Starting phenix.real_space_refine on Tue Dec 31 05:28:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh9_37535/12_2024/8wh9_37535.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh9_37535/12_2024/8wh9_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_37535/12_2024/8wh9_37535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh9_37535/12_2024/8wh9_37535.map" model { file = "/net/cci-nas-00/data/ceres_data/8wh9_37535/12_2024/8wh9_37535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh9_37535/12_2024/8wh9_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9.09, per 1000 atoms: 0.59 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: 4.19 Conformation dependent library (CDL) restraints added in 1.3 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: 6.62 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: 6.84 Time building geometry restraints manager: 4.60 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 40.560 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.340 ------------------------------------------------------------------------------- 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= 0.537 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 *********************** 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 : 1.274 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: 0.4214 time to fit residues: 196.5499 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 : 1.732 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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= 0.261 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 *********************** 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 : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7733 (tt0) cc_final: 0.6781 (tt0) REVERT: A 123 ASP cc_start: 0.8393 (m-30) cc_final: 0.8070 (m-30) REVERT: B 24 ASP cc_start: 0.6662 (p0) cc_final: 0.6110 (p0) REVERT: C 27 PRO cc_start: 0.8339 (Cg_endo) cc_final: 0.8130 (Cg_exo) REVERT: C 34 PHE cc_start: 0.8467 (m-10) cc_final: 0.8054 (m-10) REVERT: F 53 GLU cc_start: 0.8399 (tp30) cc_final: 0.8181 (tp30) REVERT: F 84 MET cc_start: 0.6886 (mmm) cc_final: 0.6635 (mmm) REVERT: G 33 ARG cc_start: 0.8510 (ttp-170) cc_final: 0.8143 (ttm170) REVERT: G 96 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8766 (ttpt) REVERT: H 111 LYS cc_start: 0.8008 (ttmm) cc_final: 0.7724 (ttmt) REVERT: K 299 THR cc_start: 0.7014 (m) cc_final: 0.6637 (m) REVERT: K 367 ASN cc_start: 0.8521 (t0) cc_final: 0.8273 (m-40) REVERT: K 466 ASN cc_start: 0.8656 (m-40) cc_final: 0.8442 (p0) REVERT: K 494 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8145 (mtp-110) REVERT: K 621 ASP cc_start: 0.6161 (p0) cc_final: 0.5830 (p0) REVERT: K 623 ASN cc_start: 0.8489 (t0) cc_final: 0.7611 (t0) REVERT: K 631 MET cc_start: 0.8476 (mtp) cc_final: 0.8168 (mtm) outliers start: 28 outliers final: 15 residues processed: 257 average time/residue: 0.3732 time to fit residues: 130.1858 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 : 1.332 ------------------------------------------------------------------------------- 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 71 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 125 GLN B 25 ASN E 55 GLN G 85 GLN H 74 HIS K 277 ASN K 282 HIS ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.7505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16193 Z= 0.315 Angle : 0.704 11.020 23080 Z= 0.395 Chirality : 0.041 0.157 2615 Planarity : 0.005 0.065 1927 Dihedral : 29.359 175.009 4404 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.91 % Favored : 93.92 % Rotamer: Outliers : 3.45 % Allowed : 15.86 % Favored : 80.69 % 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: -0.02 (0.25), residues: 1168 helix: 1.15 (0.20), residues: 723 sheet: -1.77 (0.62), residues: 64 loop : -2.00 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 327 HIS 0.006 0.001 HIS K 462 PHE 0.016 0.002 PHE K 596 TYR 0.027 0.002 TYR K 253 ARG 0.007 0.001 ARG E 129 *********************** 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 240 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.5342 (mpt180) cc_final: 0.5110 (mpt180) REVERT: A 53 LYS cc_start: 0.9271 (tttt) cc_final: 0.8965 (tttp) REVERT: B 24 ASP cc_start: 0.7057 (p0) cc_final: 0.6544 (p0) REVERT: C 93 GLU cc_start: 0.7686 (pm20) cc_final: 0.7370 (pm20) REVERT: D 105 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8817 (mp) REVERT: D 111 LYS cc_start: 0.7915 (mmtm) cc_final: 0.7572 (mtpt) REVERT: E 52 ARG cc_start: 0.8238 (ttm110) cc_final: 0.7996 (ptp-110) REVERT: F 67 ARG cc_start: 0.8126 (tmt170) cc_final: 0.7906 (ttt-90) REVERT: F 84 MET cc_start: 0.7666 (mmm) cc_final: 0.7267 (mmm) REVERT: G 39 LYS cc_start: 0.9296 (mmmm) cc_final: 0.9069 (mtmt) REVERT: G 85 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8357 (tm130) REVERT: G 96 LYS cc_start: 0.8997 (ttpt) cc_final: 0.8766 (ttpt) REVERT: G 109 MET cc_start: 0.7109 (mmp) cc_final: 0.6816 (mmm) REVERT: H 130 GLU cc_start: 0.7969 (tp30) cc_final: 0.7667 (tp30) REVERT: H 133 LYS cc_start: 0.8713 (tmmt) cc_final: 0.8491 (ttpp) REVERT: K 229 MET cc_start: 0.7962 (ptm) cc_final: 0.7664 (ptp) REVERT: K 329 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6488 (m-10) REVERT: K 448 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7765 (mpp) REVERT: K 601 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8090 (mtt180) REVERT: K 631 MET cc_start: 0.8565 (mtp) cc_final: 0.8131 (mtm) outliers start: 35 outliers final: 19 residues processed: 228 average time/residue: 0.3507 time to fit residues: 109.8704 Evaluate side-chains 190 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 74 ILE 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 G residue 102 THR Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain K residue 247 ASN Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 346 LEU Chi-restraints excluded: chain K residue 448 MET Chi-restraints excluded: chain K residue 490 VAL Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 601 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN H 134 HIS ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 466 ASN ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 644 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.8101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16193 Z= 0.217 Angle : 0.612 9.195 23080 Z= 0.347 Chirality : 0.037 0.169 2615 Planarity : 0.004 0.061 1927 Dihedral : 29.030 177.170 4404 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.48 % Favored : 94.43 % Rotamer: Outliers : 2.86 % Allowed : 17.73 % Favored : 79.41 % 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: 0.56 (0.26), residues: 1168 helix: 1.59 (0.20), residues: 724 sheet: -1.62 (0.67), residues: 54 loop : -1.71 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 373 HIS 0.004 0.001 HIS G 113 PHE 0.016 0.001 PHE K 384 TYR 0.013 0.001 TYR K 281 ARG 0.006 0.000 ARG G 72 *********************** 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 200 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.5260 (mpt180) cc_final: 0.4959 (mpt180) REVERT: A 125 GLN cc_start: 0.8511 (mt0) cc_final: 0.8302 (mt0) REVERT: E 52 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7959 (mtt90) REVERT: F 84 MET cc_start: 0.7590 (mmm) cc_final: 0.7315 (mmm) REVERT: G 85 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8552 (tm-30) REVERT: K 329 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6449 (m-10) REVERT: K 601 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8128 (mtt180) REVERT: K 631 MET cc_start: 0.8539 (mtp) cc_final: 0.8123 (mtm) outliers start: 29 outliers final: 21 residues processed: 188 average time/residue: 0.3779 time to fit residues: 96.9750 Evaluate side-chains 176 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 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 K residue 217 TRP Chi-restraints excluded: chain K residue 253 TYR Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 354 MET Chi-restraints excluded: chain K residue 570 ILE 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 77 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 117 optimal weight: 0.1980 chunk 94 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS G 85 GLN K 351 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.8913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16193 Z= 0.248 Angle : 0.630 11.059 23080 Z= 0.354 Chirality : 0.038 0.152 2615 Planarity : 0.004 0.055 1927 Dihedral : 28.948 176.612 4404 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.48 % Favored : 94.43 % Rotamer: Outliers : 3.05 % Allowed : 19.61 % Favored : 77.34 % 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: 0.71 (0.25), residues: 1168 helix: 1.68 (0.20), residues: 732 sheet: -1.48 (0.63), residues: 67 loop : -1.65 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 622 HIS 0.005 0.001 HIS D 134 PHE 0.015 0.002 PHE H 90 TYR 0.023 0.002 TYR H 108 ARG 0.007 0.001 ARG K 494 *********************** 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 188 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 25 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8245 (mp10) REVERT: C 33 ARG cc_start: 0.8948 (ttp-170) cc_final: 0.8588 (ttp80) REVERT: D 130 GLU cc_start: 0.7194 (tp30) cc_final: 0.6977 (tp30) REVERT: E 52 ARG cc_start: 0.8255 (ttm110) cc_final: 0.7885 (mtt90) REVERT: E 53 LYS cc_start: 0.8689 (tttt) cc_final: 0.8396 (tttm) REVERT: F 84 MET cc_start: 0.7652 (mmm) cc_final: 0.7347 (mmm) REVERT: K 217 TRP cc_start: 0.7622 (OUTLIER) cc_final: 0.6488 (t-100) REVERT: K 631 MET cc_start: 0.8463 (mtp) cc_final: 0.7990 (mtm) outliers start: 31 outliers final: 20 residues processed: 181 average time/residue: 0.3624 time to fit residues: 90.2877 Evaluate side-chains 164 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 102 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 136 VAL Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain K residue 217 TRP Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 570 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 120 GLN K 324 HIS K 351 HIS ** K 456 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.9532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16193 Z= 0.354 Angle : 0.678 11.291 23080 Z= 0.381 Chirality : 0.040 0.148 2615 Planarity : 0.005 0.057 1927 Dihedral : 28.996 176.775 4404 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.25 % Favored : 93.66 % Rotamer: Outliers : 3.74 % Allowed : 18.62 % 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: 0.67 (0.25), residues: 1168 helix: 1.62 (0.19), residues: 731 sheet: -1.32 (0.70), residues: 61 loop : -1.63 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 482 HIS 0.006 0.001 HIS K 541 PHE 0.018 0.002 PHE K 384 TYR 0.012 0.002 TYR A 99 ARG 0.006 0.001 ARG C 72 *********************** 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 194 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.5138 (mpt180) cc_final: 0.4481 (mpt180) REVERT: A 53 LYS cc_start: 0.9312 (tttt) cc_final: 0.9033 (tttp) REVERT: A 125 GLN cc_start: 0.8559 (mt0) cc_final: 0.8333 (mt0) REVERT: A 129 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7707 (tpt-90) REVERT: B 88 TYR cc_start: 0.8870 (m-10) cc_final: 0.8570 (m-10) REVERT: C 33 ARG cc_start: 0.9056 (ttp-170) cc_final: 0.8654 (ttp80) REVERT: C 91 ASP cc_start: 0.7673 (t0) cc_final: 0.7421 (t0) REVERT: D 101 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8070 (mm-30) REVERT: E 52 ARG cc_start: 0.8291 (ttm110) cc_final: 0.7946 (mtt90) REVERT: E 53 LYS cc_start: 0.8699 (tttt) cc_final: 0.8403 (tttm) REVERT: F 84 MET cc_start: 0.7692 (mmm) cc_final: 0.7370 (mmm) REVERT: K 217 TRP cc_start: 0.7618 (OUTLIER) cc_final: 0.6473 (t-100) REVERT: K 328 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7791 (mmtp) REVERT: K 631 MET cc_start: 0.8546 (mtp) cc_final: 0.8138 (mtm) outliers start: 38 outliers final: 22 residues processed: 187 average time/residue: 0.3625 time to fit residues: 93.4121 Evaluate side-chains 172 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 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 328 LYS Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 570 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 282 HIS K 351 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.9946 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= 0.305 Angle : 0.641 11.324 23080 Z= 0.360 Chirality : 0.039 0.152 2615 Planarity : 0.005 0.054 1927 Dihedral : 28.831 178.213 4404 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.25 % Favored : 93.66 % Rotamer: Outliers : 3.45 % Allowed : 19.61 % Favored : 76.95 % 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: 0.84 (0.26), residues: 1168 helix: 1.77 (0.20), residues: 736 sheet: -1.20 (0.71), residues: 61 loop : -1.65 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 482 HIS 0.005 0.001 HIS K 541 PHE 0.020 0.002 PHE K 384 TYR 0.023 0.002 TYR H 108 ARG 0.006 0.001 ARG C 72 *********************** 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 187 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 ARG cc_start: 0.9074 (ttp-170) cc_final: 0.8646 (ttp80) REVERT: E 52 ARG cc_start: 0.8299 (ttm110) cc_final: 0.7961 (mtt90) REVERT: E 53 LYS cc_start: 0.8735 (tttt) cc_final: 0.8456 (tttm) REVERT: F 84 MET cc_start: 0.7633 (mmm) cc_final: 0.7377 (mmm) REVERT: K 217 TRP cc_start: 0.7610 (OUTLIER) cc_final: 0.6471 (t-100) REVERT: K 328 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7683 (mmtm) REVERT: K 631 MET cc_start: 0.8543 (mtp) cc_final: 0.8100 (mtm) REVERT: K 632 ASP cc_start: 0.8508 (m-30) cc_final: 0.8182 (m-30) outliers start: 35 outliers final: 25 residues processed: 177 average time/residue: 0.3643 time to fit residues: 88.8310 Evaluate side-chains 169 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 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 328 LYS Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 487 ASN Chi-restraints excluded: chain K residue 529 LEU Chi-restraints excluded: chain K residue 570 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 67 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 1.0081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16193 Z= 0.224 Angle : 0.609 10.140 23080 Z= 0.343 Chirality : 0.036 0.150 2615 Planarity : 0.004 0.051 1927 Dihedral : 28.720 178.681 4404 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 2.66 % Allowed : 20.39 % Favored : 76.95 % 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: 1.15 (0.26), residues: 1168 helix: 1.99 (0.20), residues: 734 sheet: -0.60 (0.80), residues: 51 loop : -1.56 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 212 HIS 0.004 0.001 HIS K 541 PHE 0.016 0.001 PHE D 90 TYR 0.019 0.001 TYR H 108 ARG 0.006 0.000 ARG C 72 *********************** 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 178 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.5071 (mpt180) cc_final: 0.4795 (mpt180) REVERT: A 125 GLN cc_start: 0.8506 (mt0) cc_final: 0.8267 (mt0) REVERT: C 33 ARG cc_start: 0.9056 (ttp-170) cc_final: 0.8642 (ttp80) REVERT: E 42 ARG cc_start: 0.8377 (mtp-110) cc_final: 0.8019 (mtp85) REVERT: E 49 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7622 (ttp-170) REVERT: E 52 ARG cc_start: 0.8278 (ttm110) cc_final: 0.7949 (mtt90) REVERT: E 53 LYS cc_start: 0.8738 (tttt) cc_final: 0.8460 (tttm) REVERT: F 84 MET cc_start: 0.7585 (mmm) cc_final: 0.7308 (mmm) REVERT: K 217 TRP cc_start: 0.7544 (OUTLIER) cc_final: 0.6432 (t-100) REVERT: K 328 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7821 (mmtp) REVERT: K 631 MET cc_start: 0.8567 (mtp) cc_final: 0.8151 (mtm) outliers start: 27 outliers final: 22 residues processed: 170 average time/residue: 0.3601 time to fit residues: 84.4966 Evaluate side-chains 168 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 102 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 136 VAL Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain K residue 217 TRP Chi-restraints excluded: chain K residue 328 LYS Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 490 VAL 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 119 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 134 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 1.0135 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= 0.204 Angle : 0.602 9.761 23080 Z= 0.339 Chirality : 0.036 0.150 2615 Planarity : 0.004 0.054 1927 Dihedral : 28.652 178.934 4404 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.26 % Rotamer: Outliers : 2.27 % Allowed : 20.99 % Favored : 76.75 % 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: 1.25 (0.26), residues: 1168 helix: 2.02 (0.20), residues: 741 sheet: -0.77 (0.73), residues: 58 loop : -1.45 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 212 HIS 0.003 0.001 HIS K 541 PHE 0.018 0.001 PHE D 90 TYR 0.012 0.001 TYR H 108 ARG 0.007 0.000 ARG C 72 *********************** 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 172 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.5145 (mpt180) cc_final: 0.4824 (mpt180) REVERT: A 125 GLN cc_start: 0.8515 (mt0) cc_final: 0.8276 (mt0) REVERT: C 33 ARG cc_start: 0.9043 (ttp-170) cc_final: 0.8618 (ttp80) REVERT: E 49 ARG cc_start: 0.7986 (ttm170) cc_final: 0.7606 (ttp-170) REVERT: E 52 ARG cc_start: 0.8274 (ttm110) cc_final: 0.7944 (mtt90) REVERT: E 53 LYS cc_start: 0.8733 (tttt) cc_final: 0.8463 (tttm) REVERT: F 84 MET cc_start: 0.7571 (mmm) cc_final: 0.7360 (mmm) REVERT: H 115 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8559 (p) REVERT: K 217 TRP cc_start: 0.7504 (OUTLIER) cc_final: 0.6416 (t-100) REVERT: K 328 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7891 (mmtp) REVERT: K 631 MET cc_start: 0.8541 (mtp) cc_final: 0.8123 (mtm) outliers start: 23 outliers final: 18 residues processed: 164 average time/residue: 0.3641 time to fit residues: 81.8816 Evaluate side-chains 166 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 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 136 VAL Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain K residue 217 TRP Chi-restraints excluded: chain K residue 328 LYS Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 529 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 82 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 HIS K 351 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 1.0366 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= 0.305 Angle : 0.650 10.731 23080 Z= 0.363 Chirality : 0.039 0.151 2615 Planarity : 0.005 0.051 1927 Dihedral : 28.801 178.094 4404 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.75 % Rotamer: Outliers : 2.36 % Allowed : 21.08 % 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: 1.09 (0.26), residues: 1168 helix: 1.93 (0.20), residues: 734 sheet: -1.09 (0.71), residues: 61 loop : -1.48 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 212 HIS 0.006 0.001 HIS K 541 PHE 0.017 0.002 PHE D 90 TYR 0.013 0.002 TYR K 281 ARG 0.006 0.001 ARG C 72 ********************** 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 174 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8558 (mt0) cc_final: 0.8328 (mt0) REVERT: C 33 ARG cc_start: 0.9105 (ttp-170) cc_final: 0.8542 (ttp80) REVERT: E 49 ARG cc_start: 0.8009 (ttm170) cc_final: 0.7640 (ttp-170) REVERT: E 52 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7979 (mtt90) REVERT: E 53 LYS cc_start: 0.8724 (tttt) cc_final: 0.8439 (tttm) REVERT: F 84 MET cc_start: 0.7674 (mmm) cc_final: 0.7407 (mmm) REVERT: K 217 TRP cc_start: 0.7539 (OUTLIER) cc_final: 0.6469 (t-100) REVERT: K 328 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7725 (mmtp) REVERT: K 631 MET cc_start: 0.8677 (mtp) cc_final: 0.8276 (mtm) outliers start: 24 outliers final: 19 residues processed: 168 average time/residue: 0.3639 time to fit residues: 83.8957 Evaluate side-chains 166 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain K residue 217 TRP Chi-restraints excluded: chain K residue 299 THR Chi-restraints excluded: chain K residue 328 LYS Chi-restraints excluded: chain K residue 329 TYR Chi-restraints excluded: chain K residue 529 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 34 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 115 optimal weight: 0.0040 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 HIS K 351 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.113595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.075699 restraints weight = 40140.790| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.49 r_work: 0.2967 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 1.0469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16193 Z= 0.176 Angle : 0.588 8.569 23080 Z= 0.330 Chirality : 0.035 0.150 2615 Planarity : 0.004 0.046 1927 Dihedral : 28.538 179.128 4404 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.48 % Favored : 94.43 % Rotamer: Outliers : 1.77 % Allowed : 21.97 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (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: 1.39 (0.26), residues: 1168 helix: 2.14 (0.20), residues: 741 sheet: -0.73 (0.74), residues: 59 loop : -1.40 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 622 HIS 0.005 0.001 HIS D 134 PHE 0.024 0.001 PHE K 384 TYR 0.016 0.001 TYR H 108 ARG 0.007 0.000 ARG C 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3060.17 seconds wall clock time: 57 minutes 30.14 seconds (3450.14 seconds total)