Starting phenix.real_space_refine on Fri Jul 3 11:02:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7aiq_11802/07_2026/7aiq_11802.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aiq_11802/07_2026/7aiq_11802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7aiq_11802/07_2026/7aiq_11802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aiq_11802/07_2026/7aiq_11802.map" model { file = "/net/cci-nas-00/data/ceres_data/7aiq_11802/07_2026/7aiq_11802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aiq_11802/07_2026/7aiq_11802.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7aiq_11802/07_2026/7aiq_11802.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7aiq_11802/07_2026/7aiq_11802.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.039 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 96 5.16 5 C 8769 2.51 5 N 2223 2.21 5 O 2422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s 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: 13514 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 6695 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 38, 'TRANS': 839} Chain breaks: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 6659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6659 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 37, 'TRANS': 829} Chain breaks: 3 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.23, per 1000 atoms: 0.24 Number of scatterers: 13514 At special positions: 0 Unit cell: (107.1, 111.35, 151.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 4 15.00 O 2422 8.00 N 2223 7.00 C 8769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.04 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.04 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A1101 " - " ASN A 361 " " NAG B1101 " - " ASN B 361 " " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN B 312 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 670.9 milliseconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3210 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 61.9% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 120 through 133 removed outlier: 6.010A pdb=" N LEU A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 135 through 141 Processing helix chain 'A' and resid 141 through 177 removed outlier: 6.496A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 removed outlier: 4.234A pdb=" N MET A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 227 removed outlier: 3.518A pdb=" N LEU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 269 Processing helix chain 'A' and resid 269 through 301 removed outlier: 5.445A pdb=" N SER A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.878A pdb=" N MET A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.743A pdb=" N LEU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.605A pdb=" N LEU A 444 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 Proline residue: A 452 - end of helix Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 504 through 536 removed outlier: 4.035A pdb=" N VAL A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 539 through 547 removed outlier: 3.899A pdb=" N LEU A 542 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 543 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL A 544 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 570 Processing helix chain 'A' and resid 573 through 602 Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.824A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 661 Processing helix chain 'A' and resid 664 through 682 removed outlier: 4.127A pdb=" N GLU A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 720 removed outlier: 3.746A pdb=" N THR A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 756 removed outlier: 3.544A pdb=" N ALA A 742 " --> pdb=" O SER A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 780 Processing helix chain 'A' and resid 805 through 820 removed outlier: 3.623A pdb=" N LYS A 809 " --> pdb=" O PRO A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.527A pdb=" N TYR A 834 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 867 Proline residue: A 862 - end of helix Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 887 through 903 removed outlier: 4.000A pdb=" N MET A 891 " --> pdb=" O ASN A 887 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 932 removed outlier: 3.861A pdb=" N GLU A 924 " --> pdb=" O ALA A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1033 removed outlier: 3.604A pdb=" N ARG A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1064 removed outlier: 3.632A pdb=" N THR A1064 " --> pdb=" O LEU A1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 133 removed outlier: 5.912A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Proline residue: B 127 - end of helix Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 141 through 177 removed outlier: 6.623A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 194 Processing helix chain 'B' and resid 194 through 227 removed outlier: 3.603A pdb=" N LEU B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 269 Processing helix chain 'B' and resid 269 through 301 removed outlier: 5.652A pdb=" N SER B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 354 through 360 removed outlier: 3.937A pdb=" N MET B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.985A pdb=" N LEU B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 420 through 428 Processing helix chain 'B' and resid 429 through 432 Processing helix chain 'B' and resid 440 through 444 removed outlier: 3.685A pdb=" N LEU B 444 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 477 Proline residue: B 452 - end of helix Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'B' and resid 504 through 536 removed outlier: 3.922A pdb=" N VAL B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 509 " --> pdb=" O TRP B 505 " (cutoff:3.500A) Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 543 through 547 Processing helix chain 'B' and resid 557 through 570 Processing helix chain 'B' and resid 573 through 603 Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.630A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 661 Processing helix chain 'B' and resid 664 through 682 removed outlier: 4.081A pdb=" N GLU B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 720 removed outlier: 3.784A pdb=" N THR B 713 " --> pdb=" O PRO B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 756 removed outlier: 3.730A pdb=" N ALA B 742 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 756 " --> pdb=" O MET B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 780 removed outlier: 3.622A pdb=" N ALA B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 820 removed outlier: 3.551A pdb=" N LYS B 809 " --> pdb=" O PRO B 805 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP B 813 " --> pdb=" O LYS B 809 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 820 " --> pdb=" O ARG B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 834 removed outlier: 3.642A pdb=" N TYR B 834 " --> pdb=" O ILE B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 867 Proline residue: B 862 - end of helix Processing helix chain 'B' and resid 868 through 872 Processing helix chain 'B' and resid 888 through 903 removed outlier: 3.832A pdb=" N HIS B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 926 removed outlier: 5.263A pdb=" N ALA B 920 " --> pdb=" O SER B 916 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR B 921 " --> pdb=" O ASP B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1033 removed outlier: 3.504A pdb=" N MET B1019 " --> pdb=" O ASN B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1064 removed outlier: 3.834A pdb=" N THR B1064 " --> pdb=" O LEU B1060 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.793A pdb=" N LEU A 310 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AA3, first strand: chain 'A' and resid 761 through 767 removed outlier: 3.517A pdb=" N ILE A 726 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU A 695 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 791 " --> pdb=" O LEU A 826 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A1072 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL A1070 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL A1039 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL A1073 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A1041 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N LEU A1040 " --> pdb=" O HIS A 845 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP A 847 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ASN A1042 " --> pdb=" O ASP A 847 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 907 " --> pdb=" O MET A 876 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 880 " --> pdb=" O GLU A 909 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 783 removed outlier: 3.641A pdb=" N LEU A 783 " --> pdb=" O MET A 786 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 313 through 314 removed outlier: 3.650A pdb=" N LEU B 310 " --> pdb=" O ARG B 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AA7, first strand: chain 'B' and resid 761 through 767 removed outlier: 6.795A pdb=" N THR B 725 " --> pdb=" O PHE B 761 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N GLN B 763 " --> pdb=" O THR B 725 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL B 727 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL B 765 " --> pdb=" O VAL B 727 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER B 729 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA B 767 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE B 731 " --> pdb=" O ALA B 767 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 791 " --> pdb=" O LEU B 826 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B1072 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL B1070 " --> pdb=" O LYS B 829 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL B1039 " --> pdb=" O LEU B1071 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL B1073 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B1041 " --> pdb=" O VAL B1073 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N LEU B1040 " --> pdb=" O HIS B 845 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP B 847 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASN B1042 " --> pdb=" O ASP B 847 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 846 " --> pdb=" O ARG B 877 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N PHE B 879 " --> pdb=" O ILE B 846 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL B 848 " --> pdb=" O PHE B 879 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET B 876 " --> pdb=" O GLU B 907 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLU B 909 " --> pdb=" O MET B 876 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE B 878 " --> pdb=" O GLU B 909 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 782 through 783 removed outlier: 3.578A pdb=" N LEU B 783 " --> pdb=" O MET B 786 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 2211 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: 2.27 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4235 1.35 - 1.47: 3479 1.47 - 1.59: 5957 1.59 - 1.72: 8 1.72 - 1.84: 152 Bond restraints: 13831 Sorted by residual: bond pdb=" C4 ATP B1102 " pdb=" C5 ATP B1102 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.71e+01 bond pdb=" C4 ATP A1102 " pdb=" C5 ATP A1102 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.47e+01 bond pdb=" C5 ATP B1102 " pdb=" C6 ATP B1102 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.08e+01 bond pdb=" O1B ATP B1102 " pdb=" PB ATP B1102 " ideal model delta sigma weight residual 1.477 1.609 -0.132 2.20e-02 2.07e+03 3.58e+01 bond pdb=" O1B ATP A1102 " pdb=" PB ATP A1102 " ideal model delta sigma weight residual 1.477 1.607 -0.130 2.20e-02 2.07e+03 3.48e+01 ... (remaining 13826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 18388 2.79 - 5.58: 384 5.58 - 8.36: 51 8.36 - 11.15: 17 11.15 - 13.94: 4 Bond angle restraints: 18844 Sorted by residual: angle pdb=" PA ATP A1102 " pdb=" O3A ATP A1102 " pdb=" PB ATP A1102 " ideal model delta sigma weight residual 136.83 122.89 13.94 1.00e+00 1.00e+00 1.94e+02 angle pdb=" PA ATP B1102 " pdb=" O3A ATP B1102 " pdb=" PB ATP B1102 " ideal model delta sigma weight residual 136.83 124.70 12.13 1.00e+00 1.00e+00 1.47e+02 angle pdb=" C5 ATP B1102 " pdb=" C4 ATP B1102 " pdb=" N3 ATP B1102 " ideal model delta sigma weight residual 126.80 118.38 8.42 1.00e+00 1.00e+00 7.08e+01 angle pdb=" C5 ATP A1102 " pdb=" C4 ATP A1102 " pdb=" N3 ATP A1102 " ideal model delta sigma weight residual 126.80 118.45 8.35 1.00e+00 1.00e+00 6.97e+01 angle pdb=" N3 ATP B1102 " pdb=" C4 ATP B1102 " pdb=" N9 ATP B1102 " ideal model delta sigma weight residual 127.04 135.12 -8.08 1.15e+00 7.59e-01 4.95e+01 ... (remaining 18839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7020 17.88 - 35.77: 793 35.77 - 53.65: 189 53.65 - 71.54: 21 71.54 - 89.42: 13 Dihedral angle restraints: 8036 sinusoidal: 3025 harmonic: 5011 Sorted by residual: dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 353 " pdb=" CB CYS A 353 " ideal model delta sinusoidal sigma weight residual 93.00 138.12 -45.12 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB CYS B 343 " pdb=" SG CYS B 343 " pdb=" SG CYS B 353 " pdb=" CB CYS B 353 " ideal model delta sinusoidal sigma weight residual 93.00 134.12 -41.12 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CA GLN A 693 " pdb=" C GLN A 693 " pdb=" N LEU A 694 " pdb=" CA LEU A 694 " ideal model delta harmonic sigma weight residual -180.00 -162.47 -17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 8033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1563 0.051 - 0.103: 541 0.103 - 0.154: 103 0.154 - 0.205: 17 0.205 - 0.257: 5 Chirality restraints: 2229 Sorted by residual: chirality pdb=" CB VAL A 881 " pdb=" CA VAL A 881 " pdb=" CG1 VAL A 881 " pdb=" CG2 VAL A 881 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.60e+00 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 -2.52 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2226 not shown) Planarity restraints: 2330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 137 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU A 137 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU A 137 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE A 138 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 121 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C LEU B 121 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU B 121 " -0.014 2.00e-02 2.50e+03 pdb=" N MET B 122 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 408 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO B 409 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.028 5.00e-02 4.00e+02 ... (remaining 2327 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1919 2.74 - 3.28: 13369 3.28 - 3.82: 21304 3.82 - 4.36: 23058 4.36 - 4.90: 41742 Nonbonded interactions: 101392 Sorted by model distance: nonbonded pdb=" OG1 THR A 314 " pdb=" O VAL A 391 " model vdw 2.202 3.040 nonbonded pdb=" NE2 GLN A 152 " pdb=" OH TYR A 384 " model vdw 2.227 3.120 nonbonded pdb=" OG SER B 430 " pdb=" OH TYR B 466 " model vdw 2.245 3.040 nonbonded pdb=" O GLY A 479 " pdb=" NH2 ARG A 483 " model vdw 2.245 3.120 nonbonded pdb=" O SER B 780 " pdb=" OG SER B 780 " model vdw 2.254 3.040 ... (remaining 101387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 116 through 881 or resid 887 through 926 or resid 1014 thr \ ough 1102)) selection = (chain 'B' and (resid 116 through 233 or resid 244 through 347 or (resid 348 and \ (name N or name CA or name C or name O or name CB )) or resid 349 through 912 o \ r (resid 913 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 14 through 1019 or (resid 1020 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1021 through 1102)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue 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: 1.820 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: 0.050 Set scattering table: 0.030 Process input model: 13.240 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.009 0.132 13845 Z= 0.419 Angle : 1.024 13.940 18880 Z= 0.562 Chirality : 0.053 0.257 2229 Planarity : 0.005 0.050 2326 Dihedral : 15.712 89.422 4808 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.20 % Allowed : 20.95 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.19), residues: 1731 helix: 0.32 (0.16), residues: 953 sheet: -1.90 (0.41), residues: 136 loop : -2.74 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 440 TYR 0.021 0.002 TYR A 356 PHE 0.026 0.003 PHE B 541 TRP 0.030 0.003 TRP B 795 HIS 0.011 0.002 HIS B 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00869 / 0.42 (13831) covalent geometry : angle 1.01383 / 0.56 (18844) SS BOND : bond 0.00558 / 0.31 ( 6) SS BOND : angle 3.88512 / 1.99 ( 12) hydrogen bonds : bond 0.15785 / 10.56 ( 764) hydrogen bonds : angle 5.75474 / 4.12 ( 2211) link_BETA1-4 : bond 0.01538 / 1.01 ( 4) link_BETA1-4 : angle 3.56861 / 2.33 ( 12) link_NAG-ASN : bond 0.00733 / 0.40 ( 4) link_NAG-ASN : angle 2.85943 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 307 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8251 (mtp) cc_final: 0.7775 (tmm) REVERT: A 144 MET cc_start: 0.8485 (ttp) cc_final: 0.8037 (ptm) REVERT: A 186 TYR cc_start: 0.8882 (t80) cc_final: 0.8590 (t80) REVERT: A 188 MET cc_start: 0.7584 (mtm) cc_final: 0.7211 (ttt) REVERT: A 313 ARG cc_start: 0.6922 (mtm180) cc_final: 0.6262 (mtm-85) REVERT: A 358 MET cc_start: 0.9423 (mpp) cc_final: 0.9108 (mpp) REVERT: A 391 VAL cc_start: 0.8254 (t) cc_final: 0.7669 (t) REVERT: A 630 MET cc_start: 0.8819 (ttp) cc_final: 0.8449 (ttp) REVERT: A 658 GLU cc_start: 0.8283 (tt0) cc_final: 0.7922 (mm-30) REVERT: A 752 MET cc_start: 0.9315 (tpp) cc_final: 0.8882 (tpp) REVERT: A 859 MET cc_start: 0.9326 (mtp) cc_final: 0.8793 (mmp) REVERT: A 878 ILE cc_start: 0.8829 (mt) cc_final: 0.8614 (mm) REVERT: A 1074 ARG cc_start: 0.8646 (ttt90) cc_final: 0.8376 (ttt90) REVERT: A 1078 ARG cc_start: 0.8653 (mtm110) cc_final: 0.8316 (ptm160) REVERT: B 118 MET cc_start: 0.8444 (ptm) cc_final: 0.7770 (ptm) REVERT: B 122 MET cc_start: 0.8997 (mtp) cc_final: 0.8205 (tmm) REVERT: B 385 LEU cc_start: 0.9527 (mt) cc_final: 0.9058 (mt) REVERT: B 419 SER cc_start: 0.8543 (t) cc_final: 0.7926 (p) REVERT: B 563 LEU cc_start: 0.8774 (mp) cc_final: 0.8524 (tt) REVERT: B 596 CYS cc_start: 0.8318 (m) cc_final: 0.8034 (t) REVERT: B 630 MET cc_start: 0.9050 (ttp) cc_final: 0.8621 (ttm) REVERT: B 659 LYS cc_start: 0.9087 (tttt) cc_final: 0.8728 (ttmm) REVERT: B 696 VAL cc_start: 0.9062 (t) cc_final: 0.8849 (m) REVERT: B 746 GLU cc_start: 0.8805 (tt0) cc_final: 0.8264 (tp30) REVERT: B 750 LYS cc_start: 0.9389 (mttt) cc_final: 0.8569 (mttp) REVERT: B 752 MET cc_start: 0.8794 (tpp) cc_final: 0.8564 (tpp) REVERT: B 791 VAL cc_start: 0.9484 (t) cc_final: 0.9196 (m) REVERT: B 813 ASP cc_start: 0.9114 (m-30) cc_final: 0.8845 (t0) REVERT: B 857 MET cc_start: 0.8982 (ptm) cc_final: 0.8624 (pmm) REVERT: B 874 CYS cc_start: 0.8415 (m) cc_final: 0.6985 (t) REVERT: B 1055 ASN cc_start: 0.9231 (m110) cc_final: 0.8759 (t0) outliers start: 17 outliers final: 9 residues processed: 321 average time/residue: 0.1123 time to fit residues: 53.5018 Evaluate side-chains 174 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 427 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 699 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN A 344 HIS A 521 GLN A 655 GLN A 732 GLN A 751 ASN B 130 GLN B 152 GLN B 250 ASN B 344 HIS B 655 GLN B 717 GLN B 732 GLN B 747 GLN B 751 ASN B 763 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.095761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.070064 restraints weight = 38983.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.073006 restraints weight = 18663.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.075027 restraints weight = 11578.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.076415 restraints weight = 8407.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.077381 restraints weight = 6771.138| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13845 Z= 0.151 Angle : 0.672 8.492 18880 Z= 0.335 Chirality : 0.043 0.212 2229 Planarity : 0.004 0.048 2326 Dihedral : 5.035 48.087 1901 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.32 % Allowed : 22.36 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1731 helix: 1.48 (0.17), residues: 952 sheet: -1.09 (0.42), residues: 133 loop : -2.33 (0.21), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 317 TYR 0.016 0.001 TYR A 292 PHE 0.018 0.002 PHE B 863 TRP 0.011 0.001 TRP B 143 HIS 0.005 0.001 HIS A 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (13831) covalent geometry : angle 0.66560 / 0.33 (18844) SS BOND : bond 0.00418 / 0.29 ( 6) SS BOND : angle 1.92685 / 1.05 ( 12) hydrogen bonds : bond 0.05364 / 3.69 ( 764) hydrogen bonds : angle 4.40300 / 3.21 ( 2211) link_BETA1-4 : bond 0.01110 / 0.73 ( 4) link_BETA1-4 : angle 2.68322 / 1.70 ( 12) link_NAG-ASN : bond 0.00211 / 0.11 ( 4) link_NAG-ASN : angle 1.93075 / 1.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8196 (mtp) cc_final: 0.7803 (tmm) REVERT: A 144 MET cc_start: 0.8261 (ttp) cc_final: 0.7933 (ptm) REVERT: A 147 THR cc_start: 0.8489 (t) cc_final: 0.8236 (t) REVERT: A 186 TYR cc_start: 0.8702 (t80) cc_final: 0.8301 (t80) REVERT: A 188 MET cc_start: 0.7568 (mtm) cc_final: 0.7216 (ttt) REVERT: A 358 MET cc_start: 0.9403 (mpp) cc_final: 0.9005 (mpp) REVERT: A 484 ASP cc_start: 0.8367 (m-30) cc_final: 0.7769 (p0) REVERT: A 542 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8359 (pp) REVERT: A 631 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8442 (t80) REVERT: A 658 GLU cc_start: 0.8402 (tt0) cc_final: 0.7997 (mm-30) REVERT: A 752 MET cc_start: 0.9309 (tpp) cc_final: 0.8786 (tpp) REVERT: A 848 VAL cc_start: 0.8689 (t) cc_final: 0.8394 (m) REVERT: A 854 ASP cc_start: 0.8342 (m-30) cc_final: 0.8074 (m-30) REVERT: A 859 MET cc_start: 0.9147 (mtp) cc_final: 0.8623 (mmp) REVERT: A 864 LEU cc_start: 0.9360 (mt) cc_final: 0.9156 (mp) REVERT: A 1078 ARG cc_start: 0.8536 (mtm110) cc_final: 0.8199 (ptm160) REVERT: B 353 CYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8331 (m) REVERT: B 380 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8619 (tt) REVERT: B 390 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8609 (mm) REVERT: B 419 SER cc_start: 0.8523 (t) cc_final: 0.8182 (p) REVERT: B 542 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8304 (pp) REVERT: B 563 LEU cc_start: 0.8700 (mp) cc_final: 0.8489 (tt) REVERT: B 566 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8565 (tm-30) REVERT: B 576 MET cc_start: 0.8292 (mtp) cc_final: 0.7972 (mtp) REVERT: B 587 MET cc_start: 0.8953 (tpt) cc_final: 0.8573 (tpt) REVERT: B 623 MET cc_start: 0.9371 (tmm) cc_final: 0.8730 (tmm) REVERT: B 630 MET cc_start: 0.8856 (ttp) cc_final: 0.8575 (ttm) REVERT: B 659 LYS cc_start: 0.9072 (tttt) cc_final: 0.8678 (ttmm) REVERT: B 693 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8170 (mm110) REVERT: B 712 LEU cc_start: 0.8814 (mt) cc_final: 0.8467 (mt) REVERT: B 746 GLU cc_start: 0.8657 (tt0) cc_final: 0.7992 (tp30) REVERT: B 750 LYS cc_start: 0.9385 (mttt) cc_final: 0.8492 (mttp) REVERT: B 813 ASP cc_start: 0.9096 (m-30) cc_final: 0.8817 (t0) REVERT: B 874 CYS cc_start: 0.8552 (m) cc_final: 0.7400 (t) REVERT: B 1055 ASN cc_start: 0.9214 (m110) cc_final: 0.8756 (t0) outliers start: 61 outliers final: 30 residues processed: 261 average time/residue: 0.0861 time to fit residues: 36.0673 Evaluate side-chains 202 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 81 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 717 GLN B 615 HIS B 763 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.095199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.069876 restraints weight = 39774.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.072774 restraints weight = 19054.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.074732 restraints weight = 11824.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.076118 restraints weight = 8587.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.076965 restraints weight = 6915.710| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13845 Z= 0.164 Angle : 0.645 12.500 18880 Z= 0.316 Chirality : 0.042 0.222 2229 Planarity : 0.004 0.050 2326 Dihedral : 4.540 56.316 1888 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.17 % Allowed : 23.35 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1731 helix: 1.84 (0.17), residues: 953 sheet: -0.68 (0.42), residues: 133 loop : -2.02 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 317 TYR 0.011 0.001 TYR A 292 PHE 0.015 0.001 PHE A 541 TRP 0.012 0.001 TRP B 143 HIS 0.005 0.001 HIS B 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (13831) covalent geometry : angle 0.64019 / 0.31 (18844) SS BOND : bond 0.00340 / 0.24 ( 6) SS BOND : angle 1.74618 / 0.80 ( 12) hydrogen bonds : bond 0.04957 / 3.42 ( 764) hydrogen bonds : angle 4.13527 / 3.04 ( 2211) link_BETA1-4 : bond 0.01136 / 0.74 ( 4) link_BETA1-4 : angle 2.38575 / 1.54 ( 12) link_NAG-ASN : bond 0.00253 / 0.15 ( 4) link_NAG-ASN : angle 1.68399 / 1.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 167 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8220 (mtp) cc_final: 0.7819 (tmm) REVERT: A 144 MET cc_start: 0.8253 (ttp) cc_final: 0.7910 (ptm) REVERT: A 147 THR cc_start: 0.8611 (t) cc_final: 0.8367 (t) REVERT: A 188 MET cc_start: 0.7535 (mtm) cc_final: 0.7242 (ttm) REVERT: A 358 MET cc_start: 0.9403 (mpp) cc_final: 0.9029 (mpp) REVERT: A 376 LEU cc_start: 0.8874 (tp) cc_final: 0.8604 (tp) REVERT: A 583 MET cc_start: 0.7804 (tpp) cc_final: 0.7549 (tpp) REVERT: A 642 MET cc_start: 0.8709 (tmm) cc_final: 0.8504 (tmm) REVERT: A 658 GLU cc_start: 0.8461 (tt0) cc_final: 0.8022 (mm-30) REVERT: A 752 MET cc_start: 0.9313 (tpp) cc_final: 0.8785 (tpp) REVERT: A 854 ASP cc_start: 0.8239 (m-30) cc_final: 0.7980 (m-30) REVERT: A 859 MET cc_start: 0.9091 (mtp) cc_final: 0.8680 (mmp) REVERT: A 1041 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8064 (pt) REVERT: A 1043 MET cc_start: 0.9117 (ptt) cc_final: 0.8836 (pmm) REVERT: A 1078 ARG cc_start: 0.8589 (mtm110) cc_final: 0.8236 (ptm160) REVERT: B 171 MET cc_start: 0.8954 (tpp) cc_final: 0.8711 (tpp) REVERT: B 416 ILE cc_start: 0.9444 (tt) cc_final: 0.9091 (mm) REVERT: B 419 SER cc_start: 0.8530 (t) cc_final: 0.8304 (p) REVERT: B 542 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8330 (pp) REVERT: B 563 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8537 (tt) REVERT: B 576 MET cc_start: 0.8290 (mtp) cc_final: 0.7991 (mtp) REVERT: B 587 MET cc_start: 0.8855 (tpt) cc_final: 0.8573 (tpt) REVERT: B 630 MET cc_start: 0.8687 (ttp) cc_final: 0.8382 (ttm) REVERT: B 659 LYS cc_start: 0.9064 (tttt) cc_final: 0.8708 (ttmm) REVERT: B 750 LYS cc_start: 0.9377 (mttt) cc_final: 0.9080 (mtmm) REVERT: B 813 ASP cc_start: 0.9083 (m-30) cc_final: 0.8801 (t0) REVERT: B 874 CYS cc_start: 0.8680 (m) cc_final: 0.7473 (t) REVERT: B 900 TYR cc_start: 0.8968 (m-80) cc_final: 0.8458 (m-80) REVERT: B 1055 ASN cc_start: 0.9211 (m110) cc_final: 0.8793 (t0) outliers start: 73 outliers final: 49 residues processed: 225 average time/residue: 0.0823 time to fit residues: 30.0186 Evaluate side-chains 206 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 85 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 717 GLN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.093975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.068242 restraints weight = 40563.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.071090 restraints weight = 19444.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.073080 restraints weight = 12144.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.074418 restraints weight = 8899.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.075328 restraints weight = 7217.844| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13845 Z= 0.227 Angle : 0.681 13.316 18880 Z= 0.335 Chirality : 0.043 0.224 2229 Planarity : 0.004 0.036 2326 Dihedral : 4.268 40.955 1881 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.09 % Allowed : 24.35 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.20), residues: 1731 helix: 1.87 (0.17), residues: 953 sheet: -0.63 (0.44), residues: 121 loop : -1.82 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1074 TYR 0.011 0.001 TYR B 649 PHE 0.023 0.002 PHE A 541 TRP 0.013 0.001 TRP B 143 HIS 0.009 0.001 HIS B 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.23 (13831) covalent geometry : angle 0.67659 / 0.33 (18844) SS BOND : bond 0.00364 / 0.26 ( 6) SS BOND : angle 1.79210 / 0.92 ( 12) hydrogen bonds : bond 0.05087 / 3.50 ( 764) hydrogen bonds : angle 4.19709 / 3.08 ( 2211) link_BETA1-4 : bond 0.00811 / 0.53 ( 4) link_BETA1-4 : angle 2.17799 / 1.40 ( 12) link_NAG-ASN : bond 0.00409 / 0.23 ( 4) link_NAG-ASN : angle 1.68708 / 1.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 159 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8288 (mtp) cc_final: 0.7791 (tmm) REVERT: A 144 MET cc_start: 0.8301 (ttp) cc_final: 0.7993 (ptm) REVERT: A 147 THR cc_start: 0.8609 (t) cc_final: 0.8380 (t) REVERT: A 188 MET cc_start: 0.7591 (mtm) cc_final: 0.7273 (ttm) REVERT: A 358 MET cc_start: 0.9464 (mpp) cc_final: 0.9223 (mpp) REVERT: A 658 GLU cc_start: 0.8446 (tt0) cc_final: 0.7990 (mm-30) REVERT: A 806 ARG cc_start: 0.8579 (mmt90) cc_final: 0.8114 (mmp80) REVERT: A 859 MET cc_start: 0.9201 (mtp) cc_final: 0.8723 (mmp) REVERT: A 1041 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7995 (pt) REVERT: A 1042 ASN cc_start: 0.8217 (p0) cc_final: 0.7783 (p0) REVERT: A 1043 MET cc_start: 0.9179 (ptt) cc_final: 0.8787 (pmm) REVERT: A 1078 ARG cc_start: 0.8701 (mtm110) cc_final: 0.8337 (ptm160) REVERT: B 258 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8342 (t80) REVERT: B 416 ILE cc_start: 0.9482 (tt) cc_final: 0.9150 (mm) REVERT: B 419 SER cc_start: 0.8521 (t) cc_final: 0.8227 (p) REVERT: B 542 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8366 (pp) REVERT: B 563 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8541 (tt) REVERT: B 576 MET cc_start: 0.8321 (mtp) cc_final: 0.7975 (mtp) REVERT: B 587 MET cc_start: 0.8835 (tpt) cc_final: 0.8559 (tpt) REVERT: B 623 MET cc_start: 0.9400 (tmm) cc_final: 0.9198 (tmm) REVERT: B 630 MET cc_start: 0.8696 (ttp) cc_final: 0.8346 (ttm) REVERT: B 659 LYS cc_start: 0.9036 (tttt) cc_final: 0.8685 (ttmm) REVERT: B 750 LYS cc_start: 0.9400 (mttt) cc_final: 0.9095 (mtmm) REVERT: B 813 ASP cc_start: 0.9077 (m-30) cc_final: 0.8843 (t0) REVERT: B 874 CYS cc_start: 0.8771 (m) cc_final: 0.7529 (t) REVERT: B 876 MET cc_start: 0.8763 (ttp) cc_final: 0.8536 (ttp) REVERT: B 900 TYR cc_start: 0.8979 (m-80) cc_final: 0.8463 (m-80) REVERT: B 1055 ASN cc_start: 0.9207 (m110) cc_final: 0.8831 (t0) outliers start: 86 outliers final: 64 residues processed: 226 average time/residue: 0.0856 time to fit residues: 31.3560 Evaluate side-chains 219 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 151 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 853 HIS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 50 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 868 HIS B 763 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.095225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.069466 restraints weight = 40502.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.072385 restraints weight = 19456.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.074369 restraints weight = 12152.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.075734 restraints weight = 8898.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.076656 restraints weight = 7228.300| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13845 Z= 0.155 Angle : 0.611 10.391 18880 Z= 0.298 Chirality : 0.041 0.215 2229 Planarity : 0.003 0.036 2326 Dihedral : 4.175 39.388 1881 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.74 % Allowed : 26.26 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.80 (0.20), residues: 1731 helix: 2.06 (0.17), residues: 951 sheet: -0.59 (0.42), residues: 137 loop : -1.65 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 317 TYR 0.010 0.001 TYR B 649 PHE 0.019 0.001 PHE A 541 TRP 0.012 0.001 TRP B 143 HIS 0.004 0.001 HIS A 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (13831) covalent geometry : angle 0.60721 / 0.30 (18844) SS BOND : bond 0.00301 / 0.21 ( 6) SS BOND : angle 1.60145 / 0.83 ( 12) hydrogen bonds : bond 0.04589 / 3.18 ( 764) hydrogen bonds : angle 3.96603 / 2.91 ( 2211) link_BETA1-4 : bond 0.00900 / 0.59 ( 4) link_BETA1-4 : angle 2.00840 / 1.29 ( 12) link_NAG-ASN : bond 0.00209 / 0.12 ( 4) link_NAG-ASN : angle 1.55090 / 0.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 166 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8298 (mtp) cc_final: 0.7809 (tmm) REVERT: A 144 MET cc_start: 0.8240 (ttp) cc_final: 0.7928 (ptm) REVERT: A 147 THR cc_start: 0.8617 (t) cc_final: 0.8388 (t) REVERT: A 188 MET cc_start: 0.7514 (mtm) cc_final: 0.7313 (ttm) REVERT: A 358 MET cc_start: 0.9480 (mpp) cc_final: 0.9241 (mpp) REVERT: A 536 ASP cc_start: 0.7934 (t0) cc_final: 0.7599 (t0) REVERT: A 576 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7021 (tpp) REVERT: A 658 GLU cc_start: 0.8460 (tt0) cc_final: 0.7982 (mm-30) REVERT: A 791 VAL cc_start: 0.9055 (t) cc_final: 0.8845 (p) REVERT: A 806 ARG cc_start: 0.8558 (mmt90) cc_final: 0.8073 (mmp80) REVERT: A 859 MET cc_start: 0.9213 (mtp) cc_final: 0.8697 (mmp) REVERT: A 1042 ASN cc_start: 0.8259 (p0) cc_final: 0.7793 (p0) REVERT: A 1043 MET cc_start: 0.9160 (ptt) cc_final: 0.8820 (pmm) REVERT: A 1078 ARG cc_start: 0.8735 (mtm110) cc_final: 0.8379 (ptm160) REVERT: B 171 MET cc_start: 0.8845 (tpp) cc_final: 0.8640 (tpp) REVERT: B 258 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8256 (t80) REVERT: B 416 ILE cc_start: 0.9466 (tt) cc_final: 0.9171 (mm) REVERT: B 542 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8288 (pp) REVERT: B 576 MET cc_start: 0.8253 (mtp) cc_final: 0.7927 (mtp) REVERT: B 587 MET cc_start: 0.8768 (tpt) cc_final: 0.8479 (tpt) REVERT: B 623 MET cc_start: 0.9408 (tmm) cc_final: 0.9172 (tmm) REVERT: B 630 MET cc_start: 0.8741 (ttp) cc_final: 0.8324 (ttm) REVERT: B 659 LYS cc_start: 0.8984 (tttt) cc_final: 0.8638 (ttmm) REVERT: B 750 LYS cc_start: 0.9380 (mttt) cc_final: 0.9078 (mtmm) REVERT: B 813 ASP cc_start: 0.9049 (m-30) cc_final: 0.8804 (t0) REVERT: B 1055 ASN cc_start: 0.9223 (m110) cc_final: 0.8825 (t0) REVERT: B 1057 MET cc_start: 0.9273 (tpp) cc_final: 0.8984 (tpp) outliers start: 67 outliers final: 51 residues processed: 220 average time/residue: 0.0863 time to fit residues: 30.3835 Evaluate side-chains 204 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 853 HIS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 141 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 170 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.096754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.071275 restraints weight = 40135.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.074256 restraints weight = 19184.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.076304 restraints weight = 11944.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.077701 restraints weight = 8711.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.078564 restraints weight = 7039.273| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13845 Z= 0.114 Angle : 0.583 8.316 18880 Z= 0.279 Chirality : 0.040 0.213 2229 Planarity : 0.003 0.038 2326 Dihedral : 4.018 35.473 1881 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.89 % Allowed : 27.39 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.21), residues: 1731 helix: 2.18 (0.17), residues: 956 sheet: -0.52 (0.42), residues: 137 loop : -1.54 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 317 TYR 0.011 0.001 TYR B1056 PHE 0.022 0.001 PHE B1059 TRP 0.011 0.001 TRP B 143 HIS 0.004 0.001 HIS B 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (13831) covalent geometry : angle 0.57891 / 0.28 (18844) SS BOND : bond 0.00409 / 0.23 ( 6) SS BOND : angle 1.52066 / 0.79 ( 12) hydrogen bonds : bond 0.04150 / 2.87 ( 764) hydrogen bonds : angle 3.84099 / 2.83 ( 2211) link_BETA1-4 : bond 0.00941 / 0.62 ( 4) link_BETA1-4 : angle 1.89591 / 1.20 ( 12) link_NAG-ASN : bond 0.00118 / 0.07 ( 4) link_NAG-ASN : angle 1.50872 / 0.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8296 (mtp) cc_final: 0.7813 (tmm) REVERT: A 144 MET cc_start: 0.8163 (ttp) cc_final: 0.7887 (ptm) REVERT: A 147 THR cc_start: 0.8608 (t) cc_final: 0.8376 (t) REVERT: A 160 CYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8063 (p) REVERT: A 188 MET cc_start: 0.7529 (mtm) cc_final: 0.7270 (ttm) REVERT: A 358 MET cc_start: 0.9467 (mpp) cc_final: 0.9222 (mpp) REVERT: A 380 LEU cc_start: 0.9099 (tt) cc_final: 0.8890 (pp) REVERT: A 536 ASP cc_start: 0.7766 (t0) cc_final: 0.7387 (t0) REVERT: A 576 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.6488 (tpp) REVERT: A 630 MET cc_start: 0.8635 (tpp) cc_final: 0.8386 (tpp) REVERT: A 658 GLU cc_start: 0.8411 (tt0) cc_final: 0.8036 (tp30) REVERT: A 757 LYS cc_start: 0.9069 (mmmm) cc_final: 0.8777 (mmmm) REVERT: A 806 ARG cc_start: 0.8558 (mmt90) cc_final: 0.8069 (mmp80) REVERT: A 859 MET cc_start: 0.9217 (mtp) cc_final: 0.8688 (mmp) REVERT: A 1042 ASN cc_start: 0.8177 (p0) cc_final: 0.7811 (p0) REVERT: A 1043 MET cc_start: 0.9131 (ptt) cc_final: 0.8872 (pmm) REVERT: A 1078 ARG cc_start: 0.8724 (mtm110) cc_final: 0.8378 (ptm160) REVERT: B 171 MET cc_start: 0.8842 (tpp) cc_final: 0.8640 (tpp) REVERT: B 258 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8282 (t80) REVERT: B 416 ILE cc_start: 0.9442 (tt) cc_final: 0.9180 (mm) REVERT: B 542 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8149 (pp) REVERT: B 576 MET cc_start: 0.8271 (mtp) cc_final: 0.7956 (mtp) REVERT: B 587 MET cc_start: 0.8676 (tpt) cc_final: 0.8449 (tpt) REVERT: B 591 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8793 (m-80) REVERT: B 623 MET cc_start: 0.9379 (tmm) cc_final: 0.9102 (tmm) REVERT: B 630 MET cc_start: 0.8707 (ttp) cc_final: 0.8497 (ttm) REVERT: B 659 LYS cc_start: 0.9006 (tttt) cc_final: 0.8622 (ttmm) REVERT: B 781 CYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8276 (m) REVERT: B 813 ASP cc_start: 0.9041 (m-30) cc_final: 0.8789 (t0) REVERT: B 876 MET cc_start: 0.8714 (ttp) cc_final: 0.8287 (tmm) REVERT: B 1043 MET cc_start: 0.9026 (ptm) cc_final: 0.8560 (tmm) REVERT: B 1055 ASN cc_start: 0.9186 (m110) cc_final: 0.8769 (t0) outliers start: 55 outliers final: 34 residues processed: 223 average time/residue: 0.0905 time to fit residues: 32.3910 Evaluate side-chains 199 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 136 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 113 optimal weight: 0.0980 chunk 163 optimal weight: 5.9990 chunk 8 optimal weight: 0.0570 chunk 48 optimal weight: 0.3980 chunk 112 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.097521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.071980 restraints weight = 40138.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.075003 restraints weight = 19094.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.077114 restraints weight = 11835.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.078546 restraints weight = 8548.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.079516 restraints weight = 6869.784| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 13845 Z= 0.108 Angle : 0.594 8.462 18880 Z= 0.282 Chirality : 0.040 0.209 2229 Planarity : 0.003 0.039 2326 Dihedral : 3.898 31.438 1881 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.47 % Allowed : 28.03 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.21), residues: 1731 helix: 2.22 (0.17), residues: 957 sheet: -0.38 (0.44), residues: 131 loop : -1.44 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.014 0.001 TYR B1056 PHE 0.028 0.001 PHE B1059 TRP 0.010 0.001 TRP B 143 HIS 0.005 0.001 HIS B 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (13831) covalent geometry : angle 0.59052 / 0.28 (18844) SS BOND : bond 0.00192 / 0.13 ( 6) SS BOND : angle 1.33473 / 0.68 ( 12) hydrogen bonds : bond 0.03930 / 2.71 ( 764) hydrogen bonds : angle 3.75354 / 2.77 ( 2211) link_BETA1-4 : bond 0.00993 / 0.64 ( 4) link_BETA1-4 : angle 1.82963 / 1.14 ( 12) link_NAG-ASN : bond 0.00070 / 0.05 ( 4) link_NAG-ASN : angle 1.47694 / 0.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8297 (mtp) cc_final: 0.7817 (tmm) REVERT: A 144 MET cc_start: 0.8140 (ttp) cc_final: 0.7884 (ptm) REVERT: A 147 THR cc_start: 0.8611 (t) cc_final: 0.8378 (t) REVERT: A 160 CYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8047 (p) REVERT: A 309 MET cc_start: 0.8773 (mmm) cc_final: 0.8544 (tpp) REVERT: A 358 MET cc_start: 0.9476 (mpp) cc_final: 0.9226 (mpp) REVERT: A 536 ASP cc_start: 0.7680 (t0) cc_final: 0.7306 (t0) REVERT: A 576 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6384 (tpp) REVERT: A 630 MET cc_start: 0.8755 (tpp) cc_final: 0.8366 (tpp) REVERT: A 658 GLU cc_start: 0.8387 (tt0) cc_final: 0.7907 (mm-30) REVERT: A 859 MET cc_start: 0.9210 (mtp) cc_final: 0.8618 (mmp) REVERT: A 1041 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7821 (pt) REVERT: A 1042 ASN cc_start: 0.8127 (p0) cc_final: 0.7832 (p0) REVERT: A 1043 MET cc_start: 0.9116 (ptt) cc_final: 0.8904 (pmm) REVERT: A 1078 ARG cc_start: 0.8702 (mtm110) cc_final: 0.8357 (ptm160) REVERT: B 144 MET cc_start: 0.8761 (ttm) cc_final: 0.8552 (tmm) REVERT: B 258 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8361 (t80) REVERT: B 416 ILE cc_start: 0.9439 (tt) cc_final: 0.9148 (mm) REVERT: B 419 SER cc_start: 0.8282 (t) cc_final: 0.8038 (p) REVERT: B 450 SER cc_start: 0.9371 (t) cc_final: 0.8834 (p) REVERT: B 542 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8209 (pp) REVERT: B 576 MET cc_start: 0.8251 (mtp) cc_final: 0.7939 (mtp) REVERT: B 587 MET cc_start: 0.8622 (tpt) cc_final: 0.8395 (tpt) REVERT: B 591 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8776 (m-80) REVERT: B 623 MET cc_start: 0.9374 (tmm) cc_final: 0.9129 (tmm) REVERT: B 659 LYS cc_start: 0.8919 (tttt) cc_final: 0.8532 (ttmm) REVERT: B 750 LYS cc_start: 0.9247 (mttt) cc_final: 0.8936 (mptp) REVERT: B 781 CYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8257 (m) REVERT: B 813 ASP cc_start: 0.9012 (m-30) cc_final: 0.8729 (t0) REVERT: B 1055 ASN cc_start: 0.9190 (m110) cc_final: 0.8406 (t0) REVERT: B 1058 GLU cc_start: 0.9251 (mm-30) cc_final: 0.9042 (tm-30) REVERT: B 1059 PHE cc_start: 0.9210 (t80) cc_final: 0.8808 (t80) outliers start: 49 outliers final: 35 residues processed: 224 average time/residue: 0.0921 time to fit residues: 33.3310 Evaluate side-chains 206 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 27 optimal weight: 0.2980 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.095179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.069593 restraints weight = 40029.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.072500 restraints weight = 19268.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.074510 restraints weight = 12053.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.075893 restraints weight = 8776.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.076595 restraints weight = 7081.959| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13845 Z= 0.159 Angle : 0.631 9.788 18880 Z= 0.303 Chirality : 0.042 0.277 2229 Planarity : 0.003 0.037 2326 Dihedral : 3.946 30.598 1881 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.75 % Allowed : 27.88 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.21), residues: 1731 helix: 2.23 (0.17), residues: 953 sheet: -0.38 (0.43), residues: 131 loop : -1.38 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1074 TYR 0.012 0.001 TYR B 649 PHE 0.024 0.001 PHE B 863 TRP 0.009 0.001 TRP A 690 HIS 0.004 0.001 HIS A 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (13831) covalent geometry : angle 0.62824 / 0.30 (18844) SS BOND : bond 0.00290 / 0.19 ( 6) SS BOND : angle 1.46972 / 0.74 ( 12) hydrogen bonds : bond 0.04267 / 2.93 ( 764) hydrogen bonds : angle 3.82123 / 2.82 ( 2211) link_BETA1-4 : bond 0.00891 / 0.58 ( 4) link_BETA1-4 : angle 1.69867 / 1.08 ( 12) link_NAG-ASN : bond 0.00264 / 0.16 ( 4) link_NAG-ASN : angle 1.55090 / 0.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8311 (mtp) cc_final: 0.7814 (tmm) REVERT: A 144 MET cc_start: 0.8167 (ttp) cc_final: 0.7869 (ptm) REVERT: A 147 THR cc_start: 0.8647 (t) cc_final: 0.8421 (t) REVERT: A 160 CYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8099 (p) REVERT: A 172 SER cc_start: 0.8710 (t) cc_final: 0.8147 (p) REVERT: A 358 MET cc_start: 0.9498 (mpp) cc_final: 0.9254 (mpp) REVERT: A 536 ASP cc_start: 0.7808 (t0) cc_final: 0.7403 (t0) REVERT: A 576 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6895 (tpp) REVERT: A 630 MET cc_start: 0.8820 (tpp) cc_final: 0.8462 (tpp) REVERT: A 636 TYR cc_start: 0.7974 (p90) cc_final: 0.7726 (p90) REVERT: A 658 GLU cc_start: 0.8367 (tt0) cc_final: 0.7920 (mm-30) REVERT: A 859 MET cc_start: 0.9257 (mtp) cc_final: 0.8670 (mmp) REVERT: A 1041 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8012 (pt) REVERT: A 1042 ASN cc_start: 0.8108 (p0) cc_final: 0.7795 (p0) REVERT: A 1043 MET cc_start: 0.9164 (ptt) cc_final: 0.8857 (pmm) REVERT: A 1078 ARG cc_start: 0.8731 (mtm110) cc_final: 0.8482 (ptm160) REVERT: B 144 MET cc_start: 0.8828 (ttm) cc_final: 0.8561 (tmm) REVERT: B 258 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8295 (t80) REVERT: B 416 ILE cc_start: 0.9430 (tt) cc_final: 0.9168 (mm) REVERT: B 419 SER cc_start: 0.8438 (t) cc_final: 0.8120 (p) REVERT: B 542 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8293 (pp) REVERT: B 576 MET cc_start: 0.8228 (mtp) cc_final: 0.7900 (mtp) REVERT: B 587 MET cc_start: 0.8886 (tpt) cc_final: 0.8622 (tpt) REVERT: B 623 MET cc_start: 0.9407 (tmm) cc_final: 0.9120 (tmm) REVERT: B 630 MET cc_start: 0.8938 (ttm) cc_final: 0.8686 (ttm) REVERT: B 659 LYS cc_start: 0.8967 (tttt) cc_final: 0.8581 (ttmm) REVERT: B 750 LYS cc_start: 0.9234 (mttt) cc_final: 0.8898 (mttp) REVERT: B 781 CYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8362 (m) REVERT: B 813 ASP cc_start: 0.9032 (m-30) cc_final: 0.8762 (t0) REVERT: B 876 MET cc_start: 0.8656 (ttp) cc_final: 0.8293 (tmm) REVERT: B 1055 ASN cc_start: 0.9205 (m110) cc_final: 0.8449 (t0) REVERT: B 1059 PHE cc_start: 0.9211 (t80) cc_final: 0.8815 (t80) outliers start: 53 outliers final: 39 residues processed: 209 average time/residue: 0.0908 time to fit residues: 30.7263 Evaluate side-chains 203 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.095736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.070116 restraints weight = 40510.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.073085 restraints weight = 19358.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.075080 restraints weight = 12028.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.076488 restraints weight = 8743.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.077442 restraints weight = 7049.584| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13845 Z= 0.138 Angle : 0.629 8.736 18880 Z= 0.299 Chirality : 0.041 0.209 2229 Planarity : 0.003 0.038 2326 Dihedral : 3.959 30.900 1881 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.40 % Allowed : 28.59 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.21), residues: 1731 helix: 2.23 (0.17), residues: 953 sheet: -0.37 (0.43), residues: 132 loop : -1.32 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1074 TYR 0.011 0.001 TYR B 649 PHE 0.023 0.001 PHE B1059 TRP 0.010 0.001 TRP B 143 HIS 0.003 0.001 HIS A 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (13831) covalent geometry : angle 0.62582 / 0.30 (18844) SS BOND : bond 0.00260 / 0.17 ( 6) SS BOND : angle 1.45072 / 0.74 ( 12) hydrogen bonds : bond 0.04209 / 2.89 ( 764) hydrogen bonds : angle 3.79171 / 2.79 ( 2211) link_BETA1-4 : bond 0.00969 / 0.63 ( 4) link_BETA1-4 : angle 1.67365 / 1.05 ( 12) link_NAG-ASN : bond 0.00129 / 0.07 ( 4) link_NAG-ASN : angle 1.52775 / 0.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8279 (mtp) cc_final: 0.7803 (tmm) REVERT: A 144 MET cc_start: 0.8172 (ttp) cc_final: 0.7880 (ptm) REVERT: A 147 THR cc_start: 0.8607 (t) cc_final: 0.8386 (t) REVERT: A 160 CYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8093 (p) REVERT: A 309 MET cc_start: 0.8687 (tpp) cc_final: 0.8462 (mmm) REVERT: A 358 MET cc_start: 0.9492 (mpp) cc_final: 0.9252 (mpp) REVERT: A 536 ASP cc_start: 0.7795 (t0) cc_final: 0.7383 (t0) REVERT: A 576 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6868 (tpp) REVERT: A 630 MET cc_start: 0.8812 (tpp) cc_final: 0.8458 (tpp) REVERT: A 658 GLU cc_start: 0.8419 (tt0) cc_final: 0.7949 (mm-30) REVERT: A 859 MET cc_start: 0.9245 (mtp) cc_final: 0.8648 (mmp) REVERT: A 1041 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8008 (pt) REVERT: A 1042 ASN cc_start: 0.8112 (p0) cc_final: 0.7829 (p0) REVERT: A 1043 MET cc_start: 0.9170 (ptt) cc_final: 0.8894 (pmm) REVERT: A 1078 ARG cc_start: 0.8732 (mtm110) cc_final: 0.8375 (ptm160) REVERT: B 144 MET cc_start: 0.8800 (ttm) cc_final: 0.8590 (tmm) REVERT: B 258 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8240 (t80) REVERT: B 419 SER cc_start: 0.8374 (t) cc_final: 0.8143 (p) REVERT: B 542 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8284 (pp) REVERT: B 576 MET cc_start: 0.8227 (mtp) cc_final: 0.7902 (mtp) REVERT: B 587 MET cc_start: 0.8936 (tpt) cc_final: 0.8563 (tpt) REVERT: B 623 MET cc_start: 0.9393 (tmm) cc_final: 0.9119 (tmm) REVERT: B 630 MET cc_start: 0.8954 (ttm) cc_final: 0.8648 (ttm) REVERT: B 659 LYS cc_start: 0.8973 (tttt) cc_final: 0.8583 (ttmm) REVERT: B 750 LYS cc_start: 0.9263 (mttt) cc_final: 0.8947 (mttp) REVERT: B 781 CYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8252 (m) REVERT: B 813 ASP cc_start: 0.9050 (m-30) cc_final: 0.8780 (t0) REVERT: B 1055 ASN cc_start: 0.8962 (m110) cc_final: 0.8498 (t0) outliers start: 48 outliers final: 38 residues processed: 204 average time/residue: 0.0831 time to fit residues: 27.6336 Evaluate side-chains 207 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 64 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 109 optimal weight: 0.0980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.097242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.072051 restraints weight = 40469.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.075026 restraints weight = 19265.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.077086 restraints weight = 11909.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.078466 restraints weight = 8613.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.079424 restraints weight = 6918.737| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13845 Z= 0.119 Angle : 0.630 9.644 18880 Z= 0.296 Chirality : 0.041 0.280 2229 Planarity : 0.003 0.039 2326 Dihedral : 3.815 31.093 1879 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.33 % Allowed : 28.95 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.21), residues: 1731 helix: 2.23 (0.17), residues: 953 sheet: -0.28 (0.44), residues: 132 loop : -1.24 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1074 TYR 0.011 0.001 TYR B 649 PHE 0.025 0.001 PHE A 620 TRP 0.010 0.001 TRP B 143 HIS 0.005 0.001 HIS B 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13831) covalent geometry : angle 0.62731 / 0.30 (18844) SS BOND : bond 0.00221 / 0.15 ( 6) SS BOND : angle 1.34844 / 0.70 ( 12) hydrogen bonds : bond 0.04011 / 2.75 ( 764) hydrogen bonds : angle 3.75913 / 2.78 ( 2211) link_BETA1-4 : bond 0.00938 / 0.61 ( 4) link_BETA1-4 : angle 1.65404 / 1.02 ( 12) link_NAG-ASN : bond 0.00066 / 0.04 ( 4) link_NAG-ASN : angle 1.51558 / 0.91 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8275 (mtp) cc_final: 0.7798 (tmm) REVERT: A 144 MET cc_start: 0.8158 (ttp) cc_final: 0.7861 (ptm) REVERT: A 147 THR cc_start: 0.8616 (t) cc_final: 0.8393 (t) REVERT: A 160 CYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8064 (p) REVERT: A 174 ILE cc_start: 0.8321 (mt) cc_final: 0.8116 (mt) REVERT: A 358 MET cc_start: 0.9480 (mpp) cc_final: 0.9230 (mpp) REVERT: A 536 ASP cc_start: 0.7734 (t0) cc_final: 0.7305 (t0) REVERT: A 576 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.6810 (tpp) REVERT: A 630 MET cc_start: 0.8809 (tpp) cc_final: 0.8471 (tpp) REVERT: A 636 TYR cc_start: 0.7913 (p90) cc_final: 0.7659 (p90) REVERT: A 658 GLU cc_start: 0.8404 (tt0) cc_final: 0.8065 (tp30) REVERT: A 859 MET cc_start: 0.9226 (mtp) cc_final: 0.8627 (mmp) REVERT: A 1041 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7989 (pt) REVERT: A 1042 ASN cc_start: 0.8089 (p0) cc_final: 0.7823 (p0) REVERT: A 1043 MET cc_start: 0.9142 (ptt) cc_final: 0.8912 (pmm) REVERT: A 1078 ARG cc_start: 0.8730 (mtm110) cc_final: 0.8367 (ptm160) REVERT: B 144 MET cc_start: 0.8770 (ttm) cc_final: 0.8547 (tmm) REVERT: B 258 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8251 (t80) REVERT: B 419 SER cc_start: 0.8265 (t) cc_final: 0.8045 (p) REVERT: B 450 SER cc_start: 0.9354 (t) cc_final: 0.8847 (p) REVERT: B 542 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8270 (pp) REVERT: B 576 MET cc_start: 0.8178 (mtp) cc_final: 0.7859 (mtp) REVERT: B 587 MET cc_start: 0.8926 (tpt) cc_final: 0.8585 (tpt) REVERT: B 623 MET cc_start: 0.9386 (tmm) cc_final: 0.9124 (tmm) REVERT: B 630 MET cc_start: 0.8922 (ttm) cc_final: 0.8646 (ttm) REVERT: B 659 LYS cc_start: 0.8997 (tttt) cc_final: 0.8600 (ttmm) REVERT: B 750 LYS cc_start: 0.9252 (mttt) cc_final: 0.8939 (mttp) REVERT: B 781 CYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8145 (m) REVERT: B 813 ASP cc_start: 0.9025 (m-30) cc_final: 0.8750 (t0) REVERT: B 1055 ASN cc_start: 0.8972 (m110) cc_final: 0.8511 (t0) outliers start: 47 outliers final: 35 residues processed: 203 average time/residue: 0.0867 time to fit residues: 28.3954 Evaluate side-chains 206 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 47 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.0050 chunk 88 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.097653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.072168 restraints weight = 40023.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075211 restraints weight = 19054.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.077335 restraints weight = 11796.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078742 restraints weight = 8506.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.079707 restraints weight = 6834.505| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13845 Z= 0.111 Angle : 0.632 12.748 18880 Z= 0.294 Chirality : 0.041 0.268 2229 Planarity : 0.003 0.040 2326 Dihedral : 3.751 30.063 1879 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.18 % Allowed : 29.09 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.21), residues: 1731 helix: 2.29 (0.17), residues: 954 sheet: -0.25 (0.44), residues: 132 loop : -1.19 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 866 TYR 0.011 0.001 TYR B 649 PHE 0.028 0.001 PHE B1059 TRP 0.010 0.001 TRP B 143 HIS 0.004 0.001 HIS B 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (13831) covalent geometry : angle 0.62934 / 0.29 (18844) SS BOND : bond 0.00191 / 0.13 ( 6) SS BOND : angle 1.30273 / 0.66 ( 12) hydrogen bonds : bond 0.03797 / 2.60 ( 764) hydrogen bonds : angle 3.70147 / 2.73 ( 2211) link_BETA1-4 : bond 0.00890 / 0.58 ( 4) link_BETA1-4 : angle 1.62185 / 1.01 ( 12) link_NAG-ASN : bond 0.00161 / 0.11 ( 4) link_NAG-ASN : angle 1.51020 / 0.92 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2251.34 seconds wall clock time: 39 minutes 37.69 seconds (2377.69 seconds total)