Starting phenix.real_space_refine on Sat May 17 06:57:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yag_33711/05_2025/7yag_33711_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yag_33711/05_2025/7yag_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_33711/05_2025/7yag_33711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yag_33711/05_2025/7yag_33711.map" model { file = "/net/cci-nas-00/data/ceres_data/7yag_33711/05_2025/7yag_33711_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yag_33711/05_2025/7yag_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-5687/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: 6.97, per 1000 atoms: 0.45 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: 3.98 Conformation dependent library (CDL) restraints added in 1.2 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: 1.37 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: 6.02 Time building geometry restraints manager: 4.72 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: 0.670 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: 0.240 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.760 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.200 ------------------------------------------------------------------------------- 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 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.11837 ( 432) hydrogen bonds : angle 6.00161 ( 1356) SS BOND : bond 0.00363 ( 1) SS BOND : angle 0.71708 ( 2) covalent geometry : bond 0.00469 ( 7793) covalent geometry : angle 0.80749 (10555) *********************** 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 : 1.245 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: 0.3821 time to fit residues: 78.8115 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 : 1.103 ------------------------------------------------------------------------------- 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: 8.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.178997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.138532 restraints weight = 24552.503| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.38 r_work: 0.3505 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 7794 Z= 0.219 Angle : 0.556 5.828 10557 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 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 432) hydrogen bonds : angle 4.98257 ( 1356) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.39107 ( 2) covalent geometry : bond 0.00511 ( 7793) covalent geometry : angle 0.55584 (10555) *********************** 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 : 1.179 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: 0.7895 (tp30) cc_final: 0.7501 (tm-30) REVERT: A 262 MET cc_start: 0.8318 (mmt) cc_final: 0.8036 (mmp) REVERT: A 671 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6859 (mm-30) REVERT: A 899 GLU cc_start: 0.6630 (mp0) cc_final: 0.6170 (mp0) outliers start: 10 outliers final: 7 residues processed: 150 average time/residue: 0.3931 time to fit residues: 82.5590 Evaluate side-chains 148 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 66 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 88 optimal weight: 40.0000 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.176822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.135981 restraints weight = 24708.190| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.49 r_work: 0.3473 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7794 Z= 0.212 Angle : 0.549 5.851 10557 Z= 0.296 Chirality : 0.042 0.188 1248 Planarity : 0.005 0.058 1328 Dihedral : 8.214 106.754 1090 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.13 % Allowed : 11.94 % 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 (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: 0.89 (0.26), residues: 989 helix: 1.41 (0.23), residues: 487 sheet: -0.34 (0.42), residues: 148 loop : 0.01 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 72 HIS 0.003 0.001 HIS A 149 PHE 0.017 0.002 PHE A 176 TYR 0.013 0.001 TYR C 143 ARG 0.003 0.000 ARG A 174 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 432) hydrogen bonds : angle 4.80795 ( 1356) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.14465 ( 2) covalent geometry : bond 0.00496 ( 7793) covalent geometry : angle 0.54926 (10555) *********************** 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 164 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.117 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 213 ARG cc_start: 0.6820 (mmp80) cc_final: 0.6492 (mmp80) REVERT: A 671 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7088 (tm-30) REVERT: A 899 GLU cc_start: 0.6570 (mp0) cc_final: 0.6307 (mp0) outliers start: 18 outliers final: 15 residues processed: 157 average time/residue: 0.3677 time to fit residues: 82.0642 Evaluate side-chains 159 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 437 MET 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 751 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.179137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.139802 restraints weight = 24524.466| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.49 r_work: 0.3528 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1467 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= 0.123 Angle : 0.481 5.473 10557 Z= 0.258 Chirality : 0.040 0.178 1248 Planarity : 0.004 0.060 1328 Dihedral : 7.925 104.297 1090 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.42 % Allowed : 13.24 % 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: 1.25 (0.27), residues: 989 helix: 1.87 (0.23), residues: 486 sheet: -0.54 (0.43), residues: 137 loop : 0.09 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 72 HIS 0.002 0.001 HIS C 86 PHE 0.017 0.001 PHE A 818 TYR 0.010 0.001 TYR A 696 ARG 0.003 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 432) hydrogen bonds : angle 4.48396 ( 1356) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.16758 ( 2) covalent geometry : bond 0.00279 ( 7793) covalent geometry : angle 0.48146 (10555) *********************** 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 163 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 1.109 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: symmetry clash REVERT: A 899 GLU cc_start: 0.6545 (mp0) cc_final: 0.6339 (mp0) REVERT: C 148 TYR cc_start: 0.7072 (m-80) cc_final: 0.6851 (m-80) outliers start: 12 outliers final: 10 residues processed: 159 average time/residue: 0.4055 time to fit residues: 91.8522 Evaluate side-chains 156 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 776 ILE 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 2 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.177490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.137668 restraints weight = 24881.573| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.54 r_work: 0.3497 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7794 Z= 0.175 Angle : 0.507 5.507 10557 Z= 0.273 Chirality : 0.041 0.180 1248 Planarity : 0.004 0.059 1328 Dihedral : 7.991 105.394 1090 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.77 % Allowed : 13.95 % Favored : 84.28 % 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: 1.24 (0.27), residues: 989 helix: 1.77 (0.23), residues: 485 sheet: -0.26 (0.42), residues: 147 loop : 0.10 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 72 HIS 0.002 0.001 HIS C 86 PHE 0.018 0.001 PHE A 818 TYR 0.011 0.001 TYR A 696 ARG 0.003 0.000 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 432) hydrogen bonds : angle 4.52416 ( 1356) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.06550 ( 2) covalent geometry : bond 0.00409 ( 7793) covalent geometry : angle 0.50712 (10555) *********************** 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 162 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.126 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 899 GLU cc_start: 0.6533 (mp0) cc_final: 0.6156 (mp0) outliers start: 15 outliers final: 13 residues processed: 157 average time/residue: 0.3789 time to fit residues: 83.6964 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 : 1.233 ------------------------------------------------------------------------------- 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 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 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 68 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 606 GLN C 86 HIS ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.180308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143009 restraints weight = 24656.865| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.19 r_work: 0.3553 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7794 Z= 0.102 Angle : 0.465 5.309 10557 Z= 0.248 Chirality : 0.040 0.172 1248 Planarity : 0.004 0.059 1328 Dihedral : 7.690 101.349 1090 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.30 % Allowed : 15.01 % Favored : 83.69 % 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: 2.16 (0.23), residues: 484 sheet: -0.43 (0.44), residues: 137 loop : 0.13 (0.34), residues: 368 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 0.023 0.001 PHE A 818 TYR 0.010 0.001 TYR A 696 ARG 0.006 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 432) hydrogen bonds : angle 4.27235 ( 1356) SS BOND : bond 0.00087 ( 1) SS BOND : angle 0.16766 ( 2) covalent geometry : bond 0.00225 ( 7793) covalent geometry : angle 0.46462 (10555) *********************** 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 163 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 1.112 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 323 MET cc_start: 0.7669 (mtp) cc_final: 0.7446 (mtp) REVERT: A 605 GLN cc_start: 0.7853 (tp40) cc_final: 0.7597 (tp40) outliers start: 11 outliers final: 9 residues processed: 160 average time/residue: 0.3697 time to fit residues: 83.2736 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 : 1.112 ------------------------------------------------------------------------------- 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 564 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 870 THR 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 23 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.176833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.137076 restraints weight = 25055.367| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.54 r_work: 0.3495 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7794 Z= 0.200 Angle : 0.524 6.299 10557 Z= 0.281 Chirality : 0.042 0.180 1248 Planarity : 0.005 0.059 1328 Dihedral : 7.977 103.622 1090 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: 1.27 (0.27), residues: 989 helix: 1.82 (0.23), residues: 484 sheet: -0.16 (0.43), residues: 147 loop : 0.03 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 66 HIS 0.003 0.001 HIS A 467 PHE 0.021 0.002 PHE A 818 TYR 0.011 0.001 TYR C 143 ARG 0.007 0.001 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 432) hydrogen bonds : angle 4.47181 ( 1356) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.10948 ( 2) covalent geometry : bond 0.00467 ( 7793) covalent geometry : angle 0.52447 (10555) *********************** 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 156 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 1.254 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 248 MET cc_start: 0.7133 (mmt) cc_final: 0.6613 (mmp) REVERT: A 899 GLU cc_start: 0.6372 (mm-30) cc_final: 0.5409 (mp0) outliers start: 13 outliers final: 12 residues processed: 152 average time/residue: 0.4110 time to fit residues: 88.5134 Evaluate side-chains 151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 75 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.178760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137465 restraints weight = 24743.060| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.25 r_work: 0.3527 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1928 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= 0.125 Angle : 0.490 7.011 10557 Z= 0.260 Chirality : 0.040 0.175 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.783 102.441 1090 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.42 % Allowed : 15.60 % Favored : 82.98 % 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: 1.46 (0.27), residues: 989 helix: 2.05 (0.23), residues: 484 sheet: -0.17 (0.45), residues: 130 loop : 0.04 (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 696 ARG 0.008 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 432) hydrogen bonds : angle 4.31179 ( 1356) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.13671 ( 2) covalent geometry : bond 0.00288 ( 7793) covalent geometry : angle 0.48955 (10555) *********************** 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 162 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 1.190 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 899 GLU cc_start: 0.6243 (mm-30) cc_final: 0.5274 (mp0) outliers start: 12 outliers final: 11 residues processed: 158 average time/residue: 0.3768 time to fit residues: 83.3716 Evaluate side-chains 154 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 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 55 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 855 GLN C 86 HIS ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.179547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.142274 restraints weight = 24839.844| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.17 r_work: 0.3544 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7794 Z= 0.115 Angle : 0.489 7.866 10557 Z= 0.257 Chirality : 0.040 0.170 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.675 100.779 1090 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.65 % Allowed : 16.19 % Favored : 82.15 % 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: 1.63 (0.27), residues: 989 helix: 2.23 (0.23), residues: 484 sheet: -0.17 (0.45), residues: 130 loop : 0.10 (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 0.028 0.001 PHE A 818 TYR 0.009 0.001 TYR A 696 ARG 0.003 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 432) hydrogen bonds : angle 4.22050 ( 1356) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.16455 ( 2) covalent geometry : bond 0.00265 ( 7793) covalent geometry : angle 0.48935 (10555) *********************** 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 162 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.138 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 899 GLU cc_start: 0.6436 (mm-30) cc_final: 0.5496 (mp0) outliers start: 14 outliers final: 12 residues processed: 158 average time/residue: 0.4089 time to fit residues: 91.3409 Evaluate side-chains 158 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 25 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 87 optimal weight: 40.0000 chunk 30 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 855 GLN C 86 HIS C 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.176842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135427 restraints weight = 24888.987| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.61 r_work: 0.3473 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2048 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= 0.165 Angle : 0.520 8.076 10557 Z= 0.276 Chirality : 0.041 0.177 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.865 102.352 1090 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.65 % Allowed : 16.31 % Favored : 82.03 % 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: 1.42 (0.27), residues: 989 helix: 1.99 (0.23), residues: 483 sheet: -0.05 (0.44), residues: 142 loop : 0.01 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 66 HIS 0.003 0.001 HIS C 86 PHE 0.024 0.001 PHE A 818 TYR 0.009 0.001 TYR C 112 ARG 0.003 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 432) hydrogen bonds : angle 4.33823 ( 1356) SS BOND : bond 0.00050 ( 1) SS BOND : angle 0.08505 ( 2) covalent geometry : bond 0.00386 ( 7793) covalent geometry : angle 0.52009 (10555) ********************** 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 162 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.429 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 899 GLU cc_start: 0.6250 (mm-30) cc_final: 0.5271 (mp0) outliers start: 14 outliers final: 13 residues processed: 157 average time/residue: 0.3966 time to fit residues: 87.0423 Evaluate side-chains 156 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.176941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.135902 restraints weight = 24747.212| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.52 r_work: 0.3483 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 7794 Z= 0.195 Angle : 0.889 59.199 10557 Z= 0.524 Chirality : 0.041 0.253 1248 Planarity : 0.004 0.059 1328 Dihedral : 7.872 102.385 1090 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.54 % Allowed : 16.55 % Favored : 81.91 % Cbeta Deviations : 0.11 % 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: 1.42 (0.27), residues: 989 helix: 1.98 (0.23), residues: 483 sheet: 0.07 (0.44), residues: 139 loop : -0.03 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 66 HIS 0.003 0.001 HIS C 86 PHE 0.023 0.001 PHE A 818 TYR 0.009 0.001 TYR A 696 ARG 0.003 0.000 ARG A 174 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 432) hydrogen bonds : angle 4.33688 ( 1356) SS BOND : bond 0.00064 ( 1) SS BOND : angle 0.08358 ( 2) covalent geometry : bond 0.00452 ( 7793) covalent geometry : angle 0.88934 (10555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8576.74 seconds wall clock time: 147 minutes 29.40 seconds (8849.40 seconds total)