Starting phenix.real_space_refine on Sat Aug 23 10:41:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aua_11926/08_2025/7aua_11926.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aua_11926/08_2025/7aua_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7aua_11926/08_2025/7aua_11926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aua_11926/08_2025/7aua_11926.map" model { file = "/net/cci-nas-00/data/ceres_data/7aua_11926/08_2025/7aua_11926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aua_11926/08_2025/7aua_11926.cif" } 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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 12 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: 5.30, per 1000 atoms: 0.47 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: 1.14 Conformation dependent library (CDL) restraints added in 533.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.44 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: 1.84 Time building geometry restraints manager: 1.44 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 - 20.70: 6682 20.70 - 41.40: 364 41.40 - 62.09: 38 62.09 - 82.79: 34 82.79 - 103.49: 12 Dihedral angle restraints: 7130 sinusoidal: 3092 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 7127 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: 4.140 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.560 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 13.954 103.488 4488 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 aren 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 covalent geometry : bond 0.00756 (11618) covalent geometry : angle 0.63894 (15820) SS BOND : bond 0.00286 ( 10) SS BOND : angle 2.35719 ( 20) hydrogen bonds : bond 0.18700 ( 374) hydrogen bonds : angle 6.85160 ( 996) link_ALPHA1-3 : bond 0.01091 ( 2) link_ALPHA1-3 : angle 2.21317 ( 6) link_BETA1-4 : bond 0.00738 ( 6) link_BETA1-4 : angle 1.43132 ( 18) link_NAG-ASN : bond 0.00233 ( 4) link_NAG-ASN : angle 2.76400 ( 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 : 0.472 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.8433 time to fit residues: 107.4394 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 : 0.449 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.091233 restraints weight = 15557.207| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.22 r_work: 0.2902 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11640 Z= 0.113 Angle : 0.554 5.721 15876 Z= 0.287 Chirality : 0.044 0.148 1760 Planarity : 0.004 0.044 2008 Dihedral : 8.804 67.405 1820 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.50 % Allowed : 6.35 % Favored : 93.15 % 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 aren not related in a simple way. whole: 0.41 (0.23), residues: 1356 helix: 1.28 (0.26), residues: 424 sheet: -0.70 (0.39), residues: 174 loop : 0.03 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 854 TYR 0.014 0.001 TYR A 808 PHE 0.013 0.001 PHE B 873 TRP 0.010 0.001 TRP A 696 HIS 0.007 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00245 (11618) covalent geometry : angle 0.54504 (15820) SS BOND : bond 0.00363 ( 10) SS BOND : angle 1.19477 ( 20) hydrogen bonds : bond 0.04557 ( 374) hydrogen bonds : angle 5.37280 ( 996) link_ALPHA1-3 : bond 0.01417 ( 2) link_ALPHA1-3 : angle 1.94502 ( 6) link_BETA1-4 : bond 0.00565 ( 6) link_BETA1-4 : angle 1.43172 ( 18) link_NAG-ASN : bond 0.00127 ( 4) link_NAG-ASN : angle 2.53128 ( 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 107 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.478 Fit side-chains REVERT: A 391 LEU cc_start: 0.8597 (mp) cc_final: 0.8392 (mt) REVERT: A 669 THR cc_start: 0.9126 (p) cc_final: 0.8904 (p) REVERT: B 391 LEU cc_start: 0.8604 (mp) cc_final: 0.8402 (mt) REVERT: B 669 THR cc_start: 0.9126 (p) cc_final: 0.8906 (p) outliers start: 6 outliers final: 1 residues processed: 101 average time/residue: 0.7546 time to fit residues: 81.7797 Evaluate side-chains 75 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 75 optimal weight: 0.0470 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.089707 restraints weight = 15780.081| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.24 r_work: 0.2882 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11640 Z= 0.114 Angle : 0.523 7.046 15876 Z= 0.268 Chirality : 0.043 0.158 1760 Planarity : 0.004 0.041 2008 Dihedral : 7.224 55.585 1820 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.91 % Allowed : 8.25 % Favored : 90.84 % 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 aren not related in a simple way. whole: 0.57 (0.23), residues: 1356 helix: 1.48 (0.25), residues: 422 sheet: -0.99 (0.40), residues: 160 loop : 0.16 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 719 TYR 0.010 0.001 TYR A 811 PHE 0.012 0.001 PHE A 873 TRP 0.009 0.001 TRP B 266 HIS 0.004 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00265 (11618) covalent geometry : angle 0.50883 (15820) SS BOND : bond 0.00221 ( 10) SS BOND : angle 2.55457 ( 20) hydrogen bonds : bond 0.04165 ( 374) hydrogen bonds : angle 5.02766 ( 996) link_ALPHA1-3 : bond 0.01349 ( 2) link_ALPHA1-3 : angle 1.44255 ( 6) link_BETA1-4 : bond 0.00500 ( 6) link_BETA1-4 : angle 1.29268 ( 18) link_NAG-ASN : bond 0.00097 ( 4) link_NAG-ASN : angle 2.42192 ( 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 98 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.525 Fit side-chains REVERT: A 661 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8052 (tt0) outliers start: 11 outliers final: 4 residues processed: 94 average time/residue: 0.6612 time to fit residues: 67.4172 Evaluate side-chains 84 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 661 GLU 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: 3.9990 chunk 129 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 131 optimal weight: 0.2980 chunk 47 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 0.0040 chunk 103 optimal weight: 0.0070 chunk 25 optimal weight: 2.9990 overall best weight: 0.6412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3456 r_free = 0.3456 target = 0.117639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.089302 restraints weight = 15962.019| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.28 r_work: 0.2872 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11640 Z= 0.116 Angle : 0.508 5.252 15876 Z= 0.260 Chirality : 0.043 0.150 1760 Planarity : 0.004 0.039 2008 Dihedral : 6.302 55.107 1820 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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 aren not related in a simple way. whole: 0.62 (0.23), residues: 1356 helix: 1.53 (0.25), residues: 422 sheet: -0.88 (0.39), residues: 160 loop : 0.17 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 854 TYR 0.011 0.001 TYR A 811 PHE 0.011 0.001 PHE B 873 TRP 0.009 0.001 TRP A 266 HIS 0.005 0.001 HIS B 872 Details of bonding type rmsd covalent geometry : bond 0.00276 (11618) covalent geometry : angle 0.49779 (15820) SS BOND : bond 0.00240 ( 10) SS BOND : angle 1.54530 ( 20) hydrogen bonds : bond 0.03952 ( 374) hydrogen bonds : angle 4.87400 ( 996) link_ALPHA1-3 : bond 0.01129 ( 2) link_ALPHA1-3 : angle 1.60018 ( 6) link_BETA1-4 : bond 0.00496 ( 6) link_BETA1-4 : angle 1.31309 ( 18) link_NAG-ASN : bond 0.00144 ( 4) link_NAG-ASN : angle 2.50886 ( 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 101 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.476 Fit side-chains REVERT: A 505 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8873 (tt) REVERT: B 505 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8899 (tt) outliers start: 18 outliers final: 9 residues processed: 96 average time/residue: 0.6628 time to fit residues: 68.8763 Evaluate side-chains 89 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 503 SER 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: 3.9990 chunk 77 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.085644 restraints weight = 16050.847| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.34 r_work: 0.2807 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11640 Z= 0.148 Angle : 0.524 5.350 15876 Z= 0.269 Chirality : 0.043 0.146 1760 Planarity : 0.004 0.037 2008 Dihedral : 5.988 55.453 1820 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.49 % Allowed : 9.32 % Favored : 89.19 % 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 aren not related in a simple way. whole: 0.55 (0.22), residues: 1356 helix: 1.51 (0.25), residues: 422 sheet: -0.92 (0.38), residues: 160 loop : 0.10 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 854 TYR 0.011 0.001 TYR A 787 PHE 0.013 0.002 PHE B 452 TRP 0.011 0.001 TRP A 266 HIS 0.005 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00366 (11618) covalent geometry : angle 0.51586 (15820) SS BOND : bond 0.00275 ( 10) SS BOND : angle 1.25005 ( 20) hydrogen bonds : bond 0.04361 ( 374) hydrogen bonds : angle 4.89968 ( 996) link_ALPHA1-3 : bond 0.01005 ( 2) link_ALPHA1-3 : angle 1.41294 ( 6) link_BETA1-4 : bond 0.00540 ( 6) link_BETA1-4 : angle 1.32986 ( 18) link_NAG-ASN : bond 0.00244 ( 4) link_NAG-ASN : angle 2.53617 ( 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 105 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.477 Fit side-chains REVERT: A 397 GLU cc_start: 0.8303 (pt0) cc_final: 0.8082 (pm20) REVERT: A 505 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8886 (tt) REVERT: B 505 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8885 (tt) outliers start: 18 outliers final: 11 residues processed: 98 average time/residue: 0.7340 time to fit residues: 77.4483 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 : 0.476 ------------------------------------------------------------------------------- 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 503 SER 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: 0.9990 chunk 130 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.086079 restraints weight = 16023.690| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.28 r_work: 0.2817 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2256 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= 0.137 Angle : 0.536 6.594 15876 Z= 0.275 Chirality : 0.043 0.142 1760 Planarity : 0.004 0.037 2008 Dihedral : 5.828 55.166 1820 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.40 % Allowed : 10.15 % Favored : 88.45 % 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 aren not related in a simple way. whole: 0.50 (0.22), residues: 1356 helix: 1.49 (0.25), residues: 422 sheet: -0.89 (0.39), residues: 160 loop : 0.05 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 854 TYR 0.011 0.001 TYR A 787 PHE 0.012 0.001 PHE A 452 TRP 0.010 0.001 TRP B 266 HIS 0.004 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00336 (11618) covalent geometry : angle 0.52192 (15820) SS BOND : bond 0.00205 ( 10) SS BOND : angle 2.54063 ( 20) hydrogen bonds : bond 0.04172 ( 374) hydrogen bonds : angle 4.86331 ( 996) link_ALPHA1-3 : bond 0.00967 ( 2) link_ALPHA1-3 : angle 1.46892 ( 6) link_BETA1-4 : bond 0.00513 ( 6) link_BETA1-4 : angle 1.32081 ( 18) link_NAG-ASN : bond 0.00187 ( 4) link_NAG-ASN : angle 2.52329 ( 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 103 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.480 Fit side-chains REVERT: A 505 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8875 (tt) REVERT: B 505 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8911 (tt) outliers start: 17 outliers final: 10 residues processed: 96 average time/residue: 0.7364 time to fit residues: 75.9870 Evaluate side-chains 89 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 26 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 128 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.115153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.086557 restraints weight = 16061.991| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.29 r_work: 0.2823 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11640 Z= 0.122 Angle : 0.525 6.547 15876 Z= 0.269 Chirality : 0.042 0.149 1760 Planarity : 0.004 0.036 2008 Dihedral : 5.657 55.010 1820 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.57 % Allowed : 10.40 % Favored : 88.04 % 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 aren not related in a simple way. whole: 0.56 (0.23), residues: 1356 helix: 1.55 (0.25), residues: 420 sheet: -0.92 (0.39), residues: 160 loop : 0.10 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 854 TYR 0.011 0.001 TYR A 787 PHE 0.011 0.001 PHE B 452 TRP 0.008 0.001 TRP B 266 HIS 0.004 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00295 (11618) covalent geometry : angle 0.51358 (15820) SS BOND : bond 0.00211 ( 10) SS BOND : angle 2.00281 ( 20) hydrogen bonds : bond 0.03975 ( 374) hydrogen bonds : angle 4.82422 ( 996) link_ALPHA1-3 : bond 0.00886 ( 2) link_ALPHA1-3 : angle 1.42760 ( 6) link_BETA1-4 : bond 0.00524 ( 6) link_BETA1-4 : angle 1.31466 ( 18) link_NAG-ASN : bond 0.00172 ( 4) link_NAG-ASN : angle 2.47029 ( 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 104 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.482 Fit side-chains REVERT: A 505 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8862 (tt) REVERT: B 505 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8921 (tt) outliers start: 19 outliers final: 12 residues processed: 94 average time/residue: 0.7388 time to fit residues: 74.4929 Evaluate side-chains 92 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 A residue 517 GLU Chi-restraints excluded: chain A residue 599 ASP 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 503 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 107 optimal weight: 0.9990 chunk 94 optimal weight: 0.0270 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.085638 restraints weight = 16048.288| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.30 r_work: 0.2809 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11640 Z= 0.145 Angle : 0.538 6.537 15876 Z= 0.276 Chirality : 0.043 0.176 1760 Planarity : 0.004 0.036 2008 Dihedral : 5.669 55.458 1820 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.49 % Allowed : 11.14 % 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 aren not related in a simple way. whole: 0.51 (0.23), residues: 1356 helix: 1.49 (0.25), residues: 420 sheet: -0.94 (0.39), residues: 160 loop : 0.07 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 854 TYR 0.012 0.001 TYR A 787 PHE 0.013 0.002 PHE B 452 TRP 0.011 0.001 TRP B 266 HIS 0.005 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00356 (11618) covalent geometry : angle 0.52798 (15820) SS BOND : bond 0.00242 ( 10) SS BOND : angle 1.76888 ( 20) hydrogen bonds : bond 0.04285 ( 374) hydrogen bonds : angle 4.87050 ( 996) link_ALPHA1-3 : bond 0.00791 ( 2) link_ALPHA1-3 : angle 1.38600 ( 6) link_BETA1-4 : bond 0.00504 ( 6) link_BETA1-4 : angle 1.38129 ( 18) link_NAG-ASN : bond 0.00246 ( 4) link_NAG-ASN : angle 2.51937 ( 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 108 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.472 Fit side-chains REVERT: A 216 GLN cc_start: 0.8158 (tp40) cc_final: 0.7946 (tp40) REVERT: A 505 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8897 (tt) REVERT: B 216 GLN cc_start: 0.8160 (tp40) cc_final: 0.7947 (tp40) REVERT: B 505 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8905 (tt) outliers start: 18 outliers final: 11 residues processed: 98 average time/residue: 0.7956 time to fit residues: 83.2241 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 : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 256 LEU 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 A residue 599 ASP 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 503 SER Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.0944 > 50: distance: 65 - 142: 28.116 distance: 76 - 145: 34.213 distance: 79 - 157: 16.209 distance: 102 - 123: 31.882 distance: 109 - 115: 21.754 distance: 110 - 132: 35.731 distance: 115 - 116: 43.213 distance: 116 - 117: 42.400 distance: 116 - 119: 25.245 distance: 117 - 118: 35.170 distance: 117 - 123: 34.538 distance: 119 - 120: 47.478 distance: 120 - 121: 60.005 distance: 120 - 122: 42.300 distance: 123 - 124: 46.567 distance: 124 - 125: 29.968 distance: 124 - 127: 40.477 distance: 125 - 126: 34.930 distance: 125 - 132: 23.170 distance: 127 - 128: 59.403 distance: 128 - 129: 43.552 distance: 129 - 130: 47.141 distance: 129 - 131: 47.186 distance: 132 - 133: 19.195 distance: 133 - 134: 54.892 distance: 133 - 136: 31.078 distance: 134 - 135: 56.559 distance: 134 - 137: 26.446 distance: 137 - 138: 24.314 distance: 138 - 139: 22.391 distance: 138 - 141: 44.583 distance: 139 - 140: 49.558 distance: 139 - 142: 49.782 distance: 142 - 143: 26.928 distance: 143 - 144: 22.745 distance: 143 - 146: 42.491 distance: 144 - 145: 39.329 distance: 144 - 150: 49.993 distance: 146 - 147: 46.327 distance: 147 - 148: 27.999 distance: 147 - 149: 26.547 distance: 150 - 151: 9.775 distance: 151 - 152: 47.596 distance: 151 - 154: 63.029 distance: 152 - 153: 31.364 distance: 152 - 157: 25.719 distance: 154 - 155: 50.632 distance: 154 - 156: 32.518 distance: 157 - 158: 13.970 distance: 158 - 159: 35.385 distance: 158 - 161: 44.427 distance: 159 - 160: 16.642 distance: 159 - 164: 45.796 distance: 161 - 162: 36.192 distance: 161 - 163: 32.563 distance: 164 - 165: 46.632 distance: 164 - 170: 27.536 distance: 165 - 166: 34.697 distance: 165 - 168: 50.686 distance: 166 - 167: 40.169 distance: 166 - 171: 9.824 distance: 167 - 187: 18.884 distance: 168 - 169: 39.300 distance: 169 - 170: 18.479 distance: 171 - 172: 16.383 distance: 172 - 173: 53.247 distance: 173 - 174: 53.795 distance: 173 - 180: 14.890 distance: 174 - 195: 28.107 distance: 175 - 176: 41.997 distance: 176 - 177: 40.669 distance: 177 - 178: 10.914 distance: 178 - 179: 26.300 distance: 180 - 181: 22.874 distance: 180 - 186: 42.682 distance: 181 - 182: 40.383 distance: 181 - 184: 48.980 distance: 182 - 183: 26.288 distance: 182 - 187: 25.749 distance: 184 - 185: 44.340 distance: 185 - 186: 47.515