Starting phenix.real_space_refine on Sat Jun 21 15:44:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0s_42868/06_2025/8v0s_42868.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0s_42868/06_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_42868/06_2025/8v0s_42868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0s_42868/06_2025/8v0s_42868.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0s_42868/06_2025/8v0s_42868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0s_42868/06_2025/8v0s_42868.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.75, per 1000 atoms: 0.59 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: 5.80 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 3.69 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: 11.85 Time building geometry restraints manager: 7.05 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 1148 or resid 1301 through 1307)) selection = chain 'B' selection = (chain 'C' and (resid 24 through 1148 or resid 1301 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 58.630 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.100 ------------------------------------------------------------------------------- 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 : 4.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.002 TRP B 886 HIS 0.028 0.001 HIS A 954 PHE 0.037 0.002 PHE C 592 TYR 0.027 0.002 TYR C 170 ARG 0.016 0.001 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.01090 ( 31) link_NAG-ASN : angle 4.73004 ( 93) link_BETA1-4 : bond 0.00655 ( 6) link_BETA1-4 : angle 2.40156 ( 18) hydrogen bonds : bond 0.20601 ( 693) hydrogen bonds : angle 8.62555 ( 2004) SS BOND : bond 0.00345 ( 40) SS BOND : angle 1.61559 ( 80) covalent geometry : bond 0.00452 (25514) covalent geometry : angle 0.88308 (34708) *********************** 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 : 2.613 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: 0.7418 (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: 0.3234 time to fit residues: 157.6198 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 : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 10.0000 chunk 236 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 207 HIS ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN C 422 ASN C 448 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 935 GLN C 960 ASN C1048 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.188965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.149103 restraints weight = 37430.188| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.67 r_work: 0.3708 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25591 Z= 0.193 Angle : 0.669 18.468 34899 Z= 0.336 Chirality : 0.049 0.490 4049 Planarity : 0.005 0.072 4441 Dihedral : 6.681 55.667 4122 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.37 % Favored : 91.54 % Rotamer: Outliers : 1.29 % Allowed : 8.79 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.14), residues: 3084 helix: -0.34 (0.18), residues: 655 sheet: -1.94 (0.24), residues: 425 loop : -2.30 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 64 HIS 0.013 0.001 HIS A 954 PHE 0.022 0.002 PHE A 906 TYR 0.030 0.002 TYR B1067 ARG 0.005 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00704 ( 31) link_NAG-ASN : angle 3.70813 ( 93) link_BETA1-4 : bond 0.00385 ( 6) link_BETA1-4 : angle 1.52990 ( 18) hydrogen bonds : bond 0.04933 ( 693) hydrogen bonds : angle 6.21405 ( 2004) SS BOND : bond 0.00875 ( 40) SS BOND : angle 1.38733 ( 80) covalent geometry : bond 0.00444 (25514) covalent geometry : angle 0.63834 (34708) *********************** 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 273 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 2.757 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7435 (mt) cc_final: 0.7176 (mt) REVERT: A 104 TRP cc_start: 0.7706 (m-90) cc_final: 0.7150 (m-90) REVERT: A 465 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: A 904 TYR cc_start: 0.7848 (m-10) cc_final: 0.7577 (m-10) REVERT: B 86 PHE cc_start: 0.3312 (t80) cc_final: 0.2236 (t80) REVERT: B 556 ASN cc_start: 0.7739 (p0) cc_final: 0.7367 (p0) REVERT: C 559 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.6870 (t80) REVERT: C 985 ASP cc_start: 0.7003 (t0) cc_final: 0.6789 (t0) REVERT: C 986 LYS cc_start: 0.7648 (mtpp) cc_final: 0.7114 (tptp) outliers start: 35 outliers final: 25 residues processed: 260 average time/residue: 0.3167 time to fit residues: 136.6043 Evaluate side-chains 230 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 465 GLU 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 656 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 541 PHE 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 833 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 117 LEU 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 666 ILE 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 217 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 245 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 228 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 C 207 HIS C 339 HIS C 422 ASN C 448 ASN C 519 HIS C 690 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.187598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147854 restraints weight = 37276.331| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.60 r_work: 0.3704 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25591 Z= 0.169 Angle : 0.633 18.682 34899 Z= 0.316 Chirality : 0.048 0.482 4049 Planarity : 0.005 0.064 4441 Dihedral : 6.261 53.399 4122 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.79 % Favored : 91.12 % Rotamer: Outliers : 1.73 % Allowed : 12.18 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.14), residues: 3084 helix: 0.04 (0.19), residues: 661 sheet: -2.09 (0.23), residues: 453 loop : -2.24 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.015 0.001 HIS B 66 PHE 0.022 0.002 PHE C1089 TYR 0.029 0.002 TYR B 91 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00714 ( 31) link_NAG-ASN : angle 3.61144 ( 93) link_BETA1-4 : bond 0.00300 ( 6) link_BETA1-4 : angle 1.54349 ( 18) hydrogen bonds : bond 0.04669 ( 693) hydrogen bonds : angle 5.85405 ( 2004) SS BOND : bond 0.00431 ( 40) SS BOND : angle 1.27110 ( 80) covalent geometry : bond 0.00389 (25514) covalent geometry : angle 0.60223 (34708) *********************** 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 271 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7522 (mt) cc_final: 0.7155 (mt) REVERT: A 104 TRP cc_start: 0.7721 (m-90) cc_final: 0.7201 (m-90) REVERT: A 394 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7692 (m-40) REVERT: A 465 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: A 904 TYR cc_start: 0.7830 (m-10) cc_final: 0.7503 (m-10) REVERT: B 26 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8766 (mm110) REVERT: B 290 ASP cc_start: 0.7177 (t0) cc_final: 0.6781 (t70) REVERT: C 559 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.7028 (t80) REVERT: C 986 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7178 (tptp) REVERT: C 1089 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.5753 (p90) outliers start: 47 outliers final: 33 residues processed: 252 average time/residue: 0.3183 time to fit residues: 133.0419 Evaluate side-chains 237 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 394 ASN 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 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 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 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 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 941 THR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 51 THR 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 559 PHE Chi-restraints excluded: chain C residue 666 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 247 optimal weight: 0.0010 chunk 209 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 297 optimal weight: 0.8980 chunk 185 optimal weight: 0.6980 chunk 237 optimal weight: 0.5980 chunk 267 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 207 HIS C 81 ASN C 422 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.187653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.147662 restraints weight = 37550.384| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.64 r_work: 0.3695 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25591 Z= 0.146 Angle : 0.607 18.406 34899 Z= 0.303 Chirality : 0.047 0.487 4049 Planarity : 0.004 0.063 4441 Dihedral : 5.998 53.959 4122 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.43 % Favored : 91.47 % Rotamer: Outliers : 2.13 % Allowed : 13.32 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.14), residues: 3084 helix: 0.38 (0.20), residues: 645 sheet: -2.06 (0.23), residues: 460 loop : -2.19 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.008 0.001 HIS A 954 PHE 0.029 0.001 PHE A 275 TYR 0.029 0.001 TYR B 91 ARG 0.005 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00719 ( 31) link_NAG-ASN : angle 3.52826 ( 93) link_BETA1-4 : bond 0.00324 ( 6) link_BETA1-4 : angle 1.48598 ( 18) hydrogen bonds : bond 0.04378 ( 693) hydrogen bonds : angle 5.60937 ( 2004) SS BOND : bond 0.00416 ( 40) SS BOND : angle 1.24595 ( 80) covalent geometry : bond 0.00335 (25514) covalent geometry : angle 0.57691 (34708) *********************** 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 275 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7712 (m-90) cc_final: 0.7234 (m-90) REVERT: A 465 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: A 904 TYR cc_start: 0.7844 (m-10) cc_final: 0.7574 (m-10) REVERT: B 902 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7501 (mmm) REVERT: B 1106 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7152 (pt0) REVERT: C 559 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7061 (t80) REVERT: C 986 LYS cc_start: 0.7736 (mtpp) cc_final: 0.7259 (tptp) REVERT: C 1089 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.5810 (p90) outliers start: 58 outliers final: 46 residues processed: 259 average time/residue: 0.3161 time to fit residues: 136.1083 Evaluate side-chains 252 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 2.549 ------------------------------------------------------------------------------- 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 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 705 VAL 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 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 902 MET Chi-restraints excluded: chain B residue 1106 GLN 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 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 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 105 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 133 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 218 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A1135 ASN B 207 HIS B 405 ASN B 913 GLN C 422 ASN C 448 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.186224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.151172 restraints weight = 37555.512| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.82 r_work: 0.3649 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25591 Z= 0.164 Angle : 0.619 18.398 34899 Z= 0.308 Chirality : 0.047 0.480 4049 Planarity : 0.004 0.063 4441 Dihedral : 5.883 53.989 4122 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.75 % Favored : 91.15 % Rotamer: Outliers : 2.83 % Allowed : 14.42 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.14), residues: 3084 helix: 0.33 (0.20), residues: 649 sheet: -2.06 (0.23), residues: 474 loop : -2.20 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.008 0.001 HIS A 954 PHE 0.031 0.002 PHE A 275 TYR 0.028 0.001 TYR B 91 ARG 0.004 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 31) link_NAG-ASN : angle 3.49354 ( 93) link_BETA1-4 : bond 0.00326 ( 6) link_BETA1-4 : angle 1.47612 ( 18) hydrogen bonds : bond 0.04380 ( 693) hydrogen bonds : angle 5.56250 ( 2004) SS BOND : bond 0.00556 ( 40) SS BOND : angle 1.22595 ( 80) covalent geometry : bond 0.00383 (25514) covalent geometry : angle 0.59015 (34708) *********************** 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 287 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 210 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7636 (m-90) cc_final: 0.7113 (m-90) REVERT: A 306 PHE cc_start: 0.8194 (m-80) cc_final: 0.7953 (m-80) REVERT: A 465 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: A 904 TYR cc_start: 0.7885 (m-10) cc_final: 0.7612 (m-10) REVERT: C 33 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7677 (t) REVERT: C 338 PHE cc_start: 0.7055 (OUTLIER) cc_final: 0.4969 (t80) REVERT: C 403 ARG cc_start: 0.6838 (ttp-170) cc_final: 0.6346 (ttp-170) REVERT: C 559 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7023 (t80) REVERT: C 986 LYS cc_start: 0.7777 (mtpp) cc_final: 0.7238 (tptp) REVERT: C 1032 CYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7866 (m) REVERT: C 1089 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.5907 (p90) outliers start: 77 outliers final: 54 residues processed: 268 average time/residue: 0.3315 time to fit residues: 147.1263 Evaluate side-chains 257 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 197 time to evaluate : 2.522 ------------------------------------------------------------------------------- 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 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL 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 1104 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 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 941 THR Chi-restraints excluded: chain B residue 1032 CYS 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 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 497 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 95 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 265 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 220 optimal weight: 9.9990 chunk 302 optimal weight: 0.2980 chunk 195 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 226 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 C 422 ASN C 448 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.188077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.153125 restraints weight = 37323.828| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.75 r_work: 0.3680 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25591 Z= 0.116 Angle : 0.578 18.082 34899 Z= 0.288 Chirality : 0.046 0.486 4049 Planarity : 0.004 0.063 4441 Dihedral : 5.628 54.286 4122 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.81 % Favored : 92.09 % Rotamer: Outliers : 2.47 % Allowed : 15.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.15), residues: 3084 helix: 0.64 (0.20), residues: 650 sheet: -1.94 (0.24), residues: 457 loop : -2.17 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.006 0.001 HIS A 954 PHE 0.025 0.001 PHE A 275 TYR 0.023 0.001 TYR B 91 ARG 0.004 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 31) link_NAG-ASN : angle 3.38189 ( 93) link_BETA1-4 : bond 0.00332 ( 6) link_BETA1-4 : angle 1.42559 ( 18) hydrogen bonds : bond 0.04118 ( 693) hydrogen bonds : angle 5.30838 ( 2004) SS BOND : bond 0.00328 ( 40) SS BOND : angle 1.12935 ( 80) covalent geometry : bond 0.00261 (25514) covalent geometry : angle 0.54899 (34708) *********************** 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 286 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 219 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7646 (m-90) cc_final: 0.7091 (m-90) REVERT: A 306 PHE cc_start: 0.8164 (m-80) cc_final: 0.7942 (m-80) REVERT: A 332 ILE cc_start: 0.7878 (mp) cc_final: 0.7370 (mt) REVERT: A 465 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: A 552 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7807 (mt) REVERT: A 904 TYR cc_start: 0.7841 (m-10) cc_final: 0.7570 (m-10) REVERT: A 978 ASN cc_start: 0.7341 (m-40) cc_final: 0.7128 (m-40) REVERT: B 558 LYS cc_start: 0.8733 (tppp) cc_final: 0.8519 (tppt) REVERT: B 900 MET cc_start: 0.7617 (mtp) cc_final: 0.7250 (mtm) REVERT: B 1106 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7164 (pt0) REVERT: C 33 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7689 (t) REVERT: C 403 ARG cc_start: 0.6775 (ttp-170) cc_final: 0.6270 (ttp-170) REVERT: C 559 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7014 (t80) REVERT: C 986 LYS cc_start: 0.7716 (mtpp) cc_final: 0.7216 (tptp) REVERT: C 1089 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.5985 (p90) outliers start: 67 outliers final: 45 residues processed: 273 average time/residue: 0.3306 time to fit residues: 149.6637 Evaluate side-chains 248 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL 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 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 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 90 VAL Chi-restraints excluded: chain B residue 302 THR 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 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 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 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 497 PHE 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 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 53 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 295 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 291 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1135 ASN B 30 ASN B 207 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 = 0.4240 r_free = 0.4240 target = 0.187082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.153960 restraints weight = 36844.799| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.64 r_work: 0.3680 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2330 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= 0.182 Angle : 0.636 18.188 34899 Z= 0.317 Chirality : 0.048 0.557 4049 Planarity : 0.004 0.062 4441 Dihedral : 5.735 53.829 4122 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.40 % Favored : 90.53 % Rotamer: Outliers : 2.76 % Allowed : 16.34 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.15), residues: 3084 helix: 0.42 (0.20), residues: 656 sheet: -1.99 (0.24), residues: 462 loop : -2.19 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.007 0.001 HIS A 954 PHE 0.027 0.002 PHE A 275 TYR 0.025 0.002 TYR B 91 ARG 0.005 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00790 ( 31) link_NAG-ASN : angle 3.50992 ( 93) link_BETA1-4 : bond 0.00280 ( 6) link_BETA1-4 : angle 1.48156 ( 18) hydrogen bonds : bond 0.04404 ( 693) hydrogen bonds : angle 5.44518 ( 2004) SS BOND : bond 0.00411 ( 40) SS BOND : angle 1.40326 ( 80) covalent geometry : bond 0.00425 (25514) covalent geometry : angle 0.60695 (34708) *********************** 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 284 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 209 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7761 (m-90) cc_final: 0.7207 (m-90) REVERT: A 306 PHE cc_start: 0.8193 (m-80) cc_final: 0.7973 (m-80) REVERT: A 465 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: A 552 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8045 (mt) REVERT: A 904 TYR cc_start: 0.8157 (m-10) cc_final: 0.7907 (m-10) REVERT: B 740 MET cc_start: 0.8027 (tpt) cc_final: 0.7726 (tpt) REVERT: B 1106 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7238 (pt0) REVERT: C 33 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7684 (t) REVERT: C 319 ARG cc_start: 0.7900 (ptp-170) cc_final: 0.7398 (mmm-85) REVERT: C 338 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.4978 (t80) REVERT: C 403 ARG cc_start: 0.7034 (ttp-170) cc_final: 0.6607 (ttp-170) REVERT: C 559 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7096 (t80) REVERT: C 986 LYS cc_start: 0.7894 (mtpp) cc_final: 0.7364 (tptp) REVERT: C 1032 CYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8019 (m) REVERT: C 1089 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.6375 (p90) outliers start: 75 outliers final: 60 residues processed: 267 average time/residue: 0.3363 time to fit residues: 148.6079 Evaluate side-chains 266 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 198 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 399 SER 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 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 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS 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 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 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 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 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 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 279 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 103 optimal weight: 0.0020 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1135 ASN B 207 HIS C 422 ASN C 448 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.189304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.156940 restraints weight = 36571.861| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.83 r_work: 0.3699 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25591 Z= 0.131 Angle : 0.603 17.963 34899 Z= 0.300 Chirality : 0.046 0.483 4049 Planarity : 0.004 0.063 4441 Dihedral : 5.602 54.188 4122 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.07 % Favored : 91.86 % Rotamer: Outliers : 2.50 % Allowed : 16.85 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.15), residues: 3084 helix: 0.59 (0.20), residues: 657 sheet: -1.99 (0.25), residues: 436 loop : -2.14 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.005 0.001 HIS A 954 PHE 0.023 0.001 PHE A 275 TYR 0.022 0.001 TYR B 91 ARG 0.008 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00727 ( 31) link_NAG-ASN : angle 3.39878 ( 93) link_BETA1-4 : bond 0.00349 ( 6) link_BETA1-4 : angle 1.45268 ( 18) hydrogen bonds : bond 0.04156 ( 693) hydrogen bonds : angle 5.27401 ( 2004) SS BOND : bond 0.00413 ( 40) SS BOND : angle 1.35797 ( 80) covalent geometry : bond 0.00301 (25514) covalent geometry : angle 0.57435 (34708) *********************** 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 271 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 203 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7645 (m-90) cc_final: 0.7070 (m-90) REVERT: A 278 LYS cc_start: 0.7782 (tppt) cc_final: 0.7289 (tppt) REVERT: A 306 PHE cc_start: 0.8021 (m-80) cc_final: 0.7799 (m-80) REVERT: A 332 ILE cc_start: 0.7784 (mp) cc_final: 0.7330 (mt) REVERT: A 465 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: A 552 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7949 (mt) REVERT: A 904 TYR cc_start: 0.7884 (m-10) cc_final: 0.7570 (m-10) REVERT: A 978 ASN cc_start: 0.7323 (m-40) cc_final: 0.7084 (m-40) REVERT: B 900 MET cc_start: 0.7690 (mtp) cc_final: 0.7370 (mtm) REVERT: B 1106 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7054 (pt0) REVERT: C 33 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7849 (t) REVERT: C 338 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.5188 (t80) REVERT: C 403 ARG cc_start: 0.6958 (ttp-170) cc_final: 0.6517 (ttp-170) REVERT: C 559 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7111 (t80) REVERT: C 986 LYS cc_start: 0.7761 (mtpp) cc_final: 0.7344 (tptp) REVERT: C 1089 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6081 (p90) outliers start: 68 outliers final: 51 residues processed: 258 average time/residue: 0.3110 time to fit residues: 134.3582 Evaluate side-chains 251 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 193 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 399 SER 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 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 1094 VAL Chi-restraints excluded: chain A residue 1104 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 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 302 THR 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 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 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 418 ILE Chi-restraints excluded: chain C residue 497 PHE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 205 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 chunk 93 optimal weight: 0.0470 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A1135 ASN B 207 HIS C 448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.187489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.154769 restraints weight = 36902.402| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.77 r_work: 0.3671 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25591 Z= 0.167 Angle : 0.628 18.296 34899 Z= 0.313 Chirality : 0.047 0.541 4049 Planarity : 0.004 0.063 4441 Dihedral : 5.656 54.003 4122 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.40 % Favored : 90.56 % Rotamer: Outliers : 2.65 % Allowed : 17.07 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.15), residues: 3084 helix: 0.49 (0.20), residues: 658 sheet: -1.97 (0.24), residues: 473 loop : -2.19 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.006 0.001 HIS A 954 PHE 0.023 0.002 PHE C1089 TYR 0.023 0.002 TYR B1067 ARG 0.007 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00766 ( 31) link_NAG-ASN : angle 3.46493 ( 93) link_BETA1-4 : bond 0.00325 ( 6) link_BETA1-4 : angle 1.47155 ( 18) hydrogen bonds : bond 0.04290 ( 693) hydrogen bonds : angle 5.36220 ( 2004) SS BOND : bond 0.00425 ( 40) SS BOND : angle 1.40097 ( 80) covalent geometry : bond 0.00390 (25514) covalent geometry : angle 0.59878 (34708) *********************** 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 272 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 200 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7646 (m-90) cc_final: 0.6987 (m-90) REVERT: A 306 PHE cc_start: 0.8025 (m-80) cc_final: 0.7815 (m-80) REVERT: A 332 ILE cc_start: 0.7774 (mp) cc_final: 0.7300 (mt) REVERT: A 465 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: A 552 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8006 (mt) REVERT: A 904 TYR cc_start: 0.7924 (m-10) cc_final: 0.7662 (m-10) REVERT: B 900 MET cc_start: 0.7725 (mtp) cc_final: 0.7407 (mtm) REVERT: B 1106 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.7050 (pt0) REVERT: C 33 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7889 (t) REVERT: C 338 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.5112 (t80) REVERT: C 403 ARG cc_start: 0.7025 (ttp-170) cc_final: 0.6586 (ttp-170) REVERT: C 559 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7085 (t80) REVERT: C 986 LYS cc_start: 0.7803 (mtpp) cc_final: 0.7442 (tptp) REVERT: C 1032 CYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7657 (m) REVERT: C 1089 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6238 (p90) outliers start: 72 outliers final: 58 residues processed: 257 average time/residue: 0.3099 time to fit residues: 133.0874 Evaluate side-chains 259 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 193 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE 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 399 SER 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 534 VAL 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 950 ASP Chi-restraints excluded: chain A residue 977 LEU 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 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS 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 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 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 418 ILE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 517 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 210 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 229 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 135 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 224 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1011 GLN A1135 ASN B 30 ASN B 207 HIS C 448 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.189594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.157137 restraints weight = 36672.572| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.78 r_work: 0.3704 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25591 Z= 0.127 Angle : 0.596 17.869 34899 Z= 0.297 Chirality : 0.046 0.510 4049 Planarity : 0.004 0.063 4441 Dihedral : 5.519 54.188 4122 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.07 % Favored : 91.89 % Rotamer: Outliers : 2.61 % Allowed : 17.11 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.15), residues: 3084 helix: 0.67 (0.20), residues: 660 sheet: -1.97 (0.24), residues: 466 loop : -2.11 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.005 0.001 HIS A 954 PHE 0.021 0.001 PHE B 342 TYR 0.021 0.001 TYR B 351 ARG 0.007 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00732 ( 31) link_NAG-ASN : angle 3.34628 ( 93) link_BETA1-4 : bond 0.00358 ( 6) link_BETA1-4 : angle 1.44538 ( 18) hydrogen bonds : bond 0.04087 ( 693) hydrogen bonds : angle 5.18258 ( 2004) SS BOND : bond 0.00346 ( 40) SS BOND : angle 1.23508 ( 80) covalent geometry : bond 0.00292 (25514) covalent geometry : angle 0.56845 (34708) ********************** 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 277 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 206 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7572 (m-90) cc_final: 0.6880 (m-90) REVERT: A 278 LYS cc_start: 0.7737 (tppt) cc_final: 0.7267 (tppt) REVERT: A 306 PHE cc_start: 0.7994 (m-80) cc_final: 0.7780 (m-80) REVERT: A 332 ILE cc_start: 0.7725 (mp) cc_final: 0.7275 (mt) REVERT: A 465 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: A 552 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8004 (mt) REVERT: A 904 TYR cc_start: 0.7870 (m-10) cc_final: 0.7560 (m-10) REVERT: A 978 ASN cc_start: 0.7291 (m-40) cc_final: 0.7057 (m-40) REVERT: B 900 MET cc_start: 0.7648 (mtp) cc_final: 0.7325 (mtm) REVERT: B 1106 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.7044 (pt0) REVERT: C 117 LEU cc_start: 0.3444 (OUTLIER) cc_final: 0.2933 (pt) REVERT: C 338 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.5162 (t80) REVERT: C 403 ARG cc_start: 0.7022 (ttp-170) cc_final: 0.6599 (ttp-170) REVERT: C 559 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7088 (t80) REVERT: C 986 LYS cc_start: 0.7779 (mtpp) cc_final: 0.7368 (tptp) REVERT: C 1089 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6194 (p90) outliers start: 71 outliers final: 56 residues processed: 264 average time/residue: 0.3126 time to fit residues: 139.0881 Evaluate side-chains 264 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 201 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 399 SER 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 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN 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 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER 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 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 42 VAL Chi-restraints excluded: chain C residue 51 THR 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 418 ILE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 517 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 249 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 270 optimal weight: 0.7980 chunk 148 optimal weight: 0.0970 chunk 101 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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** A1119 ASN A1135 ASN B 207 HIS C 422 ASN C 448 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.190589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.158342 restraints weight = 36618.103| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.80 r_work: 0.3757 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2477 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= 0.113 Angle : 0.586 17.689 34899 Z= 0.291 Chirality : 0.046 0.543 4049 Planarity : 0.004 0.063 4441 Dihedral : 5.432 54.342 4122 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.37 % Favored : 91.60 % Rotamer: Outliers : 2.50 % Allowed : 17.48 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.15), residues: 3084 helix: 0.77 (0.20), residues: 669 sheet: -1.86 (0.24), residues: 469 loop : -2.09 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.004 0.001 HIS A 954 PHE 0.022 0.001 PHE B 342 TYR 0.022 0.001 TYR B 351 ARG 0.007 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00849 ( 31) link_NAG-ASN : angle 3.40772 ( 93) link_BETA1-4 : bond 0.00375 ( 6) link_BETA1-4 : angle 1.39856 ( 18) hydrogen bonds : bond 0.03974 ( 693) hydrogen bonds : angle 5.07168 ( 2004) SS BOND : bond 0.00299 ( 40) SS BOND : angle 1.16179 ( 80) covalent geometry : bond 0.00255 (25514) covalent geometry : angle 0.55732 (34708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11747.54 seconds wall clock time: 202 minutes 15.70 seconds (12135.70 seconds total)