Starting phenix.real_space_refine on Fri Jun 13 20:14:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yag_33711/06_2025/7yag_33711_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yag_33711/06_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_33711/06_2025/7yag_33711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yag_33711/06_2025/7yag_33711.map" model { file = "/net/cci-nas-00/data/ceres_data/7yag_33711/06_2025/7yag_33711_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yag_33711/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15456 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 13594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 13594 Classifications: {'peptide': 876} Link IDs: {'PTRANS': 34, 'TRANS': 841} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1830 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.92, per 1000 atoms: 0.51 Number of scatterers: 15456 At special positions: 0 Unit cell: (85.695, 83.725, 134.945, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 55 16.00 P 3 15.00 O 1450 8.00 N 1285 7.00 C 4872 6.00 H 7790 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 128 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.89 Conformation dependent library (CDL) restraints added in 1.8 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: 1.56 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: 7.17 Time building geometry restraints manager: 5.25 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.240 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.990 Find NCS groups from input model: 0.130 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.080 ------------------------------------------------------------------------------- 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 : 1.016 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: 0.4150 time to fit residues: 86.5585 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 : 1.266 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.179104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138577 restraints weight = 24560.872| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.38 r_work: 0.3507 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.0991 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= 0.218 Angle : 0.556 5.855 10557 Z= 0.301 Chirality : 0.043 0.203 1248 Planarity : 0.005 0.058 1328 Dihedral : 8.509 110.145 1092 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.49 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 0.015 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 0.04289 ( 432) hydrogen bonds : angle 4.98662 ( 1356) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.38446 ( 2) covalent geometry : bond 0.00509 ( 7793) covalent geometry : angle 0.55572 (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 : 1.392 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: 0.7887 (tp30) cc_final: 0.7502 (tm-30) REVERT: A 262 MET cc_start: 0.8320 (mmt) cc_final: 0.8039 (mmp) REVERT: A 671 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6899 (mm-30) REVERT: A 899 GLU cc_start: 0.6646 (mp0) cc_final: 0.6199 (mp0) outliers start: 10 outliers final: 7 residues processed: 150 average time/residue: 0.3807 time to fit residues: 79.9622 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 : 1.081 ------------------------------------------------------------------------------- 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: 8.9990 chunk 16 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.177361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.136591 restraints weight = 24664.153| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.47 r_work: 0.3480 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7794 Z= 0.197 Angle : 0.538 5.810 10557 Z= 0.290 Chirality : 0.042 0.185 1248 Planarity : 0.005 0.058 1328 Dihedral : 8.165 106.680 1090 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.01 % Allowed : 11.94 % Favored : 86.05 % 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: 0.95 (0.26), residues: 989 helix: 1.48 (0.23), residues: 487 sheet: -0.33 (0.42), residues: 148 loop : 0.02 (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 806 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 432) hydrogen bonds : angle 4.76217 ( 1356) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.16634 ( 2) covalent geometry : bond 0.00461 ( 7793) covalent geometry : angle 0.53831 (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 165 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.6794 (mmp80) cc_final: 0.6464 (mmp80) REVERT: A 671 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7087 (tm-30) REVERT: A 899 GLU cc_start: 0.6570 (mp0) cc_final: 0.6329 (mp0) REVERT: C 148 TYR cc_start: 0.7099 (m-80) cc_final: 0.6898 (m-80) outliers start: 17 outliers final: 15 residues processed: 159 average time/residue: 0.3755 time to fit residues: 84.6270 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 : 1.212 ------------------------------------------------------------------------------- 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: 3.9990 chunk 6 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.179250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139834 restraints weight = 24518.871| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.52 r_work: 0.3519 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1472 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= 0.125 Angle : 0.482 5.524 10557 Z= 0.258 Chirality : 0.040 0.178 1248 Planarity : 0.004 0.060 1328 Dihedral : 7.920 104.172 1090 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.42 % Allowed : 13.00 % Favored : 85.58 % 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: 1.88 (0.23), residues: 486 sheet: -0.52 (0.43), residues: 137 loop : 0.10 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 72 HIS 0.002 0.001 HIS C 86 PHE 0.014 0.001 PHE A 818 TYR 0.010 0.001 TYR A 696 ARG 0.002 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 432) hydrogen bonds : angle 4.48133 ( 1356) SS BOND : bond 0.00084 ( 1) SS BOND : angle 0.16012 ( 2) covalent geometry : bond 0.00284 ( 7793) covalent geometry : angle 0.48195 (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 161 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 1.108 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 899 GLU cc_start: 0.6573 (mp0) cc_final: 0.6347 (mp0) outliers start: 12 outliers final: 9 residues processed: 157 average time/residue: 0.3898 time to fit residues: 85.7519 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 : 1.263 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 77 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 21 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.178722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.139385 restraints weight = 24808.234| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.50 r_work: 0.3515 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1606 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= 0.143 Angle : 0.486 5.489 10557 Z= 0.260 Chirality : 0.040 0.177 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.866 104.092 1090 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.65 % Allowed : 13.59 % Favored : 84.75 % 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: 1.36 (0.27), residues: 989 helix: 1.95 (0.23), residues: 485 sheet: -0.44 (0.44), residues: 137 loop : 0.14 (0.34), residues: 367 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 0.016 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 0.03662 ( 432) hydrogen bonds : angle 4.42782 ( 1356) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.07621 ( 2) covalent geometry : bond 0.00331 ( 7793) covalent geometry : angle 0.48613 (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 165 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.328 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: 0.6603 (mp0) cc_final: 0.6343 (mp0) outliers start: 14 outliers final: 12 residues processed: 161 average time/residue: 0.4138 time to fit residues: 96.1894 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 : 1.597 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.180060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142543 restraints weight = 24681.557| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.20 r_work: 0.3537 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1683 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= 0.112 Angle : 0.471 6.301 10557 Z= 0.250 Chirality : 0.040 0.172 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.712 102.072 1090 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.54 % Allowed : 14.78 % 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: 1.56 (0.27), residues: 989 helix: 2.14 (0.23), residues: 486 sheet: -0.37 (0.44), residues: 137 loop : 0.19 (0.34), residues: 366 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 0.018 0.001 PHE A 818 TYR 0.011 0.001 TYR C 148 ARG 0.009 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 432) hydrogen bonds : angle 4.27768 ( 1356) SS BOND : bond 0.00078 ( 1) SS BOND : angle 0.15760 ( 2) covalent geometry : bond 0.00252 ( 7793) covalent geometry : angle 0.47097 (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 162 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 1.176 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: 0.7212 (mmt) cc_final: 0.6677 (mmp) outliers start: 13 outliers final: 11 residues processed: 158 average time/residue: 0.4061 time to fit residues: 90.9529 Evaluate side-chains 155 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 23 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.176193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136569 restraints weight = 25097.160| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.44 r_work: 0.3485 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7794 Z= 0.219 Angle : 0.539 5.626 10557 Z= 0.290 Chirality : 0.042 0.181 1248 Planarity : 0.005 0.059 1328 Dihedral : 8.056 103.449 1090 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.77 % Allowed : 15.48 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.27), residues: 989 helix: 1.70 (0.23), residues: 482 sheet: -0.13 (0.43), residues: 147 loop : 0.05 (0.35), residues: 360 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 0.019 0.002 PHE A 818 TYR 0.012 0.001 TYR C 143 ARG 0.003 0.000 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 432) hydrogen bonds : angle 4.53327 ( 1356) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.07047 ( 2) covalent geometry : bond 0.00515 ( 7793) covalent geometry : angle 0.53881 (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 158 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 1.232 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: 0.7291 (mmt) cc_final: 0.6772 (mmp) REVERT: A 899 GLU cc_start: 0.6332 (mm-30) cc_final: 0.5407 (mp0) outliers start: 15 outliers final: 13 residues processed: 153 average time/residue: 0.3954 time to fit residues: 84.4957 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 : 1.236 ------------------------------------------------------------------------------- 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=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: 1.9990 chunk 25 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.178072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138949 restraints weight = 24779.807| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.45 r_work: 0.3512 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1964 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= 0.140 Angle : 0.501 6.685 10557 Z= 0.267 Chirality : 0.040 0.179 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.860 102.676 1090 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.54 % Allowed : 16.08 % Favored : 82.39 % 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: 1.35 (0.27), residues: 989 helix: 1.90 (0.23), residues: 484 sheet: -0.03 (0.44), residues: 142 loop : 0.02 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 72 HIS 0.003 0.001 HIS C 86 PHE 0.025 0.001 PHE A 818 TYR 0.009 0.001 TYR A 696 ARG 0.003 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 432) hydrogen bonds : angle 4.37402 ( 1356) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.07407 ( 2) covalent geometry : bond 0.00322 ( 7793) covalent geometry : angle 0.50133 (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 156 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 1.174 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: 0.7303 (mmt) cc_final: 0.6793 (mmp) REVERT: A 899 GLU cc_start: 0.6419 (mm-30) cc_final: 0.5467 (mp0) outliers start: 13 outliers final: 12 residues processed: 152 average time/residue: 0.4176 time to fit residues: 89.6054 Evaluate side-chains 152 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 55 optimal weight: 0.1980 chunk 16 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 C 134 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.180135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.142726 restraints weight = 24793.362| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.19 r_work: 0.3547 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7794 Z= 0.105 Angle : 0.484 8.078 10557 Z= 0.256 Chirality : 0.040 0.168 1248 Planarity : 0.004 0.057 1328 Dihedral : 7.606 100.313 1090 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.30 % Allowed : 16.08 % Favored : 82.62 % 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: 1.65 (0.27), residues: 989 helix: 2.25 (0.23), residues: 484 sheet: -0.15 (0.45), residues: 130 loop : 0.10 (0.34), residues: 375 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 0.030 0.001 PHE A 818 TYR 0.010 0.001 TYR C 112 ARG 0.003 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 432) hydrogen bonds : angle 4.17781 ( 1356) SS BOND : bond 0.00101 ( 1) SS BOND : angle 0.15008 ( 2) covalent geometry : bond 0.00238 ( 7793) covalent geometry : angle 0.48438 (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 158 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.181 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 323 MET cc_start: 0.7451 (mtp) cc_final: 0.7132 (mtp) REVERT: A 899 GLU cc_start: 0.6450 (mm-30) cc_final: 0.5550 (mp0) outliers start: 11 outliers final: 10 residues processed: 155 average time/residue: 0.3935 time to fit residues: 85.2672 Evaluate side-chains 154 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 776 ILE Chi-restraints excluded: chain A residue 870 THR 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 25 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 87 optimal weight: 40.0000 chunk 30 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.177843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138224 restraints weight = 25004.394| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.47 r_work: 0.3509 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2044 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= 0.176 Angle : 0.523 8.025 10557 Z= 0.276 Chirality : 0.041 0.171 1248 Planarity : 0.004 0.059 1328 Dihedral : 7.803 102.155 1090 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.18 % Allowed : 16.55 % Favored : 82.27 % 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: 1.48 (0.27), residues: 989 helix: 2.04 (0.23), residues: 484 sheet: -0.02 (0.44), residues: 142 loop : 0.03 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 460 HIS 0.003 0.001 HIS C 86 PHE 0.026 0.002 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 0.03616 ( 432) hydrogen bonds : angle 4.30561 ( 1356) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.15147 ( 2) covalent geometry : bond 0.00412 ( 7793) covalent geometry : angle 0.52311 (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 153 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 1.132 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 323 MET cc_start: 0.7597 (mtp) cc_final: 0.7294 (mtp) REVERT: A 899 GLU cc_start: 0.6439 (mm-30) cc_final: 0.5458 (mp0) outliers start: 10 outliers final: 10 residues processed: 151 average time/residue: 0.4247 time to fit residues: 90.7429 Evaluate side-chains 151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 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: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN C 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.178141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139000 restraints weight = 24830.407| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.48 r_work: 0.3514 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2090 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= 0.149 Angle : 0.510 7.824 10557 Z= 0.269 Chirality : 0.040 0.174 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.786 101.749 1090 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.30 % Allowed : 16.67 % 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: 1.49 (0.27), residues: 989 helix: 2.03 (0.23), residues: 484 sheet: -0.00 (0.44), residues: 142 loop : 0.06 (0.35), residues: 363 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 0.025 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 0.03566 ( 432) hydrogen bonds : angle 4.27200 ( 1356) SS BOND : bond 0.00020 ( 1) SS BOND : angle 0.06188 ( 2) covalent geometry : bond 0.00347 ( 7793) covalent geometry : angle 0.50991 (10555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9313.08 seconds wall clock time: 162 minutes 18.14 seconds (9738.14 seconds total)