Starting phenix.real_space_refine on Fri Jul 3 17:50:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yag_33711/07_2026/7yag_33711_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yag_33711/07_2026/7yag_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_33711/07_2026/7yag_33711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yag_33711/07_2026/7yag_33711.map" model { file = "/net/cci-nas-00/data/ceres_data/7yag_33711/07_2026/7yag_33711_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yag_33711/07_2026/7yag_33711_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 31 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'ACP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 2.58, per 1000 atoms: 0.17 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: 1.13 Conformation dependent library (CDL) restraints added in 406.0 milliseconds 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: 0.39 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: 4.00 Time building geometry restraints manager: 1.57 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: 0.650 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: 0.100 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.080 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 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 7794 Z= 0.219 Angle : 0.807 17.070 10557 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (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 ARG 0.016 0.001 ARG A 902 TYR 0.027 0.002 TYR A 397 PHE 0.020 0.001 PHE C 80 TRP 0.007 0.001 TRP A 460 HIS 0.010 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 ( 7793) covalent geometry : angle 0.80749 / 0.42 (10555) SS BOND : bond 0.00363 / 0.19 ( 1) SS BOND : angle 0.71708 / 0.39 ( 2) hydrogen bonds : bond 0.11837 / 8.43 ( 432) hydrogen bonds : angle 6.00161 / 4.31 ( 1356) *********************** 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 : 0.305 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 outliers start: 1 outliers final: 1 residues processed: 146 average time/residue: 0.1396 time to fit residues: 29.1703 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 : 0.280 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.181906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.142493 restraints weight = 24364.350| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.42 r_work: 0.3557 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7794 Z= 0.143 Angle : 0.505 5.810 10557 Z= 0.271 Chirality : 0.041 0.190 1248 Planarity : 0.004 0.057 1328 Dihedral : 8.415 110.508 1092 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.06 % Allowed : 11.58 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.26), residues: 989 helix: 1.77 (0.23), residues: 496 sheet: -0.47 (0.41), residues: 148 loop : 0.11 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 54 TYR 0.010 0.001 TYR A 696 PHE 0.013 0.001 PHE A 702 TRP 0.004 0.001 TRP C 69 HIS 0.003 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 7793) covalent geometry : angle 0.50521 / 0.27 (10555) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 0.27514 / 0.14 ( 2) hydrogen bonds : bond 0.03974 / 2.73 ( 432) hydrogen bonds : angle 4.79571 / 3.46 ( 1356) *********************** 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 153 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.403 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 130 GLU cc_start: 0.7833 (tp30) cc_final: 0.7516 (tm-30) REVERT: A 262 MET cc_start: 0.8263 (mmt) cc_final: 0.8012 (mmp) REVERT: A 308 GLU cc_start: 0.8039 (pt0) cc_final: 0.7722 (pt0) REVERT: A 671 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6768 (mm-30) REVERT: A 899 GLU cc_start: 0.6627 (mp0) cc_final: 0.6207 (mp0) outliers start: 9 outliers final: 7 residues processed: 148 average time/residue: 0.1520 time to fit residues: 31.8651 Evaluate side-chains 143 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 ASP 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 6 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.181082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.139751 restraints weight = 24382.413| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.26 r_work: 0.3556 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7794 Z= 0.127 Angle : 0.478 5.432 10557 Z= 0.255 Chirality : 0.040 0.175 1248 Planarity : 0.004 0.056 1328 Dihedral : 8.018 107.214 1090 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.30 % Allowed : 12.06 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.27), residues: 989 helix: 1.96 (0.23), residues: 498 sheet: -0.33 (0.42), residues: 149 loop : 0.16 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 174 TYR 0.010 0.001 TYR A 696 PHE 0.011 0.001 PHE A 818 TRP 0.006 0.001 TRP A 72 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 7793) covalent geometry : angle 0.47787 / 0.25 (10555) SS BOND : bond 0.00095 / 0.05 ( 1) SS BOND : angle 0.21770 / 0.12 ( 2) hydrogen bonds : bond 0.03724 / 2.56 ( 432) hydrogen bonds : angle 4.49512 / 3.26 ( 1356) *********************** 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 160 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.259 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 130 GLU cc_start: 0.7802 (tp30) cc_final: 0.7396 (tm-30) REVERT: A 308 GLU cc_start: 0.8143 (pt0) cc_final: 0.7925 (pt0) REVERT: A 671 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6937 (tm-30) REVERT: A 899 GLU cc_start: 0.6533 (mp0) cc_final: 0.6290 (mp0) outliers start: 11 outliers final: 9 residues processed: 157 average time/residue: 0.1369 time to fit residues: 30.8501 Evaluate side-chains 151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 437 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 738 ASN 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 79 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 ASN C 86 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.181674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.143060 restraints weight = 24486.299| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.53 r_work: 0.3564 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7794 Z= 0.110 Angle : 0.466 5.405 10557 Z= 0.248 Chirality : 0.040 0.172 1248 Planarity : 0.004 0.056 1328 Dihedral : 7.831 104.883 1090 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.18 % Allowed : 12.88 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.27), residues: 989 helix: 2.10 (0.23), residues: 498 sheet: -0.35 (0.43), residues: 138 loop : 0.18 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 213 TYR 0.010 0.001 TYR A 696 PHE 0.013 0.001 PHE A 818 TRP 0.007 0.001 TRP A 72 HIS 0.002 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7793) covalent geometry : angle 0.46563 / 0.25 (10555) SS BOND : bond 0.00103 / 0.05 ( 1) SS BOND : angle 0.20622 / 0.11 ( 2) hydrogen bonds : bond 0.03511 / 2.40 ( 432) hydrogen bonds : angle 4.33762 / 3.14 ( 1356) *********************** 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 157 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.311 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 130 GLU cc_start: 0.7807 (tp30) cc_final: 0.7489 (tm-30) outliers start: 10 outliers final: 8 residues processed: 154 average time/residue: 0.1422 time to fit residues: 31.4251 Evaluate side-chains 147 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU 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 564 VAL Chi-restraints excluded: chain A residue 738 ASN 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 26 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.0870 chunk 50 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN A 606 GLN C 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.178695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139316 restraints weight = 24709.780| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.41 r_work: 0.3507 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7794 Z= 0.172 Angle : 0.511 5.634 10557 Z= 0.273 Chirality : 0.041 0.180 1248 Planarity : 0.004 0.056 1328 Dihedral : 7.961 104.959 1090 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.89 % Allowed : 12.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.27), residues: 989 helix: 1.93 (0.23), residues: 486 sheet: -0.14 (0.43), residues: 147 loop : 0.11 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 806 TYR 0.011 0.001 TYR C 143 PHE 0.016 0.001 PHE A 818 TRP 0.008 0.001 TRP A 72 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 7793) covalent geometry : angle 0.51071 / 0.27 (10555) SS BOND : bond 0.00093 / 0.05 ( 1) SS BOND : angle 0.15141 / 0.08 ( 2) hydrogen bonds : bond 0.03820 / 2.63 ( 432) hydrogen bonds : angle 4.43816 / 3.22 ( 1356) *********************** 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 158 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.304 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: A 248 MET cc_start: 0.7486 (mmt) cc_final: 0.6946 (mmp) REVERT: A 605 GLN cc_start: 0.7944 (tp40) cc_final: 0.7633 (tp40) REVERT: A 609 GLN cc_start: 0.8270 (mt0) cc_final: 0.7762 (mt0) outliers start: 16 outliers final: 13 residues processed: 153 average time/residue: 0.1396 time to fit residues: 30.4640 Evaluate side-chains 152 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 564 VAL Chi-restraints excluded: chain A residue 738 ASN 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 93 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN A 419 ASN C 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.180319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.142938 restraints weight = 24625.222| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.18 r_work: 0.3551 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7794 Z= 0.120 Angle : 0.472 5.356 10557 Z= 0.251 Chirality : 0.040 0.172 1248 Planarity : 0.004 0.056 1328 Dihedral : 7.761 103.391 1090 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.65 % Allowed : 13.83 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.27), residues: 989 helix: 2.14 (0.23), residues: 487 sheet: -0.31 (0.45), residues: 137 loop : 0.14 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 213 TYR 0.009 0.001 TYR A 696 PHE 0.020 0.001 PHE A 818 TRP 0.004 0.001 TRP A 72 HIS 0.003 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 7793) covalent geometry : angle 0.47226 / 0.25 (10555) SS BOND : bond 0.00082 / 0.04 ( 1) SS BOND : angle 0.14562 / 0.08 ( 2) hydrogen bonds : bond 0.03491 / 2.39 ( 432) hydrogen bonds : angle 4.27549 / 3.10 ( 1356) *********************** 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 156 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.396 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: A 248 MET cc_start: 0.7455 (mmt) cc_final: 0.6924 (mmp) outliers start: 14 outliers final: 11 residues processed: 152 average time/residue: 0.1413 time to fit residues: 31.0943 Evaluate side-chains 148 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 ASN ** A 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4159 r_free = 0.4159 target = 0.180605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143287 restraints weight = 24584.705| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.18 r_work: 0.3554 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7794 Z= 0.116 Angle : 0.474 5.347 10557 Z= 0.251 Chirality : 0.040 0.169 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.692 102.096 1090 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.54 % Allowed : 14.54 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.27), residues: 989 helix: 2.24 (0.23), residues: 486 sheet: -0.26 (0.44), residues: 137 loop : 0.20 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 213 TYR 0.010 0.001 TYR C 148 PHE 0.023 0.001 PHE A 818 TRP 0.004 0.001 TRP A 72 HIS 0.003 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 7793) covalent geometry : angle 0.47354 / 0.25 (10555) SS BOND : bond 0.00086 / 0.05 ( 1) SS BOND : angle 0.17878 / 0.10 ( 2) hydrogen bonds : bond 0.03418 / 2.33 ( 432) hydrogen bonds : angle 4.22047 / 3.07 ( 1356) *********************** 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 153 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.327 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: A 213 ARG cc_start: 0.6827 (mmp80) cc_final: 0.6385 (mmp80) REVERT: A 248 MET cc_start: 0.7385 (mmt) cc_final: 0.6852 (mmp) outliers start: 13 outliers final: 12 residues processed: 150 average time/residue: 0.1387 time to fit residues: 29.6449 Evaluate side-chains 147 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 88 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN ** A 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4139 r_free = 0.4139 target = 0.178871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.138923 restraints weight = 24902.331| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.51 r_work: 0.3515 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7794 Z= 0.163 Angle : 0.504 5.473 10557 Z= 0.269 Chirality : 0.041 0.173 1248 Planarity : 0.004 0.055 1328 Dihedral : 7.846 102.738 1090 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.42 % Allowed : 15.25 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.27), residues: 989 helix: 2.04 (0.23), residues: 484 sheet: -0.02 (0.43), residues: 147 loop : 0.13 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 213 TYR 0.011 0.001 TYR A 483 PHE 0.024 0.001 PHE A 818 TRP 0.004 0.001 TRP C 66 HIS 0.003 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 7793) covalent geometry : angle 0.50424 / 0.27 (10555) SS BOND : bond 0.00041 / 0.02 ( 1) SS BOND : angle 0.10963 / 0.06 ( 2) hydrogen bonds : bond 0.03659 / 2.52 ( 432) hydrogen bonds : angle 4.31285 / 3.14 ( 1356) *********************** 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 150 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.6830 (mmp80) cc_final: 0.6522 (mmp80) REVERT: A 248 MET cc_start: 0.7304 (mmt) cc_final: 0.6784 (mmp) REVERT: A 766 TRP cc_start: 0.6750 (p-90) cc_final: 0.6448 (p-90) outliers start: 12 outliers final: 12 residues processed: 147 average time/residue: 0.1445 time to fit residues: 30.9974 Evaluate side-chains 145 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 20 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 17 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 ASN ** A 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4153 r_free = 0.4153 target = 0.180228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142765 restraints weight = 24673.908| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.18 r_work: 0.3548 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7794 Z= 0.122 Angle : 0.483 6.050 10557 Z= 0.255 Chirality : 0.040 0.170 1248 Planarity : 0.004 0.054 1328 Dihedral : 7.689 101.045 1090 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.54 % Allowed : 15.13 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.27), residues: 989 helix: 2.22 (0.23), residues: 484 sheet: -0.13 (0.45), residues: 135 loop : 0.17 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 213 TYR 0.010 0.001 TYR A 483 PHE 0.027 0.001 PHE A 818 TRP 0.003 0.001 TRP A 72 HIS 0.003 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7793) covalent geometry : angle 0.48286 / 0.26 (10555) SS BOND : bond 0.00073 / 0.04 ( 1) SS BOND : angle 0.14671 / 0.08 ( 2) hydrogen bonds : bond 0.03458 / 2.36 ( 432) hydrogen bonds : angle 4.20371 / 3.05 ( 1356) *********************** 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 152 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.345 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: 0.6770 (mmp80) cc_final: 0.6456 (mmp80) REVERT: A 248 MET cc_start: 0.7270 (mmt) cc_final: 0.6749 (mmp) REVERT: A 605 GLN cc_start: 0.7959 (tp40) cc_final: 0.7732 (tp40) outliers start: 13 outliers final: 12 residues processed: 149 average time/residue: 0.1373 time to fit residues: 29.7557 Evaluate side-chains 148 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 65 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 ASN ** A 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 HIS C 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.179820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138304 restraints weight = 24762.115| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.26 r_work: 0.3534 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7794 Z= 0.133 Angle : 0.489 6.450 10557 Z= 0.259 Chirality : 0.040 0.169 1248 Planarity : 0.004 0.053 1328 Dihedral : 7.711 101.336 1090 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.54 % Allowed : 14.89 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.27), residues: 989 helix: 2.21 (0.23), residues: 484 sheet: -0.02 (0.43), residues: 147 loop : 0.18 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 213 TYR 0.010 0.001 TYR A 483 PHE 0.025 0.001 PHE A 818 TRP 0.003 0.001 TRP A 72 HIS 0.003 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7793) covalent geometry : angle 0.48927 / 0.26 (10555) SS BOND : bond 0.00071 / 0.04 ( 1) SS BOND : angle 0.10965 / 0.06 ( 2) hydrogen bonds : bond 0.03486 / 2.39 ( 432) hydrogen bonds : angle 4.19502 / 3.05 ( 1356) ********************** 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 151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.312 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: 0.6797 (mmp80) cc_final: 0.6190 (mmp80) REVERT: A 605 GLN cc_start: 0.8032 (tp40) cc_final: 0.7744 (tp40) outliers start: 13 outliers final: 13 residues processed: 147 average time/residue: 0.1432 time to fit residues: 30.2681 Evaluate side-chains 151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 84 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 ASN ** A 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 HIS C 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.180093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.142608 restraints weight = 24632.041| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.18 r_work: 0.3542 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.221 7794 Z= 0.177 Angle : 0.873 59.196 10557 Z= 0.516 Chirality : 0.040 0.259 1248 Planarity : 0.004 0.053 1328 Dihedral : 7.713 100.951 1090 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.54 % Allowed : 15.13 % Favored : 83.33 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.27), residues: 989 helix: 2.22 (0.23), residues: 484 sheet: -0.13 (0.45), residues: 135 loop : 0.17 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 213 TYR 0.010 0.001 TYR A 483 PHE 0.022 0.001 PHE A 818 TRP 0.003 0.001 TRP A 72 HIS 0.003 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 7793) covalent geometry : angle 0.87317 / 0.52 (10555) SS BOND : bond 0.00072 / 0.04 ( 1) SS BOND : angle 0.09907 / 0.05 ( 2) hydrogen bonds : bond 0.03470 / 2.38 ( 432) hydrogen bonds : angle 4.19106 / 3.04 ( 1356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3687.63 seconds wall clock time: 63 minutes 6.47 seconds (3786.47 seconds total)