Starting phenix.real_space_refine on Fri Jul 3 02:06:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7aua_11926/07_2026/7aua_11926.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aua_11926/07_2026/7aua_11926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7aua_11926/07_2026/7aua_11926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aua_11926/07_2026/7aua_11926.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7aua_11926/07_2026/7aua_11926.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7aua_11926/07_2026/7aua_11926.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aua_11926/07_2026/7aua_11926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aua_11926/07_2026/7aua_11926.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 4 5.49 5 S 56 5.16 5 C 7276 2.51 5 N 1896 2.21 5 O 2066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11300 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5546 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MN': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, E, F Time building chain proxies: 4.53, per 1000 atoms: 0.40 Number of scatterers: 11300 At special positions: 0 Unit cell: (94.785, 99.045, 104.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 56 16.00 P 4 15.00 O 2066 8.00 N 1896 7.00 C 7276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 182 " distance=2.04 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 793 " - pdb=" SG CYS B 915 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 879 " distance=2.03 Simple disulfide: pdb=" SG CYS A 915 " - pdb=" SG CYS B 793 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 182 " distance=2.04 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 831 " - pdb=" SG CYS B 879 " 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 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG C 1 " - " ASN A 592 " " NAG D 1 " - " ASN A 790 " " NAG E 1 " - " ASN B 592 " " NAG F 1 " - " ASN B 790 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 439.0 milliseconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 11 sheets defined 38.9% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 210 removed outlier: 4.568A pdb=" N TYR A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 252 through 262 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 327 through 331 removed outlier: 4.137A pdb=" N GLU A 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 removed outlier: 3.520A pdb=" N LYS A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 426 removed outlier: 4.206A pdb=" N LEU A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.547A pdb=" N VAL A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 486 through 491 removed outlier: 4.209A pdb=" N THR A 491 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.552A pdb=" N LEU A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 520 Processing helix chain 'A' and resid 522 through 538 Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.692A pdb=" N THR A 596 " --> pdb=" O ASN A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 606 Processing helix chain 'A' and resid 624 through 631 removed outlier: 3.521A pdb=" N ALA A 627 " --> pdb=" O PRO A 624 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 628 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 629 " --> pdb=" O GLU A 626 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY A 631 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.710A pdb=" N GLY A 641 " --> pdb=" O PRO A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.657A pdb=" N ALA A 652 " --> pdb=" O LYS A 648 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.558A pdb=" N LEU A 730 " --> pdb=" O ASN A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 764 Processing helix chain 'A' and resid 807 through 816 Processing helix chain 'A' and resid 818 through 828 removed outlier: 3.931A pdb=" N ARG A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 845 removed outlier: 3.925A pdb=" N ALA A 835 " --> pdb=" O CYS A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 888 removed outlier: 3.917A pdb=" N ARG A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 205 through 210 removed outlier: 4.569A pdb=" N TYR B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 327 through 331 removed outlier: 4.137A pdb=" N GLU B 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 390 removed outlier: 3.519A pdb=" N LYS B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 426 removed outlier: 4.206A pdb=" N LEU B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 457 removed outlier: 3.546A pdb=" N VAL B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 481 Processing helix chain 'B' and resid 486 through 491 removed outlier: 4.208A pdb=" N THR B 491 " --> pdb=" O PRO B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.552A pdb=" N LEU B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 520 Processing helix chain 'B' and resid 522 through 538 Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.692A pdb=" N THR B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 606 Processing helix chain 'B' and resid 624 through 631 removed outlier: 3.521A pdb=" N ALA B 627 " --> pdb=" O PRO B 624 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 628 " --> pdb=" O SER B 625 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 629 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY B 631 " --> pdb=" O LYS B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.710A pdb=" N GLY B 641 " --> pdb=" O PRO B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.657A pdb=" N ALA B 652 " --> pdb=" O LYS B 648 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 682 Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.558A pdb=" N LEU B 730 " --> pdb=" O ASN B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 764 Processing helix chain 'B' and resid 807 through 816 Processing helix chain 'B' and resid 818 through 828 removed outlier: 3.931A pdb=" N ARG B 822 " --> pdb=" O PRO B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 845 removed outlier: 3.926A pdb=" N ALA B 835 " --> pdb=" O CYS B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 888 removed outlier: 3.917A pdb=" N ARG B 876 " --> pdb=" O HIS B 872 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 198 removed outlier: 6.388A pdb=" N TYR A 238 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE A 276 " --> pdb=" O TYR A 238 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE A 240 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL A 298 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.936A pdb=" N ILE A 443 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 395 through 397 removed outlier: 8.553A pdb=" N TYR A 341 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA A 431 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE A 343 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N ILE A 433 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N PHE A 345 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR A 429 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL A 462 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA A 431 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU A 464 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE A 433 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 552 through 553 removed outlier: 4.504A pdb=" N VAL A 717 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE A 663 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL A 693 " --> pdb=" O PHE A 663 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL A 665 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL A 695 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET A 667 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A 664 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE A 743 " --> pdb=" O THR A 664 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL A 666 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 784 through 788 Processing sheet with id=AA6, first strand: chain 'A' and resid 898 through 900 Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 198 removed outlier: 6.387A pdb=" N TYR B 238 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE B 276 " --> pdb=" O TYR B 238 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 240 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL B 298 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 304 removed outlier: 3.936A pdb=" N ILE B 443 " --> pdb=" O PHE B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 395 through 397 removed outlier: 8.553A pdb=" N TYR B 341 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA B 431 " --> pdb=" O TYR B 341 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE B 343 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N ILE B 433 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N PHE B 345 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR B 429 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 462 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA B 431 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU B 464 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE B 433 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 552 through 553 removed outlier: 4.504A pdb=" N VAL B 717 " --> pdb=" O ILE B 553 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N PHE B 663 " --> pdb=" O LYS B 691 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL B 693 " --> pdb=" O PHE B 663 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL B 665 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL B 695 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET B 667 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR B 664 " --> pdb=" O LEU B 741 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE B 743 " --> pdb=" O THR B 664 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL B 666 " --> pdb=" O ILE B 743 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 784 through 788 374 hydrogen bonds defined for protein. 996 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: 2.04 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3586 1.34 - 1.46: 2953 1.46 - 1.59: 4991 1.59 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 11618 Sorted by residual: bond pdb=" C HIS B 555 " pdb=" N ARG B 556 " ideal model delta sigma weight residual 1.330 1.533 -0.204 1.32e-02 5.74e+03 2.38e+02 bond pdb=" C HIS A 555 " pdb=" N ARG A 556 " ideal model delta sigma weight residual 1.330 1.533 -0.204 1.32e-02 5.74e+03 2.38e+02 bond pdb=" O1B UDP A1002 " pdb=" PB UDP A1002 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.00e-02 1.00e+04 1.62e+01 bond pdb=" O1B UDP B1002 " pdb=" PB UDP B1002 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.00e-02 1.00e+04 1.62e+01 bond pdb=" N PHE B 918 " pdb=" CA PHE B 918 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.14e-02 7.69e+03 6.76e+00 ... (remaining 11613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 15498 1.84 - 3.67: 266 3.67 - 5.51: 43 5.51 - 7.34: 9 7.34 - 9.18: 4 Bond angle restraints: 15820 Sorted by residual: angle pdb=" O1B UDP B1002 " pdb=" PB UDP B1002 " pdb=" O3A UDP B1002 " ideal model delta sigma weight residual 102.95 112.13 -9.18 1.00e+00 1.00e+00 8.42e+01 angle pdb=" O1B UDP A1002 " pdb=" PB UDP A1002 " pdb=" O3A UDP A1002 " ideal model delta sigma weight residual 102.95 112.13 -9.18 1.00e+00 1.00e+00 8.42e+01 angle pdb=" O3A UDP A1002 " pdb=" PB UDP A1002 " pdb=" O3B UDP A1002 " ideal model delta sigma weight residual 112.01 102.98 9.03 1.00e+00 1.00e+00 8.16e+01 angle pdb=" O3A UDP B1002 " pdb=" PB UDP B1002 " pdb=" O3B UDP B1002 " ideal model delta sigma weight residual 112.01 103.00 9.01 1.00e+00 1.00e+00 8.11e+01 angle pdb=" CA TYR A 808 " pdb=" CB TYR A 808 " pdb=" CG TYR A 808 " ideal model delta sigma weight residual 113.90 117.96 -4.06 1.80e+00 3.09e-01 5.08e+00 ... (remaining 15815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 6278 17.25 - 34.51: 438 34.51 - 51.76: 72 51.76 - 69.01: 18 69.01 - 86.27: 16 Dihedral angle restraints: 6822 sinusoidal: 2784 harmonic: 4038 Sorted by residual: dihedral pdb=" CB CYS B 188 " pdb=" SG CYS B 188 " pdb=" SG CYS B 236 " pdb=" CB CYS B 236 " ideal model delta sinusoidal sigma weight residual -86.00 -167.60 81.60 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS A 188 " pdb=" SG CYS A 188 " pdb=" SG CYS A 236 " pdb=" CB CYS A 236 " ideal model delta sinusoidal sigma weight residual -86.00 -167.60 81.60 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CA ARG A 267 " pdb=" C ARG A 267 " pdb=" N THR A 268 " pdb=" CA THR A 268 " ideal model delta harmonic sigma weight residual -180.00 -152.10 -27.90 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 6819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1752 0.147 - 0.293: 6 0.293 - 0.440: 0 0.440 - 0.586: 0 0.586 - 0.733: 2 Chirality restraints: 1760 Sorted by residual: chirality pdb=" CG LEU A 251 " pdb=" CB LEU A 251 " pdb=" CD1 LEU A 251 " pdb=" CD2 LEU A 251 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CG LEU B 251 " pdb=" CB LEU B 251 " pdb=" CD1 LEU B 251 " pdb=" CD2 LEU B 251 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1757 not shown) Planarity restraints: 2012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 817 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO A 818 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 818 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 818 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 817 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO B 818 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 818 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 818 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 609 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO A 610 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 610 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 610 " 0.021 5.00e-02 4.00e+02 ... (remaining 2009 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 30 2.43 - 3.05: 7252 3.05 - 3.66: 15879 3.66 - 4.28: 25356 4.28 - 4.90: 43190 Nonbonded interactions: 91707 Sorted by model distance: nonbonded pdb="MN MN A1001 " pdb=" O2A UDP A1002 " model vdw 1.809 2.320 nonbonded pdb="MN MN B1001 " pdb=" O2A UDP B1002 " model vdw 1.809 2.320 nonbonded pdb="MN MN B1001 " pdb=" O2B UDP B1002 " model vdw 1.970 2.320 nonbonded pdb="MN MN A1001 " pdb=" O2B UDP A1002 " model vdw 1.970 2.320 nonbonded pdb=" OG1 THR B 617 " pdb=" OD1 ASP B 620 " model vdw 2.143 3.040 ... (remaining 91702 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.370 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.008 0.204 11640 Z= 0.350 Angle : 0.651 9.176 15876 Z= 0.359 Chirality : 0.052 0.733 1760 Planarity : 0.004 0.047 2008 Dihedral : 12.693 86.268 4180 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1356 helix: 0.73 (0.26), residues: 432 sheet: -1.32 (0.40), residues: 160 loop : -0.28 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 822 TYR 0.018 0.002 TYR A 808 PHE 0.019 0.002 PHE A 600 TRP 0.017 0.001 TRP B 266 HIS 0.005 0.001 HIS B 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.35 (11618) covalent geometry : angle 0.63894 / 0.36 (15820) SS BOND : bond 0.00286 / 0.18 ( 10) SS BOND : angle 2.35719 / 1.23 ( 20) hydrogen bonds : bond 0.18700 / 12.62 ( 374) hydrogen bonds : angle 6.85160 / 4.72 ( 996) link_ALPHA1-3 : bond 0.01091 / 0.65 ( 2) link_ALPHA1-3 : angle 2.21317 / 1.10 ( 6) link_BETA1-4 : bond 0.00738 / 0.51 ( 6) link_BETA1-4 : angle 1.43132 / 0.91 ( 18) link_NAG-ASN : bond 0.00233 / 0.14 ( 4) link_NAG-ASN : angle 2.76400 / 1.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.462 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.6893 time to fit residues: 88.0311 Evaluate side-chains 76 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0770 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.0980 chunk 55 optimal weight: 6.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.118968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.090970 restraints weight = 15556.503| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.23 r_work: 0.2902 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11640 Z= 0.112 Angle : 0.546 6.054 15876 Z= 0.285 Chirality : 0.043 0.149 1760 Planarity : 0.004 0.044 2008 Dihedral : 4.521 23.092 1512 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.25 % Allowed : 6.77 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.23), residues: 1356 helix: 1.29 (0.26), residues: 424 sheet: -0.70 (0.39), residues: 174 loop : 0.05 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 854 TYR 0.014 0.001 TYR B 808 PHE 0.014 0.001 PHE B 873 TRP 0.009 0.001 TRP A 696 HIS 0.006 0.001 HIS A 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (11618) covalent geometry : angle 0.53919 / 0.28 (15820) SS BOND : bond 0.00328 / 0.20 ( 10) SS BOND : angle 1.16001 / 0.70 ( 20) hydrogen bonds : bond 0.04348 / 2.86 ( 374) hydrogen bonds : angle 5.33719 / 3.68 ( 996) link_ALPHA1-3 : bond 0.00750 / 0.45 ( 2) link_ALPHA1-3 : angle 1.36305 / 0.82 ( 6) link_BETA1-4 : bond 0.00567 / 0.38 ( 6) link_BETA1-4 : angle 1.14752 / 0.74 ( 18) link_NAG-ASN : bond 0.00176 / 0.10 ( 4) link_NAG-ASN : angle 2.47315 / 1.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.454 Fit side-chains REVERT: A 391 LEU cc_start: 0.8602 (mp) cc_final: 0.8384 (mt) REVERT: A 669 THR cc_start: 0.9130 (p) cc_final: 0.8912 (p) REVERT: B 391 LEU cc_start: 0.8610 (mp) cc_final: 0.8393 (mt) REVERT: B 669 THR cc_start: 0.9130 (p) cc_final: 0.8913 (p) outliers start: 3 outliers final: 0 residues processed: 100 average time/residue: 0.5885 time to fit residues: 63.3407 Evaluate side-chains 78 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.118215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.090425 restraints weight = 15776.313| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.24 r_work: 0.2893 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11640 Z= 0.106 Angle : 0.512 6.643 15876 Z= 0.264 Chirality : 0.042 0.139 1760 Planarity : 0.004 0.041 2008 Dihedral : 4.262 19.942 1512 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.07 % Allowed : 7.92 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.23), residues: 1356 helix: 1.49 (0.25), residues: 422 sheet: -0.98 (0.40), residues: 160 loop : 0.18 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 719 TYR 0.010 0.001 TYR A 811 PHE 0.012 0.001 PHE A 873 TRP 0.009 0.001 TRP B 761 HIS 0.004 0.001 HIS A 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (11618) covalent geometry : angle 0.49867 / 0.26 (15820) SS BOND : bond 0.00220 / 0.14 ( 10) SS BOND : angle 2.43725 / 1.32 ( 20) hydrogen bonds : bond 0.04074 / 2.67 ( 374) hydrogen bonds : angle 5.02045 / 3.47 ( 996) link_ALPHA1-3 : bond 0.00908 / 0.54 ( 2) link_ALPHA1-3 : angle 1.38494 / 0.85 ( 6) link_BETA1-4 : bond 0.00467 / 0.31 ( 6) link_BETA1-4 : angle 1.14119 / 0.73 ( 18) link_NAG-ASN : bond 0.00071 / 0.04 ( 4) link_NAG-ASN : angle 2.41373 / 1.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.385 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 93 average time/residue: 0.5561 time to fit residues: 56.1448 Evaluate side-chains 83 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 12 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 0.0020 chunk 103 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 872 HIS B 872 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.088343 restraints weight = 15961.583| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.28 r_work: 0.2862 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11640 Z= 0.120 Angle : 0.504 5.670 15876 Z= 0.260 Chirality : 0.042 0.141 1760 Planarity : 0.004 0.038 2008 Dihedral : 4.159 19.239 1512 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.40 % Allowed : 9.24 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1356 helix: 1.52 (0.25), residues: 422 sheet: -0.87 (0.39), residues: 160 loop : 0.20 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 854 TYR 0.011 0.001 TYR B 811 PHE 0.011 0.001 PHE A 452 TRP 0.010 0.001 TRP A 266 HIS 0.005 0.001 HIS B 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (11618) covalent geometry : angle 0.49426 / 0.26 (15820) SS BOND : bond 0.00241 / 0.16 ( 10) SS BOND : angle 1.60103 / 0.89 ( 20) hydrogen bonds : bond 0.04018 / 2.61 ( 374) hydrogen bonds : angle 4.88616 / 3.37 ( 996) link_ALPHA1-3 : bond 0.00748 / 0.44 ( 2) link_ALPHA1-3 : angle 1.41692 / 0.86 ( 6) link_BETA1-4 : bond 0.00389 / 0.26 ( 6) link_BETA1-4 : angle 1.19300 / 0.76 ( 18) link_NAG-ASN : bond 0.00117 / 0.07 ( 4) link_NAG-ASN : angle 2.51871 / 1.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.437 Fit side-chains REVERT: A 505 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8863 (tt) REVERT: B 505 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8861 (tt) outliers start: 17 outliers final: 8 residues processed: 94 average time/residue: 0.5941 time to fit residues: 60.4661 Evaluate side-chains 89 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 67 optimal weight: 0.0670 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.086350 restraints weight = 15843.444| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.26 r_work: 0.2829 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11640 Z= 0.165 Angle : 0.533 5.422 15876 Z= 0.275 Chirality : 0.044 0.148 1760 Planarity : 0.004 0.037 2008 Dihedral : 4.244 18.266 1512 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.49 % Allowed : 9.41 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.22), residues: 1356 helix: 1.48 (0.25), residues: 422 sheet: -0.92 (0.38), residues: 160 loop : 0.08 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 854 TYR 0.011 0.001 TYR A 787 PHE 0.014 0.002 PHE A 452 TRP 0.012 0.001 TRP A 266 HIS 0.005 0.001 HIS A 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (11618) covalent geometry : angle 0.52452 / 0.27 (15820) SS BOND : bond 0.00285 / 0.19 ( 10) SS BOND : angle 1.22002 / 0.74 ( 20) hydrogen bonds : bond 0.04547 / 2.94 ( 374) hydrogen bonds : angle 4.94406 / 3.41 ( 996) link_ALPHA1-3 : bond 0.00579 / 0.34 ( 2) link_ALPHA1-3 : angle 1.37846 / 0.84 ( 6) link_BETA1-4 : bond 0.00412 / 0.28 ( 6) link_BETA1-4 : angle 1.27592 / 0.81 ( 18) link_NAG-ASN : bond 0.00225 / 0.14 ( 4) link_NAG-ASN : angle 2.60303 / 1.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.431 Fit side-chains REVERT: A 397 GLU cc_start: 0.8336 (pt0) cc_final: 0.8110 (pm20) REVERT: A 505 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8916 (tt) REVERT: B 505 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8905 (tt) outliers start: 18 outliers final: 10 residues processed: 99 average time/residue: 0.6122 time to fit residues: 65.4133 Evaluate side-chains 93 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 32 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 42 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 HIS B 321 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.086978 restraints weight = 16032.604| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.27 r_work: 0.2830 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11640 Z= 0.111 Angle : 0.517 7.158 15876 Z= 0.266 Chirality : 0.042 0.140 1760 Planarity : 0.004 0.037 2008 Dihedral : 4.146 18.360 1512 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.32 % Allowed : 10.40 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.23), residues: 1356 helix: 1.56 (0.26), residues: 420 sheet: -0.88 (0.39), residues: 160 loop : 0.12 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 854 TYR 0.011 0.001 TYR A 787 PHE 0.010 0.001 PHE A 452 TRP 0.008 0.001 TRP A 761 HIS 0.004 0.001 HIS A 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (11618) covalent geometry : angle 0.50169 / 0.26 (15820) SS BOND : bond 0.00256 / 0.17 ( 10) SS BOND : angle 2.72392 / 1.49 ( 20) hydrogen bonds : bond 0.03898 / 2.51 ( 374) hydrogen bonds : angle 4.82260 / 3.33 ( 996) link_ALPHA1-3 : bond 0.00651 / 0.39 ( 2) link_ALPHA1-3 : angle 1.39979 / 0.85 ( 6) link_BETA1-4 : bond 0.00405 / 0.27 ( 6) link_BETA1-4 : angle 1.21983 / 0.78 ( 18) link_NAG-ASN : bond 0.00081 / 0.05 ( 4) link_NAG-ASN : angle 2.47990 / 1.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.449 Fit side-chains REVERT: A 505 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8902 (tt) REVERT: B 505 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8887 (tt) outliers start: 16 outliers final: 9 residues processed: 91 average time/residue: 0.6277 time to fit residues: 61.7081 Evaluate side-chains 86 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 50 optimal weight: 0.0010 chunk 99 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.082715 restraints weight = 16174.169| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.32 r_work: 0.2760 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 11640 Z= 0.236 Angle : 0.615 7.088 15876 Z= 0.316 Chirality : 0.046 0.183 1760 Planarity : 0.005 0.036 2008 Dihedral : 4.491 18.912 1512 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.73 % Allowed : 10.31 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.23), residues: 1356 helix: 1.31 (0.25), residues: 422 sheet: -1.15 (0.38), residues: 164 loop : -0.03 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 719 TYR 0.013 0.002 TYR B 811 PHE 0.019 0.002 PHE A 452 TRP 0.017 0.002 TRP B 266 HIS 0.007 0.001 HIS A 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.24 (11618) covalent geometry : angle 0.60296 / 0.31 (15820) SS BOND : bond 0.00320 / 0.22 ( 10) SS BOND : angle 2.34580 / 1.28 ( 20) hydrogen bonds : bond 0.05313 / 3.43 ( 374) hydrogen bonds : angle 5.08132 / 3.51 ( 996) link_ALPHA1-3 : bond 0.00677 / 0.40 ( 2) link_ALPHA1-3 : angle 1.48772 / 0.91 ( 6) link_BETA1-4 : bond 0.00308 / 0.20 ( 6) link_BETA1-4 : angle 1.41855 / 0.89 ( 18) link_NAG-ASN : bond 0.00463 / 0.28 ( 4) link_NAG-ASN : angle 2.86967 / 1.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.416 Fit side-chains REVERT: A 505 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8951 (tt) REVERT: B 216 GLN cc_start: 0.8302 (tp40) cc_final: 0.8097 (tp40) REVERT: B 505 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8937 (tt) outliers start: 21 outliers final: 11 residues processed: 91 average time/residue: 0.6063 time to fit residues: 59.7710 Evaluate side-chains 92 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 107 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 95 optimal weight: 0.0050 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.116081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.087379 restraints weight = 16036.991| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.33 r_work: 0.2835 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11640 Z= 0.101 Angle : 0.509 6.661 15876 Z= 0.261 Chirality : 0.042 0.133 1760 Planarity : 0.004 0.038 2008 Dihedral : 4.128 18.265 1512 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.91 % Allowed : 11.55 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1356 helix: 1.43 (0.25), residues: 420 sheet: -0.96 (0.39), residues: 160 loop : 0.08 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 854 TYR 0.011 0.001 TYR A 787 PHE 0.008 0.001 PHE A 206 TRP 0.009 0.001 TRP B 604 HIS 0.003 0.001 HIS B 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (11618) covalent geometry : angle 0.49910 / 0.26 (15820) SS BOND : bond 0.00185 / 0.11 ( 10) SS BOND : angle 1.70911 / 0.99 ( 20) hydrogen bonds : bond 0.03684 / 2.38 ( 374) hydrogen bonds : angle 4.83238 / 3.36 ( 996) link_ALPHA1-3 : bond 0.00647 / 0.38 ( 2) link_ALPHA1-3 : angle 1.43368 / 0.87 ( 6) link_BETA1-4 : bond 0.00460 / 0.31 ( 6) link_BETA1-4 : angle 1.22649 / 0.78 ( 18) link_NAG-ASN : bond 0.00114 / 0.07 ( 4) link_NAG-ASN : angle 2.47292 / 1.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.457 Fit side-chains REVERT: A 505 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8869 (tt) REVERT: B 505 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8869 (tt) outliers start: 11 outliers final: 7 residues processed: 102 average time/residue: 0.6766 time to fit residues: 73.8975 Evaluate side-chains 92 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 743 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.084372 restraints weight = 15916.835| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.31 r_work: 0.2788 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11640 Z= 0.181 Angle : 0.573 6.630 15876 Z= 0.293 Chirality : 0.044 0.222 1760 Planarity : 0.004 0.037 2008 Dihedral : 4.286 18.335 1512 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.32 % Allowed : 11.47 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.23), residues: 1356 helix: 1.42 (0.25), residues: 420 sheet: -1.02 (0.40), residues: 158 loop : 0.08 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 719 TYR 0.011 0.001 TYR B 787 PHE 0.015 0.002 PHE A 452 TRP 0.013 0.001 TRP B 266 HIS 0.005 0.001 HIS A 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.18 (11618) covalent geometry : angle 0.56315 / 0.29 (15820) SS BOND : bond 0.00247 / 0.16 ( 10) SS BOND : angle 1.74381 / 1.00 ( 20) hydrogen bonds : bond 0.04619 / 2.98 ( 374) hydrogen bonds : angle 4.93704 / 3.41 ( 996) link_ALPHA1-3 : bond 0.00603 / 0.36 ( 2) link_ALPHA1-3 : angle 1.46311 / 0.89 ( 6) link_BETA1-4 : bond 0.00299 / 0.20 ( 6) link_BETA1-4 : angle 1.35843 / 0.86 ( 18) link_NAG-ASN : bond 0.00325 / 0.19 ( 4) link_NAG-ASN : angle 2.70099 / 1.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.444 Fit side-chains REVERT: A 505 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8835 (tt) REVERT: B 505 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8840 (tt) REVERT: B 533 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8892 (mtm) outliers start: 16 outliers final: 9 residues processed: 95 average time/residue: 0.6379 time to fit residues: 65.3317 Evaluate side-chains 94 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 533 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 71 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 105 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.084779 restraints weight = 16042.337| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.33 r_work: 0.2795 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11640 Z= 0.161 Angle : 0.558 6.848 15876 Z= 0.286 Chirality : 0.044 0.205 1760 Planarity : 0.004 0.038 2008 Dihedral : 4.286 17.845 1512 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.16 % Allowed : 11.47 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.23), residues: 1356 helix: 1.41 (0.25), residues: 420 sheet: -1.07 (0.39), residues: 158 loop : 0.07 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 719 TYR 0.012 0.001 TYR A 787 PHE 0.013 0.002 PHE A 452 TRP 0.011 0.001 TRP A 266 HIS 0.004 0.001 HIS A 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.16 (11618) covalent geometry : angle 0.54855 / 0.28 (15820) SS BOND : bond 0.00239 / 0.15 ( 10) SS BOND : angle 1.72128 / 0.99 ( 20) hydrogen bonds : bond 0.04417 / 2.85 ( 374) hydrogen bonds : angle 4.91361 / 3.40 ( 996) link_ALPHA1-3 : bond 0.00589 / 0.35 ( 2) link_ALPHA1-3 : angle 1.44997 / 0.88 ( 6) link_BETA1-4 : bond 0.00320 / 0.21 ( 6) link_BETA1-4 : angle 1.32323 / 0.84 ( 18) link_NAG-ASN : bond 0.00230 / 0.14 ( 4) link_NAG-ASN : angle 2.65683 / 1.80 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.471 Fit side-chains REVERT: A 505 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8912 (tt) REVERT: B 505 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8909 (tt) outliers start: 14 outliers final: 9 residues processed: 95 average time/residue: 0.6105 time to fit residues: 62.6658 Evaluate side-chains 95 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 125 optimal weight: 0.0060 chunk 102 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.114334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.085464 restraints weight = 16177.298| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.34 r_work: 0.2808 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11640 Z= 0.134 Angle : 0.546 6.888 15876 Z= 0.279 Chirality : 0.043 0.202 1760 Planarity : 0.004 0.039 2008 Dihedral : 4.197 17.807 1512 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.99 % Allowed : 12.21 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.23), residues: 1356 helix: 1.47 (0.25), residues: 420 sheet: -0.91 (0.40), residues: 154 loop : 0.09 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 719 TYR 0.011 0.001 TYR A 787 PHE 0.012 0.001 PHE A 452 TRP 0.009 0.001 TRP A 266 HIS 0.004 0.001 HIS B 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.13 (11618) covalent geometry : angle 0.53668 / 0.28 (15820) SS BOND : bond 0.00208 / 0.13 ( 10) SS BOND : angle 1.62133 / 0.95 ( 20) hydrogen bonds : bond 0.04124 / 2.65 ( 374) hydrogen bonds : angle 4.86162 / 3.36 ( 996) link_ALPHA1-3 : bond 0.00608 / 0.36 ( 2) link_ALPHA1-3 : angle 1.43555 / 0.87 ( 6) link_BETA1-4 : bond 0.00349 / 0.23 ( 6) link_BETA1-4 : angle 1.30671 / 0.83 ( 18) link_NAG-ASN : bond 0.00163 / 0.10 ( 4) link_NAG-ASN : angle 2.61071 / 1.76 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3232.46 seconds wall clock time: 56 minutes 4.91 seconds (3364.91 seconds total)