Starting phenix.real_space_refine on Mon Aug 25 03:34:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0s_42868/08_2025/8v0s_42868.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0s_42868/08_2025/8v0s_42868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0s_42868/08_2025/8v0s_42868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0s_42868/08_2025/8v0s_42868.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0s_42868/08_2025/8v0s_42868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0s_42868/08_2025/8v0s_42868.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 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: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 15929 2.51 5 N 4102 2.21 5 O 4805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24950 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8144 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 52, 'TRANS': 989} Chain breaks: 6 Chain: "B" Number of atoms: 8144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8144 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 52, 'TRANS': 989} Chain breaks: 6 Chain: "C" Number of atoms: 8144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8144 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 52, 'TRANS': 989} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.28, per 1000 atoms: 0.25 Number of scatterers: 24950 At special positions: 0 Unit cell: (141.48, 132.84, 176.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4805 8.00 N 4102 7.00 C 15929 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 801 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B1134 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 801 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C 709 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN B1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN C1098 " " NAG I 1 " - " ASN C 717 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5868 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 52 sheets defined 22.9% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.786A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 371 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A 372 " --> pdb=" O TYR A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 372' Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.619A pdb=" N ALA A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.544A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 836 through 842 removed outlier: 3.976A pdb=" N GLY A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.654A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.942A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 986 through 1032 Processing helix chain 'A' and resid 1116 through 1120 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.863A pdb=" N ILE B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.746A pdb=" N GLY B 545 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 546' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 removed outlier: 3.534A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 754 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.629A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 965 Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1031 Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.515A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.664A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.950A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 407' Processing helix chain 'C' and resid 416 through 420 removed outlier: 3.793A pdb=" N ALA C 419 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP C 420 " --> pdb=" O ASN C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 420' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.731A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.572A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.580A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 842 removed outlier: 3.871A pdb=" N GLY C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.594A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 906 removed outlier: 4.001A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 910 removed outlier: 3.750A pdb=" N GLY C 910 " --> pdb=" O ASN C 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 907 through 910' Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.797A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.672A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 986 through 1032 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.721A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.843A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.830A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 189 through 191 removed outlier: 3.560A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 189 through 191 removed outlier: 4.254A pdb=" N PHE A 201 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.649A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.288A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 379 through 380 removed outlier: 3.582A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 454 removed outlier: 8.184A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.910A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 670 through 673 Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 728 removed outlier: 6.521A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.537A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB7, first strand: chain 'A' and resid 1103 through 1106 removed outlier: 4.676A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.950A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.209A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.473A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.209A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.473A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.658A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.792A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 104 through 107 removed outlier: 4.007A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 129 through 130 removed outlier: 3.611A pdb=" N TYR B 170 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.735A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.993A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 586 " --> pdb=" O THR B 553 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 356 through 357 removed outlier: 3.530A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 378 through 379 Processing sheet with id=AD2, first strand: chain 'B' and resid 435 through 437 removed outlier: 3.760A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 611 through 613 Processing sheet with id=AD4, first strand: chain 'B' and resid 659 through 660 removed outlier: 4.184A pdb=" N TYR B 660 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD7, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.241A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.241A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.791A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.553A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.619A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'C' and resid 104 through 105 removed outlier: 3.514A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AE6, first strand: chain 'C' and resid 194 through 197 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 315 removed outlier: 3.525A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.524A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 357 through 358 removed outlier: 4.041A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 361 through 362 removed outlier: 5.421A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.603A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.592A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.966A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.966A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.644A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.533A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 2004 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: 5.61 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7850 1.34 - 1.46: 6123 1.46 - 1.58: 11398 1.58 - 1.71: 2 1.71 - 1.83: 141 Bond restraints: 25514 Sorted by residual: bond pdb=" N PRO C 225 " pdb=" CD PRO C 225 " ideal model delta sigma weight residual 1.473 1.411 0.062 1.40e-02 5.10e+03 1.94e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" CB PRO C 225 " pdb=" CG PRO C 225 " ideal model delta sigma weight residual 1.492 1.642 -0.150 5.00e-02 4.00e+02 9.02e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.35e+00 ... (remaining 25509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 34446 3.84 - 7.68: 225 7.68 - 11.51: 33 11.51 - 15.35: 2 15.35 - 19.19: 2 Bond angle restraints: 34708 Sorted by residual: angle pdb=" CA PRO C 225 " pdb=" N PRO C 225 " pdb=" CD PRO C 225 " ideal model delta sigma weight residual 112.00 94.86 17.14 1.40e+00 5.10e-01 1.50e+02 angle pdb=" C GLY A1131 " pdb=" N ILE A1132 " pdb=" CA ILE A1132 " ideal model delta sigma weight residual 121.97 133.66 -11.69 1.80e+00 3.09e-01 4.22e+01 angle pdb=" N GLY A 103 " pdb=" CA GLY A 103 " pdb=" C GLY A 103 " ideal model delta sigma weight residual 111.01 121.08 -10.07 1.86e+00 2.89e-01 2.93e+01 angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 123.31 -10.97 2.04e+00 2.40e-01 2.89e+01 angle pdb=" C GLY A1099 " pdb=" N THR A1100 " pdb=" CA THR A1100 " ideal model delta sigma weight residual 121.54 131.65 -10.11 1.91e+00 2.74e-01 2.80e+01 ... (remaining 34703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.54: 14005 18.54 - 37.08: 1402 37.08 - 55.62: 232 55.62 - 74.15: 41 74.15 - 92.69: 25 Dihedral angle restraints: 15705 sinusoidal: 6591 harmonic: 9114 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -0.11 -85.89 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -159.69 73.69 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -12.51 -73.49 1 1.00e+01 1.00e-02 6.87e+01 ... (remaining 15702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 3954 0.141 - 0.282: 82 0.282 - 0.422: 6 0.422 - 0.563: 5 0.563 - 0.704: 2 Chirality restraints: 4049 Sorted by residual: chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.56e+00 ... (remaining 4046 not shown) Planarity restraints: 4472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 224 " 0.078 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO C 225 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO C 225 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 225 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 61 " -0.007 2.00e-02 2.50e+03 3.59e-02 1.61e+01 pdb=" CG ASN C 61 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN C 61 " -0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN C 61 " 0.039 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 433 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.31e+01 pdb=" C VAL C 433 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL C 433 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE C 434 " -0.021 2.00e-02 2.50e+03 ... (remaining 4469 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5776 2.79 - 3.32: 21305 3.32 - 3.85: 40708 3.85 - 4.37: 45329 4.37 - 4.90: 79684 Nonbonded interactions: 192802 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR C 393 " pdb=" O HIS C 519 " model vdw 2.279 3.040 nonbonded pdb=" O LEU A 966 " pdb=" OG SER A 975 " model vdw 2.288 3.040 nonbonded pdb=" OE1 GLU C 819 " pdb=" OG SER C1055 " model vdw 2.295 3.040 nonbonded pdb=" O SER B 758 " pdb=" OG SER B 758 " model vdw 2.297 3.040 ... (remaining 192797 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 24 through 1307) selection = chain 'B' selection = (chain 'C' and resid 24 through 1307) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.310 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 25591 Z= 0.219 Angle : 0.919 22.972 34899 Z= 0.461 Chirality : 0.061 0.704 4049 Planarity : 0.007 0.107 4441 Dihedral : 14.639 92.693 9717 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.37 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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 aren not related in a simple way. whole: -3.00 (0.13), residues: 3084 helix: -1.34 (0.16), residues: 631 sheet: -1.60 (0.28), residues: 348 loop : -2.43 (0.12), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 237 TYR 0.027 0.002 TYR C 170 PHE 0.037 0.002 PHE C 592 TRP 0.021 0.002 TRP B 886 HIS 0.028 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00452 (25514) covalent geometry : angle 0.88308 (34708) SS BOND : bond 0.00345 ( 40) SS BOND : angle 1.61559 ( 80) hydrogen bonds : bond 0.20601 ( 693) hydrogen bonds : angle 8.62555 ( 2004) link_BETA1-4 : bond 0.00655 ( 6) link_BETA1-4 : angle 2.40156 ( 18) link_NAG-ASN : bond 0.01090 ( 31) link_NAG-ASN : angle 4.73004 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7567 (m-90) cc_final: 0.6883 (m-90) REVERT: A 904 TYR cc_start: 0.7406 (m-10) cc_final: 0.6971 (m-10) REVERT: B 556 ASN cc_start: 0.7749 (p0) cc_final: 0.7417 (p0) REVERT: B 1138 TYR cc_start: 0.6128 (t80) cc_final: 0.5811 (t80) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1623 time to fit residues: 79.4549 Evaluate side-chains 203 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 66 HIS B 196 ASN B 339 HIS ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN C 405 ASN C 422 ASN C 448 ASN C 895 GLN C 913 GLN C 935 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.193222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.153942 restraints weight = 37461.567| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.65 r_work: 0.3775 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25591 Z= 0.129 Angle : 0.613 18.339 34899 Z= 0.306 Chirality : 0.047 0.485 4049 Planarity : 0.005 0.072 4441 Dihedral : 6.555 57.873 4122 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.62 % Favored : 92.28 % Rotamer: Outliers : 0.85 % Allowed : 8.17 % Favored : 90.99 % 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 aren not related in a simple way. whole: -2.41 (0.14), residues: 3084 helix: -0.07 (0.19), residues: 651 sheet: -1.57 (0.26), residues: 392 loop : -2.27 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.025 0.001 TYR B1067 PHE 0.021 0.001 PHE B 342 TRP 0.007 0.001 TRP C 436 HIS 0.012 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00286 (25514) covalent geometry : angle 0.58141 (34708) SS BOND : bond 0.00542 ( 40) SS BOND : angle 1.22576 ( 80) hydrogen bonds : bond 0.04605 ( 693) hydrogen bonds : angle 6.12621 ( 2004) link_BETA1-4 : bond 0.00359 ( 6) link_BETA1-4 : angle 1.46683 ( 18) link_NAG-ASN : bond 0.00688 ( 31) link_NAG-ASN : angle 3.61814 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7258 (mt) cc_final: 0.7014 (mt) REVERT: A 104 TRP cc_start: 0.7567 (m-90) cc_final: 0.7005 (m-90) REVERT: A 904 TYR cc_start: 0.7941 (m-10) cc_final: 0.7610 (m-10) REVERT: B 542 ASN cc_start: 0.7160 (OUTLIER) cc_final: 0.6888 (t0) REVERT: B 556 ASN cc_start: 0.7843 (p0) cc_final: 0.7479 (p0) REVERT: C 559 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.6843 (t80) REVERT: C 986 LYS cc_start: 0.7510 (mtpp) cc_final: 0.6993 (tptp) outliers start: 23 outliers final: 14 residues processed: 246 average time/residue: 0.1599 time to fit residues: 65.5271 Evaluate side-chains 219 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 23 optimal weight: 0.9980 chunk 244 optimal weight: 0.0370 chunk 54 optimal weight: 0.9980 chunk 291 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 chunk 126 optimal weight: 0.0370 chunk 153 optimal weight: 1.9990 chunk 299 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 305 optimal weight: 0.0040 chunk 182 optimal weight: 4.9990 overall best weight: 0.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS C 339 HIS C 422 ASN C 448 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.194058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.160276 restraints weight = 37382.365| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.95 r_work: 0.3739 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25591 Z= 0.102 Angle : 0.564 18.018 34899 Z= 0.281 Chirality : 0.045 0.499 4049 Planarity : 0.004 0.063 4441 Dihedral : 5.978 54.188 4122 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.68 % Favored : 92.22 % Rotamer: Outliers : 0.92 % Allowed : 10.96 % Favored : 88.12 % 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 aren not related in a simple way. whole: -2.12 (0.14), residues: 3084 helix: 0.50 (0.20), residues: 658 sheet: -1.46 (0.26), residues: 385 loop : -2.19 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 466 TYR 0.020 0.001 TYR B1067 PHE 0.023 0.001 PHE B 342 TRP 0.008 0.001 TRP B 64 HIS 0.009 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00221 (25514) covalent geometry : angle 0.53423 (34708) SS BOND : bond 0.00381 ( 40) SS BOND : angle 1.04695 ( 80) hydrogen bonds : bond 0.04228 ( 693) hydrogen bonds : angle 5.57277 ( 2004) link_BETA1-4 : bond 0.00395 ( 6) link_BETA1-4 : angle 1.42371 ( 18) link_NAG-ASN : bond 0.00722 ( 31) link_NAG-ASN : angle 3.41742 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7281 (mt) cc_final: 0.7005 (mt) REVERT: A 104 TRP cc_start: 0.7497 (m-90) cc_final: 0.7030 (m-90) REVERT: A 465 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: A 904 TYR cc_start: 0.7956 (m-10) cc_final: 0.7623 (m-10) REVERT: B 556 ASN cc_start: 0.7798 (p0) cc_final: 0.7410 (p0) REVERT: B 864 LEU cc_start: 0.7519 (tt) cc_final: 0.7064 (tp) REVERT: B 900 MET cc_start: 0.7479 (mtp) cc_final: 0.7251 (mtm) REVERT: C 559 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7042 (t80) REVERT: C 986 LYS cc_start: 0.7676 (mtpp) cc_final: 0.7068 (tptp) outliers start: 25 outliers final: 16 residues processed: 238 average time/residue: 0.1619 time to fit residues: 63.7862 Evaluate side-chains 219 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 172 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 33 optimal weight: 0.0060 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A 487 ASN A 777 ASN A1135 ASN B 66 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 914 ASN C1048 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.185730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146970 restraints weight = 37452.068| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.63 r_work: 0.3662 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 25591 Z= 0.245 Angle : 0.702 18.211 34899 Z= 0.352 Chirality : 0.050 0.494 4049 Planarity : 0.005 0.065 4441 Dihedral : 6.199 53.001 4122 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.60 % Favored : 90.27 % Rotamer: Outliers : 2.32 % Allowed : 12.55 % Favored : 85.14 % 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 aren not related in a simple way. whole: -2.46 (0.14), residues: 3084 helix: 0.03 (0.19), residues: 659 sheet: -2.04 (0.23), residues: 499 loop : -2.23 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 273 TYR 0.033 0.002 TYR B1067 PHE 0.030 0.002 PHE C1089 TRP 0.021 0.002 TRP A 64 HIS 0.010 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00579 (25514) covalent geometry : angle 0.67436 (34708) SS BOND : bond 0.00526 ( 40) SS BOND : angle 1.39411 ( 80) hydrogen bonds : bond 0.04892 ( 693) hydrogen bonds : angle 5.83356 ( 2004) link_BETA1-4 : bond 0.00324 ( 6) link_BETA1-4 : angle 1.59976 ( 18) link_NAG-ASN : bond 0.00747 ( 31) link_NAG-ASN : angle 3.64015 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 225 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7646 (mt) cc_final: 0.7345 (mt) REVERT: A 104 TRP cc_start: 0.7665 (m-90) cc_final: 0.7142 (m-90) REVERT: A 364 ASP cc_start: 0.7012 (m-30) cc_final: 0.6118 (m-30) REVERT: A 465 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: A 904 TYR cc_start: 0.7878 (m-10) cc_final: 0.7565 (m-10) REVERT: B 556 ASN cc_start: 0.7743 (p0) cc_final: 0.7355 (p0) REVERT: C 338 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.5053 (t80) REVERT: C 559 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7274 (t80) REVERT: C 986 LYS cc_start: 0.7788 (mtpp) cc_final: 0.7332 (tptp) REVERT: C 1089 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.5916 (p90) outliers start: 63 outliers final: 46 residues processed: 269 average time/residue: 0.1581 time to fit residues: 70.9410 Evaluate side-chains 245 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1139 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 55 optimal weight: 1.9990 chunk 309 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 291 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 199 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 207 HIS B1011 GLN C 207 HIS C 422 ASN C 448 ASN C 690 GLN C1088 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.187247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.147655 restraints weight = 37286.800| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.59 r_work: 0.3706 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 25591 Z= 0.140 Angle : 0.602 18.245 34899 Z= 0.300 Chirality : 0.046 0.483 4049 Planarity : 0.004 0.062 4441 Dihedral : 5.864 54.048 4122 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.91 % Favored : 91.99 % Rotamer: Outliers : 2.17 % Allowed : 14.35 % Favored : 83.48 % 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 aren not related in a simple way. whole: -2.29 (0.14), residues: 3084 helix: 0.38 (0.20), residues: 654 sheet: -1.91 (0.24), residues: 469 loop : -2.22 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 319 TYR 0.022 0.001 TYR B1067 PHE 0.024 0.001 PHE A1095 TRP 0.014 0.001 TRP A 64 HIS 0.008 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00323 (25514) covalent geometry : angle 0.57259 (34708) SS BOND : bond 0.00418 ( 40) SS BOND : angle 1.27812 ( 80) hydrogen bonds : bond 0.04288 ( 693) hydrogen bonds : angle 5.48958 ( 2004) link_BETA1-4 : bond 0.00297 ( 6) link_BETA1-4 : angle 1.50945 ( 18) link_NAG-ASN : bond 0.00691 ( 31) link_NAG-ASN : angle 3.46376 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7484 (mt) cc_final: 0.7235 (mt) REVERT: A 104 TRP cc_start: 0.7655 (m-90) cc_final: 0.7137 (m-90) REVERT: A 306 PHE cc_start: 0.8185 (m-80) cc_final: 0.7965 (m-80) REVERT: A 364 ASP cc_start: 0.7062 (m-30) cc_final: 0.6153 (m-30) REVERT: A 465 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: A 904 TYR cc_start: 0.7828 (m-10) cc_final: 0.7537 (m-10) REVERT: B 556 ASN cc_start: 0.7632 (p0) cc_final: 0.7211 (p0) REVERT: C 33 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7743 (t) REVERT: C 54 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6215 (pp) REVERT: C 338 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.5147 (t80) REVERT: C 559 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7053 (t80) REVERT: C 986 LYS cc_start: 0.7738 (mtpp) cc_final: 0.7272 (tptp) REVERT: C 1032 CYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7759 (m) REVERT: C 1089 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.5878 (p90) outliers start: 59 outliers final: 41 residues processed: 251 average time/residue: 0.1530 time to fit residues: 65.1735 Evaluate side-chains 239 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 302 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 128 optimal weight: 0.0170 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 255 optimal weight: 10.0000 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1135 ASN B 913 GLN C 81 ASN C 207 HIS C 422 ASN C 448 ASN C1023 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.185547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146537 restraints weight = 37450.219| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.75 r_work: 0.3663 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25591 Z= 0.172 Angle : 0.624 19.464 34899 Z= 0.311 Chirality : 0.047 0.478 4049 Planarity : 0.004 0.063 4441 Dihedral : 5.818 54.018 4122 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.34 % Favored : 90.56 % Rotamer: Outliers : 2.83 % Allowed : 14.79 % Favored : 82.38 % 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 aren not related in a simple way. whole: -2.30 (0.14), residues: 3084 helix: 0.43 (0.20), residues: 651 sheet: -2.05 (0.23), residues: 476 loop : -2.20 (0.13), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.025 0.002 TYR B1067 PHE 0.024 0.002 PHE C1089 TRP 0.015 0.001 TRP A 64 HIS 0.007 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00402 (25514) covalent geometry : angle 0.59455 (34708) SS BOND : bond 0.00481 ( 40) SS BOND : angle 1.23973 ( 80) hydrogen bonds : bond 0.04372 ( 693) hydrogen bonds : angle 5.47800 ( 2004) link_BETA1-4 : bond 0.00290 ( 6) link_BETA1-4 : angle 1.49496 ( 18) link_NAG-ASN : bond 0.00752 ( 31) link_NAG-ASN : angle 3.55706 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 198 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7529 (mt) cc_final: 0.7304 (mt) REVERT: A 104 TRP cc_start: 0.7673 (m-90) cc_final: 0.7167 (m-90) REVERT: A 306 PHE cc_start: 0.8174 (m-80) cc_final: 0.7959 (m-80) REVERT: A 364 ASP cc_start: 0.7085 (m-30) cc_final: 0.6161 (m-30) REVERT: A 465 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: A 552 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7911 (mt) REVERT: A 904 TYR cc_start: 0.7909 (m-10) cc_final: 0.7605 (m-10) REVERT: B 556 ASN cc_start: 0.7712 (p0) cc_final: 0.7303 (p0) REVERT: B 1106 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7054 (pt0) REVERT: C 33 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7821 (t) REVERT: C 54 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6269 (pp) REVERT: C 338 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.5123 (t80) REVERT: C 403 ARG cc_start: 0.6955 (ttp-170) cc_final: 0.6572 (ttp-170) REVERT: C 559 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7071 (t80) REVERT: C 986 LYS cc_start: 0.7805 (mtpp) cc_final: 0.7326 (tptp) REVERT: C 1032 CYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7833 (m) REVERT: C 1089 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.5991 (p90) outliers start: 77 outliers final: 58 residues processed: 259 average time/residue: 0.1585 time to fit residues: 68.4633 Evaluate side-chains 259 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 192 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 200 optimal weight: 0.7980 chunk 270 optimal weight: 0.8980 chunk 304 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 279 optimal weight: 3.9990 chunk 281 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 99 optimal weight: 0.0470 chunk 119 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN C 422 ASN C 448 ASN C 935 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.189918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.156975 restraints weight = 36534.316| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.65 r_work: 0.3709 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25591 Z= 0.125 Angle : 0.587 17.773 34899 Z= 0.291 Chirality : 0.046 0.504 4049 Planarity : 0.004 0.062 4441 Dihedral : 5.620 54.306 4122 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.04 % Favored : 91.89 % Rotamer: Outliers : 2.54 % Allowed : 15.53 % Favored : 81.94 % 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 aren not related in a simple way. whole: -2.15 (0.15), residues: 3084 helix: 0.64 (0.20), residues: 654 sheet: -1.91 (0.24), residues: 463 loop : -2.16 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.020 0.001 TYR B1067 PHE 0.027 0.001 PHE A 275 TRP 0.012 0.001 TRP A 64 HIS 0.006 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00285 (25514) covalent geometry : angle 0.55734 (34708) SS BOND : bond 0.00339 ( 40) SS BOND : angle 1.17640 ( 80) hydrogen bonds : bond 0.04120 ( 693) hydrogen bonds : angle 5.27434 ( 2004) link_BETA1-4 : bond 0.00331 ( 6) link_BETA1-4 : angle 1.44670 ( 18) link_NAG-ASN : bond 0.00717 ( 31) link_NAG-ASN : angle 3.40299 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 205 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7722 (m-90) cc_final: 0.7241 (m-90) REVERT: A 364 ASP cc_start: 0.7195 (m-30) cc_final: 0.6256 (m-30) REVERT: A 465 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: A 552 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8034 (mt) REVERT: A 904 TYR cc_start: 0.8130 (m-10) cc_final: 0.7835 (m-10) REVERT: A 978 ASN cc_start: 0.7478 (m-40) cc_final: 0.7217 (m-40) REVERT: B 556 ASN cc_start: 0.7693 (p0) cc_final: 0.7296 (p0) REVERT: B 558 LYS cc_start: 0.8933 (tppp) cc_final: 0.8718 (tppt) REVERT: B 1106 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7201 (pt0) REVERT: C 24 ARG cc_start: 0.4598 (tpt170) cc_final: 0.4193 (ttt90) REVERT: C 33 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7826 (t) REVERT: C 54 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6319 (pp) REVERT: C 338 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.5145 (t80) REVERT: C 403 ARG cc_start: 0.6939 (ttp-170) cc_final: 0.6575 (ttp-170) REVERT: C 559 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7156 (t80) REVERT: C 986 LYS cc_start: 0.7883 (mtpp) cc_final: 0.7336 (tptp) REVERT: C 1089 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6268 (p90) outliers start: 69 outliers final: 55 residues processed: 259 average time/residue: 0.1391 time to fit residues: 60.8299 Evaluate side-chains 259 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 196 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 288 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 304 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A1135 ASN B 30 ASN C 422 ASN C 448 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 960 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.185663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.152555 restraints weight = 36734.362| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.74 r_work: 0.3657 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25591 Z= 0.213 Angle : 0.669 19.511 34899 Z= 0.335 Chirality : 0.049 0.503 4049 Planarity : 0.004 0.062 4441 Dihedral : 5.860 53.600 4122 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.99 % Favored : 89.95 % Rotamer: Outliers : 2.83 % Allowed : 16.00 % Favored : 81.16 % 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 aren not related in a simple way. whole: -2.38 (0.14), residues: 3084 helix: 0.34 (0.20), residues: 649 sheet: -2.12 (0.23), residues: 479 loop : -2.23 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 273 TYR 0.027 0.002 TYR B1067 PHE 0.032 0.002 PHE A 275 TRP 0.019 0.002 TRP A 64 HIS 0.008 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00501 (25514) covalent geometry : angle 0.63984 (34708) SS BOND : bond 0.00495 ( 40) SS BOND : angle 1.53824 ( 80) hydrogen bonds : bond 0.04559 ( 693) hydrogen bonds : angle 5.54479 ( 2004) link_BETA1-4 : bond 0.00259 ( 6) link_BETA1-4 : angle 1.54410 ( 18) link_NAG-ASN : bond 0.00737 ( 31) link_NAG-ASN : angle 3.59364 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 203 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7709 (m-90) cc_final: 0.7144 (m-90) REVERT: A 364 ASP cc_start: 0.7188 (m-30) cc_final: 0.6290 (m-30) REVERT: A 465 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: A 552 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8007 (mt) REVERT: A 904 TYR cc_start: 0.7921 (m-10) cc_final: 0.7641 (m-10) REVERT: B 556 ASN cc_start: 0.7640 (p0) cc_final: 0.7239 (p0) REVERT: B 1106 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6927 (pt0) REVERT: C 24 ARG cc_start: 0.4622 (tpt170) cc_final: 0.4220 (ttt90) REVERT: C 33 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7890 (t) REVERT: C 54 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6367 (pp) REVERT: C 319 ARG cc_start: 0.7737 (ptp-170) cc_final: 0.7426 (mmm-85) REVERT: C 338 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.5133 (t80) REVERT: C 403 ARG cc_start: 0.7004 (ttp-170) cc_final: 0.6626 (ttp-170) REVERT: C 559 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7097 (t80) REVERT: C 986 LYS cc_start: 0.7794 (mtpp) cc_final: 0.7387 (tptp) REVERT: C 1089 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6166 (p90) outliers start: 77 outliers final: 58 residues processed: 265 average time/residue: 0.1291 time to fit residues: 56.9342 Evaluate side-chains 260 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 194 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 108 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 230 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 308 optimal weight: 0.5980 chunk 212 optimal weight: 20.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A1135 ASN C 422 ASN C 448 ASN C 505 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.187804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.155171 restraints weight = 36731.780| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.76 r_work: 0.3687 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25591 Z= 0.150 Angle : 0.622 18.276 34899 Z= 0.309 Chirality : 0.047 0.500 4049 Planarity : 0.004 0.063 4441 Dihedral : 5.728 54.032 4122 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.46 % Favored : 91.47 % Rotamer: Outliers : 2.65 % Allowed : 16.41 % Favored : 80.94 % 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 aren not related in a simple way. whole: -2.28 (0.15), residues: 3084 helix: 0.51 (0.20), residues: 649 sheet: -2.05 (0.24), residues: 459 loop : -2.20 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 44 TYR 0.022 0.001 TYR B1067 PHE 0.029 0.001 PHE A 275 TRP 0.014 0.001 TRP A 64 HIS 0.006 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00347 (25514) covalent geometry : angle 0.59178 (34708) SS BOND : bond 0.00390 ( 40) SS BOND : angle 1.50737 ( 80) hydrogen bonds : bond 0.04249 ( 693) hydrogen bonds : angle 5.39114 ( 2004) link_BETA1-4 : bond 0.00315 ( 6) link_BETA1-4 : angle 1.48725 ( 18) link_NAG-ASN : bond 0.00694 ( 31) link_NAG-ASN : angle 3.46022 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 202 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7628 (m-90) cc_final: 0.7134 (m-90) REVERT: A 278 LYS cc_start: 0.7754 (tppt) cc_final: 0.7259 (tppt) REVERT: A 364 ASP cc_start: 0.7202 (m-30) cc_final: 0.6314 (m-30) REVERT: A 465 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: A 904 TYR cc_start: 0.7934 (m-10) cc_final: 0.7674 (m-10) REVERT: B 556 ASN cc_start: 0.7614 (p0) cc_final: 0.7217 (p0) REVERT: B 740 MET cc_start: 0.7957 (tpt) cc_final: 0.7649 (tpt) REVERT: B 1106 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6991 (pt0) REVERT: C 24 ARG cc_start: 0.4625 (tpt170) cc_final: 0.4293 (ttt90) REVERT: C 33 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7880 (t) REVERT: C 54 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6334 (pp) REVERT: C 338 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.5212 (t80) REVERT: C 403 ARG cc_start: 0.6985 (ttp-170) cc_final: 0.6653 (ttp-170) REVERT: C 559 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7136 (t80) REVERT: C 986 LYS cc_start: 0.7773 (mtpp) cc_final: 0.7350 (tptp) REVERT: C 1089 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6147 (p90) outliers start: 72 outliers final: 56 residues processed: 258 average time/residue: 0.1335 time to fit residues: 58.1657 Evaluate side-chains 257 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 194 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 279 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1135 ASN C 207 HIS C 422 ASN C 448 ASN C 505 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.187320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.154464 restraints weight = 36824.647| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.72 r_work: 0.3682 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25591 Z= 0.167 Angle : 0.635 18.298 34899 Z= 0.316 Chirality : 0.047 0.502 4049 Planarity : 0.004 0.063 4441 Dihedral : 5.733 54.053 4122 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.37 % Favored : 90.56 % Rotamer: Outliers : 2.61 % Allowed : 16.63 % Favored : 80.76 % 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 aren not related in a simple way. whole: -2.30 (0.15), residues: 3084 helix: 0.50 (0.20), residues: 648 sheet: -2.07 (0.23), residues: 494 loop : -2.21 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 44 TYR 0.023 0.001 TYR B1067 PHE 0.029 0.002 PHE A 275 TRP 0.015 0.001 TRP A 64 HIS 0.006 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00393 (25514) covalent geometry : angle 0.60559 (34708) SS BOND : bond 0.00409 ( 40) SS BOND : angle 1.45257 ( 80) hydrogen bonds : bond 0.04298 ( 693) hydrogen bonds : angle 5.41065 ( 2004) link_BETA1-4 : bond 0.00297 ( 6) link_BETA1-4 : angle 1.49094 ( 18) link_NAG-ASN : bond 0.00693 ( 31) link_NAG-ASN : angle 3.45944 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 198 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7666 (m-90) cc_final: 0.7097 (m-90) REVERT: A 364 ASP cc_start: 0.7296 (m-30) cc_final: 0.6421 (m-30) REVERT: A 465 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: A 904 TYR cc_start: 0.7928 (m-10) cc_final: 0.7667 (m-10) REVERT: B 556 ASN cc_start: 0.7539 (p0) cc_final: 0.7150 (p0) REVERT: B 1106 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6932 (pt0) REVERT: C 33 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7899 (t) REVERT: C 54 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6344 (pp) REVERT: C 319 ARG cc_start: 0.7716 (ptp-170) cc_final: 0.7313 (mmm-85) REVERT: C 338 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.5202 (t80) REVERT: C 403 ARG cc_start: 0.6992 (ttp-170) cc_final: 0.6621 (ttp-170) REVERT: C 559 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7140 (t80) REVERT: C 986 LYS cc_start: 0.7816 (mtpp) cc_final: 0.7392 (tptp) REVERT: C 1089 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6170 (p90) outliers start: 71 outliers final: 60 residues processed: 253 average time/residue: 0.1269 time to fit residues: 54.1032 Evaluate side-chains 261 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 194 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 53 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 248 optimal weight: 0.0670 chunk 9 optimal weight: 9.9990 chunk 233 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1135 ASN C 422 ASN C 448 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.190036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.157624 restraints weight = 36584.368| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.63 r_work: 0.3727 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25591 Z= 0.117 Angle : 0.595 18.311 34899 Z= 0.295 Chirality : 0.046 0.518 4049 Planarity : 0.004 0.063 4441 Dihedral : 5.515 54.585 4122 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.98 % Favored : 91.96 % Rotamer: Outliers : 2.28 % Allowed : 17.03 % Favored : 80.68 % 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 aren not related in a simple way. whole: -2.10 (0.15), residues: 3084 helix: 0.75 (0.20), residues: 655 sheet: -2.00 (0.24), residues: 470 loop : -2.11 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 44 TYR 0.023 0.001 TYR B 351 PHE 0.024 0.001 PHE A 275 TRP 0.010 0.001 TRP A 64 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00264 (25514) covalent geometry : angle 0.56680 (34708) SS BOND : bond 0.00312 ( 40) SS BOND : angle 1.21952 ( 80) hydrogen bonds : bond 0.04023 ( 693) hydrogen bonds : angle 5.17362 ( 2004) link_BETA1-4 : bond 0.00350 ( 6) link_BETA1-4 : angle 1.40925 ( 18) link_NAG-ASN : bond 0.00715 ( 31) link_NAG-ASN : angle 3.34715 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5548.72 seconds wall clock time: 96 minutes 15.20 seconds (5775.20 seconds total)