Starting phenix.real_space_refine on Tue Dec 31 09:55:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yag_33711/12_2024/7yag_33711_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yag_33711/12_2024/7yag_33711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yag_33711/12_2024/7yag_33711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yag_33711/12_2024/7yag_33711.map" model { file = "/net/cci-nas-00/data/ceres_data/7yag_33711/12_2024/7yag_33711_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yag_33711/12_2024/7yag_33711_trim.cif" } resolution = 3.1 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= 0.005 sd= 0.048 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 Ca 1 9.91 5 P 3 5.49 5 S 55 5.16 5 C 4872 2.51 5 N 1285 2.21 5 O 1450 1.98 5 H 7790 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 15456 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 13594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 13594 Classifications: {'peptide': 876} Link IDs: {'PTRANS': 34, 'TRANS': 841} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1830 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.44, per 1000 atoms: 0.48 Number of scatterers: 15456 At special positions: 0 Unit cell: (85.695, 83.725, 134.945, 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) Ca 1 19.99 S 55 16.00 P 3 15.00 O 1450 8.00 N 1285 7.00 C 4872 6.00 H 7790 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 128 " distance=2.03 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: 4.23 Conformation dependent library (CDL) restraints added in 1.3 seconds 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 8 sheets defined 51.7% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.618A pdb=" N PHE A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 78 removed outlier: 3.649A pdb=" N GLN A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 99 through 134 removed outlier: 3.722A pdb=" N LEU A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.897A pdb=" N SER A 239 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 removed outlier: 4.177A pdb=" N PHE A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 288 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 308 through 328 removed outlier: 4.214A pdb=" N ILE A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 removed outlier: 4.305A pdb=" N GLU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 411 removed outlier: 3.532A pdb=" N CYS A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.502A pdb=" N LEU A 442 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.705A pdb=" N TYR A 489 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 520 Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 596 through 602 Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 621 through 635 Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.598A pdb=" N MET A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 723 Processing helix chain 'A' and resid 730 through 743 Processing helix chain 'A' and resid 743 through 751 removed outlier: 4.308A pdb=" N LEU A 749 " --> pdb=" O PRO A 745 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 751 " --> pdb=" O GLN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 761 removed outlier: 4.221A pdb=" N ILE A 759 " --> pdb=" O ASP A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 798 Processing helix chain 'A' and resid 804 through 827 removed outlier: 3.523A pdb=" N THR A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 removed outlier: 3.526A pdb=" N ILE A 836 " --> pdb=" O SER A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 861 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 874 through 904 removed outlier: 4.038A pdb=" N SER A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N CYS A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 123 removed outlier: 4.194A pdb=" N THR C 123 " --> pdb=" O PRO C 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 151 removed outlier: 4.495A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 222 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 151 removed outlier: 4.495A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 222 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 332 removed outlier: 6.254A pdb=" N GLY A 658 " --> pdb=" O MET A 675 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU A 677 " --> pdb=" O GLY A 658 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA A 660 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 639 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL A 659 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N MET A 641 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N MET A 661 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N CYS A 344 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA A 640 " --> pdb=" O CYS A 344 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 346 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR A 642 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS A 348 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASN A 345 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LYS A 567 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE A 347 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE A 569 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER A 349 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 566 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N PHE A 617 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N MET A 568 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLN A 592 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N PHE A 617 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 594 " --> pdb=" O PHE A 617 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 392 removed outlier: 4.696A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU A 536 " --> pdb=" O PRO A 531 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE A 538 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER A 529 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 540 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 450 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392 removed outlier: 4.696A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N CYS A 490 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE A 538 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR A 492 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLY A 540 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N GLN A 494 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 14.074A pdb=" N VAL A 542 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 37 through 40 Processing sheet with id=AA7, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.543A pdb=" N TRP C 69 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY C 83 " --> pdb=" O MET C 67 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N MET C 67 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP C 66 " --> pdb=" O GLN C 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.543A pdb=" N TRP C 69 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY C 83 " --> pdb=" O MET C 67 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N MET C 67 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP C 66 " --> pdb=" O GLN C 131 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.45 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7770 1.03 - 1.23: 42 1.23 - 1.43: 3083 1.43 - 1.62: 4598 1.62 - 1.82: 90 Bond restraints: 15583 Sorted by residual: bond pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 1.698 1.605 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C3B ACP A1001 " pdb=" PG ACP A1001 " ideal model delta sigma weight residual 1.875 1.793 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O5' ACP A1001 " pdb=" PA ACP A1001 " ideal model delta sigma weight residual 1.659 1.580 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" N ASP A 290 " pdb=" H ASP A 290 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" N TRP A 285 " pdb=" H TRP A 285 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.35e+00 ... (remaining 15578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 28123 3.41 - 6.83: 124 6.83 - 10.24: 7 10.24 - 13.66: 1 13.66 - 17.07: 1 Bond angle restraints: 28256 Sorted by residual: angle pdb=" PA ACP A1001 " pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 125.06 107.99 17.07 3.00e+00 1.11e-01 3.24e+01 angle pdb=" CA ASP A 290 " pdb=" C ASP A 290 " pdb=" O ASP A 290 " ideal model delta sigma weight residual 120.80 116.55 4.25 1.08e+00 8.57e-01 1.55e+01 angle pdb=" C3B ACP A1001 " pdb=" PB ACP A1001 " pdb=" O3A ACP A1001 " ideal model delta sigma weight residual 98.05 108.41 -10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" N ASP A 290 " pdb=" CA ASP A 290 " pdb=" C ASP A 290 " ideal model delta sigma weight residual 110.30 105.20 5.10 1.50e+00 4.44e-01 1.15e+01 angle pdb=" N VAL A 179 " pdb=" CA VAL A 179 " pdb=" C VAL A 179 " ideal model delta sigma weight residual 110.30 107.01 3.29 9.70e-01 1.06e+00 1.15e+01 ... (remaining 28251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.91: 6826 24.91 - 49.83: 391 49.83 - 74.74: 80 74.74 - 99.65: 9 99.65 - 124.56: 2 Dihedral angle restraints: 7308 sinusoidal: 4055 harmonic: 3253 Sorted by residual: dihedral pdb=" CA MET A 97 " pdb=" C MET A 97 " pdb=" N HIS A 98 " pdb=" CA HIS A 98 " ideal model delta harmonic sigma weight residual 180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA VAL C 111 " pdb=" C VAL C 111 " pdb=" N TYR C 112 " pdb=" CA TYR C 112 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CB CYS C 55 " pdb=" SG CYS C 55 " pdb=" SG CYS C 128 " pdb=" CB CYS C 128 " ideal model delta sinusoidal sigma weight residual 93.00 55.30 37.70 1 1.00e+01 1.00e-02 2.00e+01 ... (remaining 7305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1109 0.070 - 0.141: 133 0.141 - 0.211: 4 0.211 - 0.281: 1 0.281 - 0.351: 1 Chirality restraints: 1248 Sorted by residual: chirality pdb=" C3' ACP A1001 " pdb=" C2' ACP A1001 " pdb=" C4' ACP A1001 " pdb=" O3' ACP A1001 " both_signs ideal model delta sigma weight residual False -2.57 -2.92 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C2' ACP A1001 " pdb=" C1' ACP A1001 " pdb=" C3' ACP A1001 " pdb=" O2' ACP A1001 " both_signs ideal model delta sigma weight residual False -2.75 -2.99 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C4' ACP A1001 " pdb=" C3' ACP A1001 " pdb=" C5' ACP A1001 " pdb=" O4' ACP A1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.09e-01 ... (remaining 1245 not shown) Planarity restraints: 2286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 391 " -0.015 2.00e-02 2.50e+03 2.84e-02 8.08e+00 pdb=" N VAL A 392 " 0.049 2.00e-02 2.50e+03 pdb=" CA VAL A 392 " -0.013 2.00e-02 2.50e+03 pdb=" H VAL A 392 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 902 " 0.215 9.50e-02 1.11e+02 7.21e-02 6.63e+00 pdb=" NE ARG A 902 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 902 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 902 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 902 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 902 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG A 902 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 902 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 902 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 862 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.12e+00 pdb=" N PRO A 863 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 863 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 863 " 0.035 5.00e-02 4.00e+02 ... (remaining 2283 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 2308 2.27 - 2.85: 35765 2.85 - 3.44: 40790 3.44 - 4.02: 55884 4.02 - 4.60: 86495 Nonbonded interactions: 221242 Sorted by model distance: nonbonded pdb=" H VAL A 833 " pdb=" OE2 GLU A 893 " model vdw 1.688 2.450 nonbonded pdb=" OE1 GLU A 33 " pdb=" H GLU A 33 " model vdw 1.719 2.450 nonbonded pdb=" O TRP A 285 " pdb=" HD1 TRP A 285 " model vdw 1.726 2.450 nonbonded pdb=" OE1 GLU A 374 " pdb=" H GLN C 134 " model vdw 1.740 2.450 nonbonded pdb=" O THR A 570 " pdb=" H ALA A 620 " model vdw 1.746 2.450 ... (remaining 221237 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.450 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: 0.260 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 35.680 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 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 : 0.005 0.093 7793 Z= 0.295 Angle : 0.807 17.070 10555 Z= 0.418 Chirality : 0.046 0.351 1248 Planarity : 0.006 0.096 1328 Dihedral : 15.720 124.564 2884 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.12 % Allowed : 11.47 % Favored : 88.42 % 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: 0.92 (0.26), residues: 989 helix: 1.54 (0.23), residues: 484 sheet: -0.61 (0.43), residues: 131 loop : -0.03 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 460 HIS 0.010 0.001 HIS C 86 PHE 0.020 0.001 PHE C 80 TYR 0.027 0.002 TYR A 397 ARG 0.016 0.001 ARG A 902 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 146 average time/residue: 0.3935 time to fit residues: 80.9873 Evaluate side-chains 138 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7793 Z= 0.326 Angle : 0.556 5.828 10555 Z= 0.301 Chirality : 0.042 0.203 1248 Planarity : 0.005 0.058 1328 Dihedral : 8.489 110.156 1092 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.18 % Allowed : 11.82 % Favored : 87.00 % 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: 0.96 (0.26), residues: 989 helix: 1.49 (0.22), residues: 495 sheet: -0.47 (0.41), residues: 148 loop : 0.05 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 460 HIS 0.003 0.001 HIS A 149 PHE 0.014 0.002 PHE A 176 TYR 0.012 0.001 TYR C 143 ARG 0.004 0.001 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 MET cc_start: 0.8468 (mmt) cc_final: 0.8174 (mmp) REVERT: A 671 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6936 (mm-30) REVERT: A 899 GLU cc_start: 0.6802 (mp0) cc_final: 0.6552 (mp0) outliers start: 10 outliers final: 7 residues processed: 150 average time/residue: 0.3868 time to fit residues: 81.0842 Evaluate side-chains 147 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 871 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 89 optimal weight: 20.0000 chunk 30 optimal weight: 0.0670 chunk 72 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7793 Z= 0.149 Angle : 0.477 5.419 10555 Z= 0.254 Chirality : 0.040 0.178 1248 Planarity : 0.004 0.058 1328 Dihedral : 8.037 106.645 1090 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.06 % Allowed : 11.94 % Favored : 87.00 % 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: 1.33 (0.27), residues: 989 helix: 1.92 (0.23), residues: 498 sheet: -0.55 (0.43), residues: 136 loop : 0.10 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 72 HIS 0.002 0.001 HIS A 624 PHE 0.011 0.001 PHE A 818 TYR 0.010 0.001 TYR A 696 ARG 0.002 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 MET cc_start: 0.8424 (mmt) cc_final: 0.8190 (mmp) outliers start: 9 outliers final: 6 residues processed: 155 average time/residue: 0.4290 time to fit residues: 93.7252 Evaluate side-chains 147 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 30.0000 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 47 optimal weight: 0.0980 chunk 85 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN C 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7793 Z= 0.221 Angle : 0.492 5.420 10555 Z= 0.265 Chirality : 0.040 0.177 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.967 105.521 1090 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.54 % Allowed : 12.17 % Favored : 86.29 % 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: 1.33 (0.27), residues: 989 helix: 1.91 (0.23), residues: 492 sheet: -0.33 (0.42), residues: 150 loop : 0.07 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 72 HIS 0.002 0.001 HIS A 149 PHE 0.015 0.001 PHE A 818 TYR 0.010 0.001 TYR A 696 ARG 0.006 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 MET cc_start: 0.8363 (mmt) cc_final: 0.8131 (mmp) outliers start: 13 outliers final: 10 residues processed: 153 average time/residue: 0.4251 time to fit residues: 90.8781 Evaluate side-chains 151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN C 86 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7793 Z= 0.259 Angle : 0.507 5.547 10555 Z= 0.273 Chirality : 0.041 0.179 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.993 105.631 1090 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.65 % Allowed : 13.00 % Favored : 85.34 % 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: 1.27 (0.27), residues: 989 helix: 1.84 (0.23), residues: 486 sheet: -0.37 (0.42), residues: 149 loop : 0.10 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 72 HIS 0.003 0.001 HIS C 86 PHE 0.020 0.002 PHE A 818 TYR 0.011 0.001 TYR C 143 ARG 0.008 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 MET cc_start: 0.8448 (mmt) cc_final: 0.8211 (mmp) outliers start: 14 outliers final: 13 residues processed: 155 average time/residue: 0.4054 time to fit residues: 88.6509 Evaluate side-chains 154 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 56 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN C 86 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7793 Z= 0.150 Angle : 0.469 5.938 10555 Z= 0.249 Chirality : 0.040 0.171 1248 Planarity : 0.004 0.057 1328 Dihedral : 7.715 102.233 1090 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.30 % Allowed : 14.54 % Favored : 84.16 % 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: 1.59 (0.27), residues: 989 helix: 2.17 (0.23), residues: 486 sheet: -0.41 (0.44), residues: 137 loop : 0.22 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 72 HIS 0.003 0.001 HIS C 86 PHE 0.021 0.001 PHE A 818 TYR 0.010 0.001 TYR A 696 ARG 0.006 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.7406 (mmt) cc_final: 0.6918 (mmp) REVERT: A 262 MET cc_start: 0.8379 (mmm) cc_final: 0.8168 (mmp) outliers start: 11 outliers final: 9 residues processed: 156 average time/residue: 0.3984 time to fit residues: 87.6578 Evaluate side-chains 152 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN C 86 HIS ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7793 Z= 0.304 Angle : 0.528 5.595 10555 Z= 0.284 Chirality : 0.042 0.178 1248 Planarity : 0.005 0.065 1328 Dihedral : 8.021 103.909 1090 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.89 % Allowed : 15.01 % Favored : 83.10 % 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: 1.29 (0.27), residues: 989 helix: 1.83 (0.23), residues: 482 sheet: -0.15 (0.43), residues: 147 loop : 0.09 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 66 HIS 0.003 0.001 HIS C 86 PHE 0.024 0.002 PHE A 818 TYR 0.012 0.001 TYR C 143 ARG 0.012 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.6793 (mmp80) cc_final: 0.6578 (mmp80) REVERT: A 248 MET cc_start: 0.7420 (mmt) cc_final: 0.6933 (mmp) REVERT: A 262 MET cc_start: 0.8497 (mmm) cc_final: 0.8248 (mmp) outliers start: 16 outliers final: 14 residues processed: 151 average time/residue: 0.4148 time to fit residues: 88.0453 Evaluate side-chains 149 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN C 86 HIS ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7793 Z= 0.171 Angle : 0.481 5.383 10555 Z= 0.256 Chirality : 0.040 0.172 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.750 102.212 1090 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.42 % Allowed : 15.84 % Favored : 82.74 % 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: 1.52 (0.27), residues: 989 helix: 2.10 (0.23), residues: 484 sheet: -0.28 (0.44), residues: 135 loop : 0.13 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 72 HIS 0.003 0.001 HIS C 86 PHE 0.026 0.001 PHE A 818 TYR 0.010 0.001 TYR A 483 ARG 0.011 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.6699 (mmp80) cc_final: 0.6461 (mmp80) REVERT: A 248 MET cc_start: 0.7399 (mmt) cc_final: 0.6909 (mmp) REVERT: A 262 MET cc_start: 0.8406 (mmm) cc_final: 0.8179 (mmp) outliers start: 12 outliers final: 12 residues processed: 157 average time/residue: 0.4529 time to fit residues: 101.3984 Evaluate side-chains 157 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 94 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN C 86 HIS C 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7793 Z= 0.188 Angle : 0.495 7.678 10555 Z= 0.262 Chirality : 0.040 0.170 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.720 101.298 1090 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.54 % Allowed : 15.60 % Favored : 82.86 % 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: 1.59 (0.27), residues: 989 helix: 2.16 (0.23), residues: 484 sheet: -0.13 (0.46), residues: 130 loop : 0.12 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 72 HIS 0.003 0.001 HIS C 86 PHE 0.027 0.001 PHE A 818 TYR 0.009 0.001 TYR A 483 ARG 0.011 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.6650 (mmp80) cc_final: 0.6436 (mmp80) REVERT: A 262 MET cc_start: 0.8403 (mmm) cc_final: 0.8175 (mmp) outliers start: 13 outliers final: 13 residues processed: 156 average time/residue: 0.3932 time to fit residues: 85.5643 Evaluate side-chains 157 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN C 86 HIS C 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7793 Z= 0.226 Angle : 0.513 8.206 10555 Z= 0.271 Chirality : 0.040 0.170 1248 Planarity : 0.004 0.059 1328 Dihedral : 7.778 101.818 1090 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.54 % Allowed : 15.72 % Favored : 82.74 % 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: 1.55 (0.27), residues: 989 helix: 2.07 (0.23), residues: 484 sheet: 0.02 (0.44), residues: 142 loop : 0.11 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 72 HIS 0.003 0.001 HIS C 86 PHE 0.025 0.001 PHE A 818 TYR 0.009 0.001 TYR A 696 ARG 0.010 0.000 ARG A 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.6653 (mmp80) cc_final: 0.6387 (mmp80) REVERT: A 262 MET cc_start: 0.8436 (mmm) cc_final: 0.8211 (mmp) outliers start: 13 outliers final: 13 residues processed: 155 average time/residue: 0.4155 time to fit residues: 89.8400 Evaluate side-chains 157 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN C 86 HIS ** C 109 ASN ** 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 = 0.4152 r_free = 0.4152 target = 0.180039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142853 restraints weight = 24742.955| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.17 r_work: 0.3553 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7793 Z= 0.167 Angle : 0.499 8.572 10555 Z= 0.263 Chirality : 0.040 0.171 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.675 100.746 1090 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.54 % Allowed : 15.60 % Favored : 82.86 % 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: 1.67 (0.27), residues: 989 helix: 2.23 (0.23), residues: 484 sheet: -0.09 (0.46), residues: 130 loop : 0.15 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 72 HIS 0.003 0.001 HIS C 86 PHE 0.024 0.001 PHE A 818 TYR 0.010 0.001 TYR A 483 ARG 0.010 0.000 ARG A 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3967.78 seconds wall clock time: 71 minutes 46.39 seconds (4306.39 seconds total)