Starting phenix.real_space_refine on Fri May 16 21:45:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh9_37535/05_2025/8wh9_37535.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh9_37535/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wh9_37535/05_2025/8wh9_37535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh9_37535/05_2025/8wh9_37535.map" model { file = "/net/cci-nas-00/data/ceres_data/8wh9_37535/05_2025/8wh9_37535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh9_37535/05_2025/8wh9_37535.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.76, per 1000 atoms: 0.64 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: 4.09 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 7.66 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: 7.17 Time building geometry restraints manager: 4.78 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: 0.870 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: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 44.550 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.780 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.038 0.002 TRP K 217 HIS 0.014 0.001 HIS K 541 PHE 0.048 0.003 PHE C 26 TYR 0.040 0.003 TYR K 329 ARG 0.009 0.001 ARG G 89 Details of bonding type rmsd hydrogen bonds : bond 0.22158 ( 755) hydrogen bonds : angle 8.38174 ( 1989) covalent geometry : bond 0.00897 (16193) covalent geometry : angle 1.18513 (23080) *********************** 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 : 1.373 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: 0.3775 time to fit residues: 175.5544 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 : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 539 ASN K 548 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.128949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.091667 restraints weight = 41044.387| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.56 r_work: 0.3259 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16193 Z= 0.209 Angle : 0.742 8.326 23080 Z= 0.416 Chirality : 0.043 0.216 2615 Planarity : 0.006 0.058 1927 Dihedral : 29.515 179.738 4404 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.22 % Favored : 94.61 % Rotamer: Outliers : 2.76 % Allowed : 13.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.24), residues: 1168 helix: 0.51 (0.19), residues: 728 sheet: -2.56 (0.58), residues: 60 loop : -2.14 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 327 HIS 0.005 0.001 HIS G 113 PHE 0.030 0.002 PHE K 240 TYR 0.009 0.002 TYR A 99 ARG 0.007 0.001 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.06255 ( 755) hydrogen bonds : angle 3.57943 ( 1989) covalent geometry : bond 0.00466 (16193) covalent geometry : angle 0.74235 (23080) *********************** 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 266 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 238 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8175 (tt0) cc_final: 0.7422 (tt0) REVERT: A 123 ASP cc_start: 0.8594 (m-30) cc_final: 0.8298 (m-30) REVERT: B 24 ASP cc_start: 0.6999 (p0) cc_final: 0.6372 (p0) REVERT: B 74 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8364 (tt0) REVERT: C 27 PRO cc_start: 0.8479 (Cg_endo) cc_final: 0.8258 (Cg_exo) REVERT: C 34 PHE cc_start: 0.8562 (m-10) cc_final: 0.8145 (m-10) REVERT: C 96 LYS cc_start: 0.8983 (mtmt) cc_final: 0.8664 (mmtm) REVERT: F 53 GLU cc_start: 0.8856 (tp30) cc_final: 0.8628 (tp30) REVERT: F 84 MET cc_start: 0.8024 (mmm) cc_final: 0.7700 (mmm) REVERT: G 33 ARG cc_start: 0.8793 (ttp-170) cc_final: 0.8427 (ttm170) REVERT: G 93 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8247 (mm-30) REVERT: G 96 LYS cc_start: 0.9110 (ttpt) cc_final: 0.8867 (ttpt) REVERT: H 100 SER cc_start: 0.8609 (m) cc_final: 0.8405 (m) REVERT: H 111 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7858 (ttmt) REVERT: K 299 THR cc_start: 0.7206 (m) cc_final: 0.6836 (m) REVERT: K 367 ASN cc_start: 0.8530 (t0) cc_final: 0.8252 (m-40) REVERT: K 466 ASN cc_start: 0.8773 (m-40) cc_final: 0.8495 (p0) REVERT: K 494 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8136 (mtp-110) REVERT: K 621 ASP cc_start: 0.6270 (p0) cc_final: 0.5949 (p0) REVERT: K 623 ASN cc_start: 0.8585 (t0) cc_final: 0.7642 (t0) REVERT: K 631 MET cc_start: 0.8575 (mtp) cc_final: 0.8278 (mtm) outliers start: 28 outliers final: 15 residues processed: 257 average time/residue: 0.3440 time to fit residues: 120.5352 Evaluate side-chains 195 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 70 VAL 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 105 optimal weight: 0.0030 chunk 104 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 25 ASN E 55 GLN G 85 GLN H 74 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.123022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.084359 restraints weight = 40258.313| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.55 r_work: 0.3118 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.6499 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= 0.174 Angle : 0.635 8.498 23080 Z= 0.360 Chirality : 0.038 0.146 2615 Planarity : 0.005 0.050 1927 Dihedral : 29.207 176.931 4404 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 2.96 % Allowed : 15.76 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1168 helix: 1.45 (0.20), residues: 725 sheet: -1.51 (0.69), residues: 54 loop : -1.76 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 327 HIS 0.005 0.001 HIS K 462 PHE 0.017 0.001 PHE K 384 TYR 0.023 0.002 TYR K 253 ARG 0.007 0.001 ARG C 33 Details of bonding type rmsd hydrogen bonds : bond 0.05431 ( 755) hydrogen bonds : angle 3.19053 ( 1989) covalent geometry : bond 0.00374 (16193) covalent geometry : angle 0.63474 (23080) *********************** 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 231 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8466 (pp20) cc_final: 0.8231 (pm20) REVERT: B 24 ASP cc_start: 0.7231 (p0) cc_final: 0.6727 (p0) REVERT: C 27 PRO cc_start: 0.8937 (Cg_endo) cc_final: 0.8577 (Cg_exo) REVERT: C 33 ARG cc_start: 0.8320 (ttp80) cc_final: 0.8082 (ttp80) REVERT: C 93 GLU cc_start: 0.7830 (pm20) cc_final: 0.7493 (pm20) REVERT: C 96 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8747 (mmtm) REVERT: D 130 GLU cc_start: 0.7502 (tp30) cc_final: 0.7130 (tp30) REVERT: E 52 ARG cc_start: 0.8565 (ttm110) cc_final: 0.7952 (ptp90) REVERT: E 73 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8633 (tm-30) REVERT: F 53 GLU cc_start: 0.8769 (tp30) cc_final: 0.8547 (tp30) REVERT: F 84 MET cc_start: 0.8507 (mmm) cc_final: 0.7923 (mmm) REVERT: F 88 TYR cc_start: 0.9085 (m-10) cc_final: 0.8766 (m-10) REVERT: G 93 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8349 (mm-30) REVERT: G 109 MET cc_start: 0.7123 (mmp) cc_final: 0.6921 (mmm) REVERT: H 60 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7811 (mm-30) REVERT: H 130 GLU cc_start: 0.8439 (tp30) cc_final: 0.8189 (tp30) REVERT: H 141 LYS cc_start: 0.9293 (tttp) cc_final: 0.9059 (ttmt) REVERT: K 329 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6484 (m-10) REVERT: K 359 LEU cc_start: 0.7676 (mt) cc_final: 0.7451 (mp) REVERT: K 466 ASN cc_start: 0.8583 (m-40) cc_final: 0.8329 (p0) REVERT: K 570 ILE cc_start: 0.7443 (mt) cc_final: 0.7204 (mp) REVERT: K 601 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7436 (mtm180) outliers start: 30 outliers final: 17 residues processed: 218 average time/residue: 0.3284 time to fit residues: 99.1396 Evaluate side-chains 189 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 85 GLN 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 299 THR Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 490 VAL Chi-restraints excluded: chain K residue 576 LEU 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 41 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 65 optimal weight: 0.0970 chunk 115 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 69 ASN E 39 HIS H 134 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.120073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.081228 restraints weight = 40193.602| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.58 r_work: 0.3059 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.7500 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= 0.162 Angle : 0.611 8.195 23080 Z= 0.345 Chirality : 0.037 0.189 2615 Planarity : 0.004 0.048 1927 Dihedral : 28.954 177.545 4404 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.22 % Favored : 94.69 % Rotamer: Outliers : 2.36 % Allowed : 17.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1168 helix: 1.72 (0.20), residues: 730 sheet: -1.46 (0.66), residues: 54 loop : -1.43 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 373 HIS 0.005 0.001 HIS G 113 PHE 0.016 0.001 PHE K 384 TYR 0.011 0.001 TYR K 281 ARG 0.007 0.000 ARG K 320 Details of bonding type rmsd hydrogen bonds : bond 0.04782 ( 755) hydrogen bonds : angle 3.09633 ( 1989) covalent geometry : bond 0.00354 (16193) covalent geometry : angle 0.61054 (23080) *********************** 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 195 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7199 (p0) cc_final: 0.6636 (p0) REVERT: C 25 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8254 (mp10) REVERT: C 33 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8244 (ttm170) REVERT: C 93 GLU cc_start: 0.7720 (pm20) cc_final: 0.7494 (pm20) REVERT: C 96 LYS cc_start: 0.9087 (mtmt) cc_final: 0.8819 (mttm) REVERT: E 52 ARG cc_start: 0.8647 (ttm110) cc_final: 0.8036 (ptp90) REVERT: E 73 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8841 (tm-30) REVERT: F 84 MET cc_start: 0.8585 (mmm) cc_final: 0.8064 (mmm) REVERT: G 89 ARG cc_start: 0.8763 (mmp80) cc_final: 0.8383 (mmt180) REVERT: K 217 TRP cc_start: 0.7680 (OUTLIER) cc_final: 0.6287 (t-100) REVERT: K 329 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.5107 (m-10) REVERT: K 359 LEU cc_start: 0.7672 (mt) cc_final: 0.7389 (mp) REVERT: K 601 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7336 (mtm180) outliers start: 24 outliers final: 13 residues processed: 186 average time/residue: 0.3667 time to fit residues: 92.7122 Evaluate side-chains 176 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR 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 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 H residue 144 THR Chi-restraints excluded: chain K residue 217 TRP Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 576 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 59 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 122 optimal weight: 30.0000 chunk 108 optimal weight: 5.9990 chunk 105 optimal weight: 0.1980 chunk 126 optimal weight: 0.2980 chunk 84 optimal weight: 10.0000 chunk 134 optimal weight: 0.0050 chunk 93 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 456 GLN ** 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 = 0.3985 r_free = 0.3985 target = 0.121224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.082950 restraints weight = 40867.490| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.60 r_work: 0.3098 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.7830 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= 0.136 Angle : 0.574 7.814 23080 Z= 0.325 Chirality : 0.035 0.158 2615 Planarity : 0.004 0.061 1927 Dihedral : 28.877 178.084 4404 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 1.77 % Allowed : 18.52 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1168 helix: 2.03 (0.20), residues: 732 sheet: -1.17 (0.69), residues: 54 loop : -1.34 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 622 HIS 0.005 0.001 HIS B 75 PHE 0.011 0.001 PHE K 384 TYR 0.009 0.001 TYR K 281 ARG 0.007 0.000 ARG K 494 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 755) hydrogen bonds : angle 2.85648 ( 1989) covalent geometry : bond 0.00291 (16193) covalent geometry : angle 0.57443 (23080) *********************** 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 187 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7198 (p0) cc_final: 0.6656 (p0) REVERT: C 25 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8313 (mp10) REVERT: C 33 ARG cc_start: 0.8640 (ttp80) cc_final: 0.8368 (ttp80) REVERT: C 82 ARG cc_start: 0.8667 (tpt170) cc_final: 0.8461 (tpt170) REVERT: C 91 ASP cc_start: 0.7844 (t0) cc_final: 0.7390 (t0) REVERT: C 93 GLU cc_start: 0.7729 (pm20) cc_final: 0.7513 (pm20) REVERT: C 96 LYS cc_start: 0.9044 (mtmt) cc_final: 0.8762 (mttm) REVERT: E 51 ILE cc_start: 0.8190 (mt) cc_final: 0.7921 (mt) REVERT: E 52 ARG cc_start: 0.8626 (ttm110) cc_final: 0.8021 (ptp90) REVERT: E 73 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8821 (tm-30) REVERT: F 84 MET cc_start: 0.8558 (mmm) cc_final: 0.8070 (mmm) REVERT: G 85 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8390 (tm-30) REVERT: G 89 ARG cc_start: 0.8776 (mmp80) cc_final: 0.8302 (mmt180) REVERT: H 111 LYS cc_start: 0.8392 (ttmm) cc_final: 0.7987 (tptt) REVERT: H 141 LYS cc_start: 0.9293 (tttp) cc_final: 0.9075 (ttmt) REVERT: K 329 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6576 (m-10) REVERT: K 359 LEU cc_start: 0.7650 (mt) cc_final: 0.7330 (mp) REVERT: K 601 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7388 (mtm180) outliers start: 18 outliers final: 13 residues processed: 181 average time/residue: 0.3325 time to fit residues: 82.6683 Evaluate side-chains 164 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 63 GLU 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 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 372 LEU Chi-restraints excluded: chain K residue 463 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 Chi-restraints excluded: chain K residue 669 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 56 optimal weight: 7.9990 chunk 106 optimal weight: 0.0010 chunk 107 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 45 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 overall best weight: 2.0170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 351 HIS K 456 GLN ** K 492 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 = 0.117071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.078053 restraints weight = 40207.930| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.55 r_work: 0.2995 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.8425 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= 0.177 Angle : 0.606 9.261 23080 Z= 0.340 Chirality : 0.036 0.156 2615 Planarity : 0.004 0.046 1927 Dihedral : 28.893 177.620 4404 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 2.27 % Allowed : 19.11 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1168 helix: 2.00 (0.20), residues: 736 sheet: -1.10 (0.64), residues: 64 loop : -1.42 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 622 HIS 0.005 0.001 HIS B 75 PHE 0.015 0.001 PHE H 90 TYR 0.033 0.002 TYR H 108 ARG 0.005 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.04938 ( 755) hydrogen bonds : angle 3.00382 ( 1989) covalent geometry : bond 0.00395 (16193) covalent geometry : angle 0.60593 (23080) *********************** 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 184 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.4695 (mpt180) cc_final: 0.4472 (mpt180) REVERT: C 79 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8516 (mt) REVERT: C 91 ASP cc_start: 0.7893 (t0) cc_final: 0.7362 (t0) REVERT: C 96 LYS cc_start: 0.9121 (mtmt) cc_final: 0.8825 (mttm) REVERT: E 52 ARG cc_start: 0.8615 (ttm110) cc_final: 0.8079 (ptp90) REVERT: E 73 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8821 (tm-30) REVERT: E 105 GLU cc_start: 0.8992 (tt0) cc_final: 0.8756 (mt-10) REVERT: F 84 MET cc_start: 0.8786 (mmm) cc_final: 0.8294 (mmm) REVERT: G 39 LYS cc_start: 0.9432 (mmmm) cc_final: 0.9135 (mtmt) REVERT: G 85 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8656 (tm-30) REVERT: H 120 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8333 (tp40) REVERT: K 217 TRP cc_start: 0.7603 (OUTLIER) cc_final: 0.6035 (t-100) REVERT: K 329 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.5155 (m-10) REVERT: K 359 LEU cc_start: 0.7778 (mt) cc_final: 0.7471 (mp) REVERT: K 448 MET cc_start: 0.8083 (mpp) cc_final: 0.7801 (mpp) REVERT: K 601 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8244 (mtt180) outliers start: 23 outliers final: 11 residues processed: 178 average time/residue: 0.3441 time to fit residues: 84.0648 Evaluate side-chains 169 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 137 SER 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 372 LEU Chi-restraints excluded: chain K residue 463 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 57 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 122 optimal weight: 50.0000 chunk 95 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 41 optimal weight: 0.1980 chunk 118 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 85 GLN ** K 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 471 HIS ** K 492 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 = 0.3848 r_free = 0.3848 target = 0.111991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.072634 restraints weight = 40074.662| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.56 r_work: 0.2895 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.9518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16193 Z= 0.242 Angle : 0.682 12.576 23080 Z= 0.381 Chirality : 0.040 0.167 2615 Planarity : 0.005 0.052 1927 Dihedral : 29.090 177.396 4404 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.74 % Favored : 94.18 % Rotamer: Outliers : 2.96 % Allowed : 19.41 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1168 helix: 1.75 (0.20), residues: 729 sheet: -1.34 (0.65), residues: 67 loop : -1.46 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 265 HIS 0.006 0.001 HIS K 541 PHE 0.018 0.002 PHE K 384 TYR 0.058 0.002 TYR B 88 ARG 0.008 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.06184 ( 755) hydrogen bonds : angle 3.40717 ( 1989) covalent geometry : bond 0.00551 (16193) covalent geometry : angle 0.68197 (23080) *********************** 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 196 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.411 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9290 (tttt) cc_final: 0.9040 (tttp) REVERT: C 25 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8551 (mp10) REVERT: C 93 GLU cc_start: 0.8206 (pm20) cc_final: 0.8001 (pm20) REVERT: C 96 LYS cc_start: 0.9215 (mtmt) cc_final: 0.8964 (mttm) REVERT: D 101 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8215 (tm-30) REVERT: D 130 GLU cc_start: 0.7820 (tp30) cc_final: 0.7591 (tp30) REVERT: E 52 ARG cc_start: 0.8627 (ttm110) cc_final: 0.8270 (mtt90) REVERT: E 53 LYS cc_start: 0.8591 (tttt) cc_final: 0.8300 (tttm) REVERT: E 73 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8831 (tm-30) REVERT: F 84 MET cc_start: 0.8937 (mmm) cc_final: 0.8377 (mmm) REVERT: G 39 LYS cc_start: 0.9473 (mmmm) cc_final: 0.9226 (mtmt) REVERT: G 85 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8769 (tm130) REVERT: G 91 ASP cc_start: 0.8424 (t0) cc_final: 0.8208 (t0) REVERT: K 217 TRP cc_start: 0.7483 (OUTLIER) cc_final: 0.6278 (t-100) REVERT: K 448 MET cc_start: 0.8362 (mpp) cc_final: 0.8118 (mpp) REVERT: K 632 ASP cc_start: 0.8522 (m-30) cc_final: 0.8204 (m-30) outliers start: 30 outliers final: 14 residues processed: 187 average time/residue: 0.3572 time to fit residues: 91.3090 Evaluate side-chains 165 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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 101 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 108 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 463 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 23 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 120 GLN ** K 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 HIS ** K 492 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 = 0.3903 r_free = 0.3903 target = 0.115375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.077046 restraints weight = 40183.656| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.53 r_work: 0.2989 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.9665 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= 0.144 Angle : 0.602 9.710 23080 Z= 0.336 Chirality : 0.036 0.217 2615 Planarity : 0.004 0.051 1927 Dihedral : 28.761 179.426 4404 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 1.77 % Allowed : 20.79 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1168 helix: 1.99 (0.20), residues: 738 sheet: -0.99 (0.65), residues: 64 loop : -1.49 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 265 HIS 0.004 0.001 HIS B 75 PHE 0.011 0.001 PHE A 67 TYR 0.032 0.002 TYR B 88 ARG 0.007 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 755) hydrogen bonds : angle 2.95109 ( 1989) covalent geometry : bond 0.00313 (16193) covalent geometry : angle 0.60212 (23080) *********************** 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 174 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9091 (mttm) cc_final: 0.8651 (mtpp) REVERT: C 25 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8404 (mp10) REVERT: C 91 ASP cc_start: 0.7661 (t0) cc_final: 0.7227 (t0) REVERT: C 96 LYS cc_start: 0.9140 (mtmt) cc_final: 0.8894 (mttm) REVERT: D 101 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8324 (tm-30) REVERT: E 52 ARG cc_start: 0.8606 (ttm110) cc_final: 0.8225 (mtt90) REVERT: E 53 LYS cc_start: 0.8638 (tttt) cc_final: 0.8330 (tttm) REVERT: E 73 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8838 (tm-30) REVERT: F 84 MET cc_start: 0.8773 (mmm) cc_final: 0.8293 (mmm) REVERT: G 36 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8809 (mptt) REVERT: G 39 LYS cc_start: 0.9440 (mmmm) cc_final: 0.9210 (mtmt) REVERT: G 85 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8906 (tp-100) REVERT: K 217 TRP cc_start: 0.7379 (OUTLIER) cc_final: 0.6241 (t-100) REVERT: K 448 MET cc_start: 0.8385 (mpp) cc_final: 0.8130 (mpp) REVERT: K 632 ASP cc_start: 0.8519 (m-30) cc_final: 0.7990 (m-30) outliers start: 18 outliers final: 11 residues processed: 168 average time/residue: 0.3387 time to fit residues: 77.8433 Evaluate side-chains 157 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 108 VAL 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 K residue 217 TRP Chi-restraints excluded: chain K residue 241 LEU Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 463 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 73 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 104 optimal weight: 0.0020 chunk 75 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 85 GLN ** K 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 HIS ** K 492 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 = 0.3918 r_free = 0.3918 target = 0.116243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.078035 restraints weight = 40252.567| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.54 r_work: 0.3009 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.9832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16193 Z= 0.142 Angle : 0.596 10.410 23080 Z= 0.331 Chirality : 0.036 0.228 2615 Planarity : 0.004 0.053 1927 Dihedral : 28.659 178.919 4404 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 1.48 % Allowed : 21.28 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1168 helix: 2.17 (0.20), residues: 737 sheet: -0.87 (0.64), residues: 64 loop : -1.45 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 212 HIS 0.004 0.001 HIS B 75 PHE 0.021 0.001 PHE K 384 TYR 0.033 0.001 TYR B 88 ARG 0.008 0.000 ARG K 636 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 755) hydrogen bonds : angle 2.91402 ( 1989) covalent geometry : bond 0.00309 (16193) covalent geometry : angle 0.59648 (23080) *********************** 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 171 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9272 (tttt) cc_final: 0.9025 (tttp) REVERT: B 79 LYS cc_start: 0.9108 (mttm) cc_final: 0.8693 (mtpp) REVERT: C 25 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8480 (mp10) REVERT: C 91 ASP cc_start: 0.7648 (t0) cc_final: 0.7056 (t0) REVERT: C 96 LYS cc_start: 0.9132 (mtmt) cc_final: 0.8851 (mttm) REVERT: D 101 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8325 (tm-30) REVERT: E 52 ARG cc_start: 0.8617 (ttm110) cc_final: 0.8416 (ptp-110) REVERT: E 73 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8826 (tm-30) REVERT: F 84 MET cc_start: 0.8787 (mmm) cc_final: 0.8300 (mmm) REVERT: G 39 LYS cc_start: 0.9417 (mmmm) cc_final: 0.9156 (mtmt) REVERT: G 85 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8729 (tm130) REVERT: K 217 TRP cc_start: 0.7392 (OUTLIER) cc_final: 0.6129 (t-100) REVERT: K 448 MET cc_start: 0.8302 (mpp) cc_final: 0.8033 (mpp) REVERT: K 512 LEU cc_start: 0.8801 (pt) cc_final: 0.8461 (tp) REVERT: K 554 ASP cc_start: 0.8564 (t0) cc_final: 0.8320 (t0) REVERT: K 632 ASP cc_start: 0.8440 (m-30) cc_final: 0.8116 (m-30) outliers start: 15 outliers final: 10 residues processed: 166 average time/residue: 0.3457 time to fit residues: 78.8576 Evaluate side-chains 157 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain G residue 85 GLN 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 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 463 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 15 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 85 GLN ** K 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 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 = 0.3872 r_free = 0.3872 target = 0.113294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.074396 restraints weight = 40219.859| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.52 r_work: 0.2931 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.9950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16193 Z= 0.201 Angle : 0.640 9.946 23080 Z= 0.355 Chirality : 0.038 0.187 2615 Planarity : 0.004 0.048 1927 Dihedral : 28.714 178.804 4404 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 1.28 % Allowed : 22.17 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1168 helix: 2.11 (0.20), residues: 734 sheet: -0.98 (0.65), residues: 66 loop : -1.35 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 373 HIS 0.005 0.001 HIS B 75 PHE 0.027 0.002 PHE K 384 TYR 0.036 0.002 TYR H 108 ARG 0.007 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.05324 ( 755) hydrogen bonds : angle 3.08527 ( 1989) covalent geometry : bond 0.00455 (16193) covalent geometry : angle 0.63982 (23080) ********************** 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 167 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: C 25 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8457 (mp10) REVERT: C 96 LYS cc_start: 0.9176 (mtmt) cc_final: 0.8916 (mttm) REVERT: D 130 GLU cc_start: 0.7449 (tp30) cc_final: 0.7105 (tp30) REVERT: E 52 ARG cc_start: 0.8625 (ttm110) cc_final: 0.8276 (mtt90) REVERT: E 53 LYS cc_start: 0.8654 (tttt) cc_final: 0.8397 (tttm) REVERT: E 73 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8851 (tm-30) REVERT: F 84 MET cc_start: 0.8882 (mmm) cc_final: 0.8616 (mmm) REVERT: G 39 LYS cc_start: 0.9432 (mmmm) cc_final: 0.9168 (mtmt) REVERT: G 85 GLN cc_start: 0.9270 (mm-40) cc_final: 0.8871 (tm-30) REVERT: K 217 TRP cc_start: 0.7371 (OUTLIER) cc_final: 0.6090 (t-100) REVERT: K 448 MET cc_start: 0.8272 (mpp) cc_final: 0.7983 (mpp) REVERT: K 512 LEU cc_start: 0.8839 (pt) cc_final: 0.8481 (tp) REVERT: K 632 ASP cc_start: 0.8538 (m-30) cc_final: 0.8274 (m-30) outliers start: 13 outliers final: 10 residues processed: 165 average time/residue: 0.3359 time to fit residues: 76.5951 Evaluate side-chains 160 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain G residue 80 VAL 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 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 463 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 30 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 20.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 HIS ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 629 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.111902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.073143 restraints weight = 40001.405| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.51 r_work: 0.2909 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 1.0260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16193 Z= 0.213 Angle : 0.648 10.351 23080 Z= 0.361 Chirality : 0.038 0.206 2615 Planarity : 0.005 0.051 1927 Dihedral : 28.790 179.460 4404 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.35 % Rotamer: Outliers : 1.38 % Allowed : 22.27 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1168 helix: 1.93 (0.20), residues: 737 sheet: -1.31 (0.66), residues: 62 loop : -1.39 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 373 HIS 0.005 0.001 HIS K 541 PHE 0.028 0.002 PHE K 384 TYR 0.038 0.002 TYR B 88 ARG 0.007 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.05342 ( 755) hydrogen bonds : angle 3.19203 ( 1989) covalent geometry : bond 0.00487 (16193) covalent geometry : angle 0.64841 (23080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8151.61 seconds wall clock time: 141 minutes 13.88 seconds (8473.88 seconds total)