193) covalent geometry : angle 0.66020 (23080) hydrogen bonds : bond 0.05774 ( 755) hydrogen bonds : angle 3.17758 ( 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 168 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: C 25 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8515 (mp10) REVERT: C 96 LYS cc_start: 0.9199 (mtmt) cc_final: 0.8951 (mttm) REVERT: E 52 ARG cc_start: 0.8611 (ttm110) cc_final: 0.8374 (ptp-110) REVERT: E 73 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8879 (tm-30) REVERT: F 84 MET cc_start: 0.8888 (mmm) cc_final: 0.8445 (mmm) REVERT: G 39 LYS cc_start: 0.9452 (mmmm) cc_final: 0.9209 (mtmt) REVERT: K 217 TRP cc_start: 0.7492 (OUTLIER) cc_final: 0.6291 (t-100) REVERT: K 448 MET cc_start: 0.8326 (mpp) cc_final: 0.8039 (mpp) REVERT: K 632 ASP cc_start: 0.8510 (m-30) cc_final: 0.8149 (m-30) outliers start: 20 outliers final: 16 residues processed: 164 average time/residue: 0.1764 time to fit residues: 39.9287 Evaluate side-chains 156 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain K residue 217 TRP Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 325 TYR Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 570 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 3 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 105 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.113712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.075271 restraints weight = 40409.313| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.51 r_work: 0.2954 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.9951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16193 Z= 0.181 Angle : 0.613 8.769 23080 Z= 0.344 Chirality : 0.037 0.158 2615 Planarity : 0.004 0.065 1927 Dihedral : 28.693 179.975 4404 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.39 % Favored : 94.52 % Rotamer: Outliers : 1.67 % Allowed : 21.87 % Favored : 76.45 % 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 aren not related in a simple way. whole: 1.32 (0.26), residues: 1168 helix: 2.12 (0.20), residues: 740 sheet: -1.14 (0.66), residues: 64 loop : -1.43 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 72 TYR 0.033 0.002 TYR H 108 PHE 0.018 0.001 PHE D 90 TRP 0.006 0.001 TRP K 212 HIS 0.003 0.001 HIS K 541 Details of bonding type rmsd covalent geometry : bond 0.00411 (16193) covalent geometry : angle 0.61266 (23080) hydrogen bonds : bond 0.04769 ( 755) hydrogen bonds : angle 2.94802 ( 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 170 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.4734 (mpt180) cc_final: 0.4515 (mpt180) REVERT: C 25 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8499 (mp10) REVERT: C 96 LYS cc_start: 0.9193 (mtmt) cc_final: 0.8946 (mttm) REVERT: D 111 LYS cc_start: 0.7989 (mmtm) cc_final: 0.7512 (mtpt) REVERT: E 52 ARG cc_start: 0.8632 (ttm110) cc_final: 0.8192 (mtt90) REVERT: E 53 LYS cc_start: 0.8612 (tttt) cc_final: 0.8335 (tttm) REVERT: E 73 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8875 (tm-30) REVERT: F 84 MET cc_start: 0.8781 (mmm) cc_final: 0.8485 (mmm) REVERT: G 39 LYS cc_start: 0.9414 (mmmm) cc_final: 0.9161 (mtmt) REVERT: K 217 TRP cc_start: 0.7425 (OUTLIER) cc_final: 0.6367 (t-100) REVERT: K 448 MET cc_start: 0.8342 (mpp) cc_final: 0.8098 (mpp) REVERT: K 512 LEU cc_start: 0.8852 (pt) cc_final: 0.8501 (tp) REVERT: K 632 ASP cc_start: 0.8497 (m-30) cc_final: 0.8152 (m-30) outliers start: 17 outliers final: 13 residues processed: 165 average time/residue: 0.1796 time to fit residues: 40.2961 Evaluate side-chains 157 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain K residue 217 TRP Chi-restraints excluded: chain K residue 241 LEU Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 570 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.113395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.074897 restraints weight = 40025.847| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.50 r_work: 0.2941 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 1.0154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16193 Z= 0.176 Angle : 0.617 9.598 23080 Z= 0.346 Chirality : 0.037 0.167 2615 Planarity : 0.004 0.055 1927 Dihedral : 28.675 179.307 4404 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.35 % Rotamer: Outliers : 1.77 % Allowed : 21.77 % Favored : 76.45 % 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 aren not related in a simple way. whole: 1.36 (0.26), residues: 1168 helix: 2.16 (0.20), residues: 738 sheet: -1.30 (0.67), residues: 59 loop : -1.38 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 72 TYR 0.035 0.002 TYR H 108 PHE 0.036 0.001 PHE K 384 TRP 0.008 0.001 TRP K 622 HIS 0.004 0.001 HIS K 541 Details of bonding type rmsd covalent geometry : bond 0.00397 (16193) covalent geometry : angle 0.61727 (23080) hydrogen bonds : bond 0.04988 ( 755) hydrogen bonds : angle 2.95142 ( 1989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4193.94 seconds wall clock time: 72 minutes 28.12 seconds (4348.12 seconds total)