Starting phenix.real_space_refine on Thu Mar 5 18:52:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wz1_32901/03_2026/7wz1_32901.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wz1_32901/03_2026/7wz1_32901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wz1_32901/03_2026/7wz1_32901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wz1_32901/03_2026/7wz1_32901.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wz1_32901/03_2026/7wz1_32901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wz1_32901/03_2026/7wz1_32901.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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 111 5.16 5 C 15661 2.51 5 N 4033 2.21 5 O 4662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24467 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8032 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 973} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 8000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8000 Classifications: {'peptide': 1027} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 970} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 5.11, per 1000 atoms: 0.21 Number of scatterers: 24467 At special positions: 0 Unit cell: (139.384, 145.768, 167.048, 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 111 16.00 O 4662 8.00 N 4033 7.00 C 15661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.03 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=2.03 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=2.03 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 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 336 " - pdb=" SG CYS B 361 " 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 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 131 " - pdb=" SG CYS C 166 " 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=2.03 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 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 NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 61 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 709 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 947.9 milliseconds 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5814 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 49 sheets defined 22.8% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.936A pdb=" N TYR A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.525A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.142A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.613A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.142A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.549A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 782 removed outlier: 3.555A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.721A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.363A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 937 removed outlier: 3.858A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.857A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) 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 removed outlier: 4.169A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.512A pdb=" N ALA A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.646A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.415A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.903A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.579A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 761 through 778 removed outlier: 3.817A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.640A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.926A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.629A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.579A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.518A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 979 through 983 removed outlier: 3.589A pdb=" N ARG B 983 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.528A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.980A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.913A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 444 through 448 removed outlier: 3.863A pdb=" N GLY C 447 " --> pdb=" O LYS C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 605 removed outlier: 3.858A pdb=" N THR C 604 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 605 " --> pdb=" O THR C 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 601 through 605' Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 761 through 780 Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 929 Processing helix chain 'C' and resid 930 through 940 removed outlier: 3.602A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 945 No H-bonds generated for 'chain 'C' and resid 943 through 945' Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.034A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 977 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.182A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.995A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.510A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.652A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.984A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.792A pdb=" N ILE A 201 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL A 227 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER A 203 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 95 through 96 removed outlier: 3.742A pdb=" N GLU A 96 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 186 " --> pdb=" O GLU A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 103 through 104 removed outlier: 3.608A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.662A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.884A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.160A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 394 through 400 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.543A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.357A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.274A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.291A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.291A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 735 removed outlier: 3.773A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AC3, first strand: chain 'B' and resid 34 through 37 removed outlier: 6.343A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 42 through 43 removed outlier: 7.161A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.618A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 90 through 94 removed outlier: 7.285A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.332A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.631A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.521A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.106A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AD4, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.762A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD6, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.145A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.642A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B1086 " --> pdb=" O HIS B1083 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.764A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP C 64 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 226 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU C 224 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.538A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.556A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.842A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 130 through 131 removed outlier: 3.502A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.511A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 326 removed outlier: 7.462A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 376 through 377 removed outlier: 3.859A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.972A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 722 removed outlier: 3.564A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.552A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1121 701 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 2.24 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: 7763 1.34 - 1.46: 4999 1.46 - 1.58: 12140 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25040 Sorted by residual: bond pdb=" CA VAL C 67 " pdb=" C VAL C 67 " ideal model delta sigma weight residual 1.526 1.490 0.035 1.13e-02 7.83e+03 9.83e+00 bond pdb=" CA SER A 937 " pdb=" C SER A 937 " ideal model delta sigma weight residual 1.522 1.486 0.037 1.43e-02 4.89e+03 6.60e+00 bond pdb=" CA HIS C 66 " pdb=" C HIS C 66 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.22e-02 6.72e+03 6.59e+00 bond pdb=" C GLN C 173 " pdb=" N PRO C 174 " ideal model delta sigma weight residual 1.332 1.358 -0.026 1.12e-02 7.97e+03 5.39e+00 bond pdb=" CA LEU A 938 " pdb=" C LEU A 938 " ideal model delta sigma weight residual 1.520 1.489 0.031 1.37e-02 5.33e+03 5.11e+00 ... (remaining 25035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 33998 3.35 - 6.70: 94 6.70 - 10.05: 2 10.05 - 13.39: 0 13.39 - 16.74: 1 Bond angle restraints: 34095 Sorted by residual: angle pdb=" N LEU A 938 " pdb=" CA LEU A 938 " pdb=" C LEU A 938 " ideal model delta sigma weight residual 114.64 97.90 16.74 1.52e+00 4.33e-01 1.21e+02 angle pdb=" C VAL C 67 " pdb=" CA VAL C 67 " pdb=" CB VAL C 67 " ideal model delta sigma weight residual 111.23 104.99 6.24 1.08e+00 8.57e-01 3.34e+01 angle pdb=" C PHE C 79 " pdb=" N ASP C 80 " pdb=" CA ASP C 80 " ideal model delta sigma weight residual 122.99 115.36 7.63 1.41e+00 5.03e-01 2.93e+01 angle pdb=" C ASP B 80 " pdb=" N ASN B 81 " pdb=" CA ASN B 81 " ideal model delta sigma weight residual 123.16 117.63 5.53 1.23e+00 6.61e-01 2.02e+01 angle pdb=" N ILE B 909 " pdb=" CA ILE B 909 " pdb=" C ILE B 909 " ideal model delta sigma weight residual 113.47 109.11 4.36 1.01e+00 9.80e-01 1.86e+01 ... (remaining 34090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14570 17.89 - 35.77: 614 35.77 - 53.66: 97 53.66 - 71.54: 19 71.54 - 89.43: 5 Dihedral angle restraints: 15305 sinusoidal: 6285 harmonic: 9020 Sorted by residual: dihedral pdb=" CA CYS A 291 " pdb=" C CYS A 291 " pdb=" N ALA A 292 " pdb=" CA ALA A 292 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -113.52 27.52 1 1.00e+01 1.00e-02 1.09e+01 dihedral pdb=" CA SER B 112 " pdb=" C SER B 112 " pdb=" N LYS B 113 " pdb=" CA LYS B 113 " ideal model delta harmonic sigma weight residual -180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 15302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3191 0.051 - 0.102: 657 0.102 - 0.152: 101 0.152 - 0.203: 5 0.203 - 0.254: 3 Chirality restraints: 3957 Sorted by residual: chirality pdb=" CA ILE C 68 " pdb=" N ILE C 68 " pdb=" C ILE C 68 " pdb=" CB ILE C 68 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA LEU A 938 " pdb=" N LEU A 938 " pdb=" C LEU A 938 " pdb=" CB LEU A 938 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 3954 not shown) Planarity restraints: 4407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 986 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO C 373 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO B 986 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.026 5.00e-02 4.00e+02 ... (remaining 4404 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2437 2.75 - 3.29: 24591 3.29 - 3.82: 40055 3.82 - 4.36: 46190 4.36 - 4.90: 79010 Nonbonded interactions: 192283 Sorted by model distance: nonbonded pdb=" O PHE A 106 " pdb=" OG SER A 116 " model vdw 2.212 3.040 nonbonded pdb=" OD2 ASP C 808 " pdb=" OG SER C 810 " model vdw 2.245 3.040 nonbonded pdb=" OG1 THR C 29 " pdb=" OD1 ASP C 215 " model vdw 2.250 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.260 3.040 nonbonded pdb=" O GLN B 957 " pdb=" OG1 THR B 961 " model vdw 2.262 3.040 ... (remaining 192278 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 26 through 243 or resid 262 through 1309)) selection = (chain 'B' and (resid 26 through 68 or resid 80 through 1309)) selection = (chain 'C' and (resid 26 through 68 or resid 80 through 243 or resid 262 through \ 1309)) } 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.850 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 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 : 0.003 0.043 25107 Z= 0.170 Angle : 0.659 16.744 34257 Z= 0.410 Chirality : 0.042 0.254 3957 Planarity : 0.004 0.055 4379 Dihedral : 9.689 89.429 9374 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 5.40 % Allowed : 8.25 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.13), residues: 3044 helix: -0.37 (0.20), residues: 645 sheet: -3.05 (0.19), residues: 530 loop : -3.76 (0.11), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1014 TYR 0.008 0.001 TYR A 160 PHE 0.011 0.001 PHE C 375 TRP 0.005 0.000 TRP A 886 HIS 0.001 0.000 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00283 (25040) covalent geometry : angle 0.65832 (34095) SS BOND : bond 0.00130 ( 39) SS BOND : angle 0.46817 ( 78) hydrogen bonds : bond 0.23227 ( 695) hydrogen bonds : angle 8.01793 ( 1938) link_NAG-ASN : bond 0.00287 ( 28) link_NAG-ASN : angle 1.04248 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 802 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7739 (m-80) cc_final: 0.6732 (m-80) REVERT: A 45 SER cc_start: 0.7843 (t) cc_final: 0.7639 (p) REVERT: A 52 GLN cc_start: 0.6968 (tp40) cc_final: 0.6728 (tm-30) REVERT: A 104 TRP cc_start: 0.7833 (OUTLIER) cc_final: 0.7365 (m-90) REVERT: A 129 LYS cc_start: 0.7751 (mtmm) cc_final: 0.7300 (mtmm) REVERT: A 188 ARG cc_start: 0.7391 (ptp-110) cc_final: 0.7098 (ptp90) REVERT: A 235 ILE cc_start: 0.8470 (mm) cc_final: 0.8006 (mm) REVERT: A 237 ARG cc_start: 0.7340 (ttm110) cc_final: 0.7069 (mtp-110) REVERT: A 238 PHE cc_start: 0.6719 (t80) cc_final: 0.6509 (t80) REVERT: A 267 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8047 (p) REVERT: A 269 TYR cc_start: 0.7780 (m-80) cc_final: 0.7562 (m-10) REVERT: A 280 ASN cc_start: 0.7510 (t0) cc_final: 0.7264 (t0) REVERT: A 281 GLU cc_start: 0.7475 (pp20) cc_final: 0.6994 (pp20) REVERT: A 340 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5791 (pm20) REVERT: A 351 TYR cc_start: 0.6501 (p90) cc_final: 0.6073 (p90) REVERT: A 380 TYR cc_start: 0.6929 (m-80) cc_final: 0.6495 (m-10) REVERT: A 452 LEU cc_start: 0.7930 (tt) cc_final: 0.7248 (mm) REVERT: A 546 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7707 (tm) REVERT: A 558 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7540 (mtpp) REVERT: A 565 PHE cc_start: 0.6229 (m-10) cc_final: 0.5954 (m-10) REVERT: A 574 ASP cc_start: 0.7682 (t70) cc_final: 0.7419 (t0) REVERT: A 578 ASP cc_start: 0.7183 (t0) cc_final: 0.6952 (t0) REVERT: A 586 ASP cc_start: 0.7163 (t0) cc_final: 0.6814 (t0) REVERT: A 599 THR cc_start: 0.8313 (m) cc_final: 0.7920 (t) REVERT: A 654 GLU cc_start: 0.6872 (pm20) cc_final: 0.6592 (pm20) REVERT: A 660 TYR cc_start: 0.8417 (m-80) cc_final: 0.7493 (m-80) REVERT: A 670 ILE cc_start: 0.8420 (mm) cc_final: 0.8062 (mt) REVERT: A 675 GLN cc_start: 0.7193 (mm-40) cc_final: 0.6632 (mm-40) REVERT: A 691 SER cc_start: 0.8092 (t) cc_final: 0.7886 (p) REVERT: A 693 ILE cc_start: 0.8539 (pt) cc_final: 0.8300 (pt) REVERT: A 707 TYR cc_start: 0.7594 (t80) cc_final: 0.7334 (t80) REVERT: A 745 ASP cc_start: 0.7155 (m-30) cc_final: 0.6822 (p0) REVERT: A 751 ASN cc_start: 0.7843 (m-40) cc_final: 0.7615 (m110) REVERT: A 768 THR cc_start: 0.8174 (m) cc_final: 0.7896 (p) REVERT: A 774 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6785 (mp10) REVERT: A 779 GLN cc_start: 0.7848 (tt0) cc_final: 0.7537 (mt0) REVERT: A 787 GLN cc_start: 0.7659 (mt0) cc_final: 0.7167 (mt0) REVERT: A 819 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6509 (mt-10) REVERT: A 825 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8233 (mtpp) REVERT: A 867 ASP cc_start: 0.7254 (m-30) cc_final: 0.7005 (m-30) REVERT: A 869 MET cc_start: 0.7895 (mtt) cc_final: 0.7680 (mtp) REVERT: A 904 TYR cc_start: 0.6676 (m-10) cc_final: 0.6307 (m-10) REVERT: A 918 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7346 (mt-10) REVERT: A 949 GLN cc_start: 0.7550 (mm110) cc_final: 0.7201 (mm-40) REVERT: A 993 ILE cc_start: 0.8343 (tp) cc_final: 0.7777 (tp) REVERT: A 998 THR cc_start: 0.7934 (m) cc_final: 0.7660 (p) REVERT: A 1030 SER cc_start: 0.8746 (m) cc_final: 0.8209 (t) REVERT: A 1072 GLU cc_start: 0.7842 (pm20) cc_final: 0.7524 (pm20) REVERT: A 1073 LYS cc_start: 0.8162 (mtpm) cc_final: 0.7957 (mtpp) REVERT: A 1081 ILE cc_start: 0.8006 (pt) cc_final: 0.7793 (mt) REVERT: A 1097 SER cc_start: 0.8430 (t) cc_final: 0.8081 (p) REVERT: A 1102 TRP cc_start: 0.8570 (m100) cc_final: 0.8083 (m100) REVERT: A 1111 GLU cc_start: 0.7608 (tt0) cc_final: 0.7212 (tt0) REVERT: A 1125 ASN cc_start: 0.7410 (p0) cc_final: 0.6916 (p0) REVERT: B 54 LEU cc_start: 0.7359 (mm) cc_final: 0.7142 (mt) REVERT: B 83 VAL cc_start: 0.5712 (OUTLIER) cc_final: 0.5433 (t) REVERT: B 105 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7643 (pt) REVERT: B 106 PHE cc_start: 0.7818 (m-80) cc_final: 0.7571 (m-10) REVERT: B 169 GLU cc_start: 0.7077 (pm20) cc_final: 0.6813 (pm20) REVERT: B 201 ILE cc_start: 0.8500 (mt) cc_final: 0.7986 (tt) REVERT: B 202 TYR cc_start: 0.7675 (m-80) cc_final: 0.7475 (m-80) REVERT: B 224 GLU cc_start: 0.6684 (pm20) cc_final: 0.6390 (pm20) REVERT: B 273 ARG cc_start: 0.8013 (ttm-80) cc_final: 0.7446 (mtm180) REVERT: B 289 VAL cc_start: 0.7477 (t) cc_final: 0.7140 (m) REVERT: B 356 LYS cc_start: 0.8340 (mtpp) cc_final: 0.7872 (mtpp) REVERT: B 360 ASN cc_start: 0.8290 (m110) cc_final: 0.8069 (m110) REVERT: B 380 TYR cc_start: 0.7965 (m-80) cc_final: 0.7122 (m-80) REVERT: B 557 LYS cc_start: 0.8278 (ptpp) cc_final: 0.8034 (ptpt) REVERT: B 558 LYS cc_start: 0.8190 (mppt) cc_final: 0.7659 (mppt) REVERT: B 644 GLN cc_start: 0.8208 (tp40) cc_final: 0.7978 (tp40) REVERT: B 650 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7798 (tp) REVERT: B 654 GLU cc_start: 0.7375 (pm20) cc_final: 0.7155 (pm20) REVERT: B 698 SER cc_start: 0.7918 (t) cc_final: 0.7184 (p) REVERT: B 699 LEU cc_start: 0.8223 (mt) cc_final: 0.7904 (mt) REVERT: B 705 VAL cc_start: 0.8642 (t) cc_final: 0.8269 (m) REVERT: B 736 VAL cc_start: 0.8582 (m) cc_final: 0.8300 (t) REVERT: B 810 SER cc_start: 0.8275 (t) cc_final: 0.8075 (p) REVERT: B 819 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6701 (mt-10) REVERT: B 821 LEU cc_start: 0.8392 (tp) cc_final: 0.7939 (tt) REVERT: B 850 ILE cc_start: 0.8635 (mm) cc_final: 0.8359 (tp) REVERT: B 868 GLU cc_start: 0.6479 (tp30) cc_final: 0.6011 (tp30) REVERT: B 922 LEU cc_start: 0.8209 (tp) cc_final: 0.8002 (tt) REVERT: B 950 ASP cc_start: 0.6919 (t70) cc_final: 0.6536 (t70) REVERT: B 975 SER cc_start: 0.8453 (m) cc_final: 0.8190 (t) REVERT: B 988 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6695 (tp30) REVERT: B 990 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6199 (mp0) REVERT: B 993 ILE cc_start: 0.8414 (tp) cc_final: 0.8166 (tp) REVERT: B 1029 MET cc_start: 0.8273 (tpp) cc_final: 0.7902 (tpp) REVERT: B 1081 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7525 (pt) REVERT: B 1097 SER cc_start: 0.8855 (t) cc_final: 0.8488 (p) REVERT: B 1104 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8283 (p) REVERT: B 1111 GLU cc_start: 0.7654 (tt0) cc_final: 0.7433 (tt0) REVERT: C 40 ASP cc_start: 0.6741 (p0) cc_final: 0.6461 (p0) REVERT: C 51 THR cc_start: 0.8419 (p) cc_final: 0.8190 (p) REVERT: C 105 ILE cc_start: 0.7383 (mm) cc_final: 0.7134 (mp) REVERT: C 117 LEU cc_start: 0.7543 (mt) cc_final: 0.7187 (mt) REVERT: C 212 GLU cc_start: 0.5157 (OUTLIER) cc_final: 0.4756 (pm20) REVERT: C 224 GLU cc_start: 0.7319 (pm20) cc_final: 0.7112 (pm20) REVERT: C 238 PHE cc_start: 0.7618 (t80) cc_final: 0.7345 (t80) REVERT: C 347 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6039 (t80) REVERT: C 349 SER cc_start: 0.7428 (p) cc_final: 0.7170 (t) REVERT: C 377 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.6907 (m-80) REVERT: C 398 ASP cc_start: 0.6622 (t70) cc_final: 0.6403 (t70) REVERT: C 414 GLN cc_start: 0.7182 (mp-120) cc_final: 0.6838 (mp10) REVERT: C 420 ASP cc_start: 0.6935 (t0) cc_final: 0.6574 (t0) REVERT: C 427 ASP cc_start: 0.6600 (t70) cc_final: 0.6333 (t70) REVERT: C 442 ASP cc_start: 0.7161 (m-30) cc_final: 0.6930 (m-30) REVERT: C 553 THR cc_start: 0.8226 (p) cc_final: 0.8015 (t) REVERT: C 565 PHE cc_start: 0.6584 (m-10) cc_final: 0.6160 (m-10) REVERT: C 675 GLN cc_start: 0.7063 (mm-40) cc_final: 0.6816 (mm-40) REVERT: C 707 TYR cc_start: 0.7533 (t80) cc_final: 0.6644 (t80) REVERT: C 725 GLU cc_start: 0.6769 (tt0) cc_final: 0.6227 (tt0) REVERT: C 750 SER cc_start: 0.8746 (m) cc_final: 0.8255 (p) REVERT: C 751 ASN cc_start: 0.7961 (m-40) cc_final: 0.7515 (m-40) REVERT: C 776 LYS cc_start: 0.8326 (ttpt) cc_final: 0.8058 (tttp) REVERT: C 779 GLN cc_start: 0.6789 (tt0) cc_final: 0.6550 (tm-30) REVERT: C 788 ILE cc_start: 0.8369 (mm) cc_final: 0.8120 (mm) REVERT: C 825 LYS cc_start: 0.8249 (tppt) cc_final: 0.7904 (ttmm) REVERT: C 868 GLU cc_start: 0.7078 (tp30) cc_final: 0.6740 (tp30) REVERT: C 904 TYR cc_start: 0.6811 (m-10) cc_final: 0.6428 (m-10) REVERT: C 914 ASN cc_start: 0.7475 (p0) cc_final: 0.6939 (p0) REVERT: C 921 LYS cc_start: 0.8335 (mmmt) cc_final: 0.8125 (mmmm) REVERT: C 964 LYS cc_start: 0.8118 (ttpp) cc_final: 0.7885 (ttmm) REVERT: C 975 SER cc_start: 0.8527 (m) cc_final: 0.8305 (t) REVERT: C 983 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7858 (ttm110) REVERT: C 1018 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8015 (mt) REVERT: C 1105 THR cc_start: 0.7596 (t) cc_final: 0.7324 (t) REVERT: C 1111 GLU cc_start: 0.7003 (tt0) cc_final: 0.6746 (tt0) REVERT: C 1139 ASP cc_start: 0.7929 (t70) cc_final: 0.7720 (t0) outliers start: 144 outliers final: 45 residues processed: 909 average time/residue: 0.1631 time to fit residues: 232.3844 Evaluate side-chains 704 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 644 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.0770 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 173 GLN A 181 GLN A 314 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 437 ASN A 450 ASN A 519 HIS A 540 ASN A 544 ASN A 563 GLN A 580 GLN A 613 GLN A 784 GLN A 853 GLN A 901 GLN A 907 ASN A 913 GLN A1002 GLN A1083 HIS A1101 HIS B 99 ASN B 314 GLN B 321 GLN B 370 ASN B 409 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 580 GLN B 644 GLN B 690 GLN B 779 GLN B 784 GLN B 853 GLN B 895 GLN B 901 GLN B 907 ASN B 955 ASN B1010 GLN B1011 GLN B1048 HIS C 52 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 321 GLN C 360 ASN C 394 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 563 GLN C 658 ASN C 762 GLN C 784 GLN C 824 ASN C 853 GLN C 901 GLN C 957 GLN C 965 GLN C1002 GLN C1011 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.146721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120138 restraints weight = 40250.111| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.74 r_work: 0.3442 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 25107 Z= 0.179 Angle : 0.650 13.067 34257 Z= 0.330 Chirality : 0.047 0.342 3957 Planarity : 0.005 0.054 4379 Dihedral : 7.662 82.356 4027 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 5.51 % Allowed : 14.85 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.14), residues: 3044 helix: 0.45 (0.21), residues: 650 sheet: -2.57 (0.20), residues: 502 loop : -3.27 (0.12), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 328 TYR 0.022 0.002 TYR B 495 PHE 0.037 0.002 PHE C1121 TRP 0.015 0.001 TRP B 104 HIS 0.010 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00397 (25040) covalent geometry : angle 0.63258 (34095) SS BOND : bond 0.00748 ( 39) SS BOND : angle 2.58952 ( 78) hydrogen bonds : bond 0.04110 ( 695) hydrogen bonds : angle 5.31221 ( 1938) link_NAG-ASN : bond 0.00349 ( 28) link_NAG-ASN : angle 1.87910 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 699 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8089 (t) cc_final: 0.7837 (p) REVERT: A 65 PHE cc_start: 0.7256 (m-10) cc_final: 0.6972 (m-10) REVERT: A 102 ARG cc_start: 0.7494 (mtm-85) cc_final: 0.6906 (mtm-85) REVERT: A 104 TRP cc_start: 0.7774 (OUTLIER) cc_final: 0.7453 (m-90) REVERT: A 129 LYS cc_start: 0.8052 (mtmm) cc_final: 0.7413 (mtmm) REVERT: A 188 ARG cc_start: 0.7899 (ptp-110) cc_final: 0.7444 (ptp90) REVERT: A 189 GLU cc_start: 0.8158 (pm20) cc_final: 0.7812 (pt0) REVERT: A 267 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8132 (p) REVERT: A 269 TYR cc_start: 0.8246 (m-80) cc_final: 0.7917 (m-10) REVERT: A 281 GLU cc_start: 0.7970 (pp20) cc_final: 0.7653 (pp20) REVERT: A 307 THR cc_start: 0.8254 (m) cc_final: 0.7961 (p) REVERT: A 340 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6317 (pm20) REVERT: A 351 TYR cc_start: 0.6652 (p90) cc_final: 0.6191 (p90) REVERT: A 355 ARG cc_start: 0.7006 (ttm170) cc_final: 0.6746 (ttm170) REVERT: A 358 ILE cc_start: 0.6487 (OUTLIER) cc_final: 0.6186 (pt) REVERT: A 359 SER cc_start: 0.8289 (m) cc_final: 0.7664 (p) REVERT: A 380 TYR cc_start: 0.7324 (m-80) cc_final: 0.6754 (m-10) REVERT: A 386 LYS cc_start: 0.8284 (mttp) cc_final: 0.7999 (mttt) REVERT: A 452 LEU cc_start: 0.8101 (tt) cc_final: 0.7527 (mm) REVERT: A 533 LEU cc_start: 0.8544 (tp) cc_final: 0.8337 (tt) REVERT: A 558 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7983 (mtpp) REVERT: A 569 ILE cc_start: 0.8038 (pt) cc_final: 0.7686 (mp) REVERT: A 586 ASP cc_start: 0.7580 (t0) cc_final: 0.7243 (t0) REVERT: A 643 PHE cc_start: 0.8232 (t80) cc_final: 0.7929 (t80) REVERT: A 654 GLU cc_start: 0.7334 (pm20) cc_final: 0.7077 (pm20) REVERT: A 670 ILE cc_start: 0.8464 (mm) cc_final: 0.8264 (mp) REVERT: A 675 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7378 (mm-40) REVERT: A 707 TYR cc_start: 0.7977 (t80) cc_final: 0.7741 (t80) REVERT: A 740 MET cc_start: 0.7872 (tpp) cc_final: 0.7575 (ttm) REVERT: A 745 ASP cc_start: 0.7357 (m-30) cc_final: 0.7054 (p0) REVERT: A 751 ASN cc_start: 0.8230 (m-40) cc_final: 0.7934 (m-40) REVERT: A 768 THR cc_start: 0.8375 (m) cc_final: 0.8097 (p) REVERT: A 774 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7279 (mp10) REVERT: A 787 GLN cc_start: 0.8070 (mt0) cc_final: 0.7706 (mt0) REVERT: A 803 SER cc_start: 0.8386 (m) cc_final: 0.8008 (t) REVERT: A 808 ASP cc_start: 0.7911 (t0) cc_final: 0.7657 (t0) REVERT: A 855 PHE cc_start: 0.8106 (m-80) cc_final: 0.7441 (m-80) REVERT: A 868 GLU cc_start: 0.7813 (tp30) cc_final: 0.7556 (tp30) REVERT: A 949 GLN cc_start: 0.7900 (mm110) cc_final: 0.7553 (mm-40) REVERT: A 970 PHE cc_start: 0.7853 (m-10) cc_final: 0.7640 (m-10) REVERT: A 993 ILE cc_start: 0.8651 (tp) cc_final: 0.8400 (tp) REVERT: A 998 THR cc_start: 0.8105 (m) cc_final: 0.7789 (p) REVERT: A 1030 SER cc_start: 0.8820 (m) cc_final: 0.8318 (t) REVERT: A 1094 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8078 (m) REVERT: A 1097 SER cc_start: 0.8607 (t) cc_final: 0.8010 (p) REVERT: A 1103 PHE cc_start: 0.8491 (m-10) cc_final: 0.8047 (m-80) REVERT: B 53 ASP cc_start: 0.7348 (t0) cc_final: 0.7059 (t0) REVERT: B 54 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8034 (mt) REVERT: B 83 VAL cc_start: 0.6273 (OUTLIER) cc_final: 0.5840 (t) REVERT: B 105 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7572 (pt) REVERT: B 106 PHE cc_start: 0.7929 (m-80) cc_final: 0.7616 (m-10) REVERT: B 169 GLU cc_start: 0.7844 (pm20) cc_final: 0.7363 (pm20) REVERT: B 177 MET cc_start: 0.6539 (tmt) cc_final: 0.6177 (tmt) REVERT: B 189 GLU cc_start: 0.7244 (pm20) cc_final: 0.6696 (mp0) REVERT: B 201 ILE cc_start: 0.8517 (mt) cc_final: 0.7973 (tt) REVERT: B 204 LYS cc_start: 0.8776 (tttp) cc_final: 0.8505 (tttp) REVERT: B 224 GLU cc_start: 0.6902 (pm20) cc_final: 0.6589 (pm20) REVERT: B 289 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8125 (m) REVERT: B 319 ARG cc_start: 0.7881 (ttm110) cc_final: 0.7648 (ttm110) REVERT: B 365 TYR cc_start: 0.7982 (m-80) cc_final: 0.7730 (m-10) REVERT: B 547 LYS cc_start: 0.8225 (mttm) cc_final: 0.7834 (mttp) REVERT: B 557 LYS cc_start: 0.8527 (ptpp) cc_final: 0.8158 (ptpt) REVERT: B 558 LYS cc_start: 0.8558 (mppt) cc_final: 0.8121 (mppt) REVERT: B 580 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7558 (mm-40) REVERT: B 589 PRO cc_start: 0.8776 (Cg_exo) cc_final: 0.8417 (Cg_endo) REVERT: B 644 GLN cc_start: 0.8425 (tp-100) cc_final: 0.8166 (tp40) REVERT: B 698 SER cc_start: 0.8195 (t) cc_final: 0.7793 (p) REVERT: B 703 ASN cc_start: 0.8638 (t0) cc_final: 0.7709 (m-40) REVERT: B 705 VAL cc_start: 0.8723 (t) cc_final: 0.8334 (m) REVERT: B 711 SER cc_start: 0.8625 (t) cc_final: 0.8407 (t) REVERT: B 773 GLU cc_start: 0.7701 (tm-30) cc_final: 0.6809 (tm-30) REVERT: B 774 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7788 (mm-40) REVERT: B 810 SER cc_start: 0.8644 (t) cc_final: 0.8429 (p) REVERT: B 819 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6915 (mt-10) REVERT: B 821 LEU cc_start: 0.8800 (tp) cc_final: 0.8319 (tt) REVERT: B 868 GLU cc_start: 0.7331 (tp30) cc_final: 0.6726 (tp30) REVERT: B 914 ASN cc_start: 0.8270 (p0) cc_final: 0.7326 (p0) REVERT: B 918 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7523 (mt-10) REVERT: B 922 LEU cc_start: 0.8495 (tp) cc_final: 0.8271 (tt) REVERT: B 950 ASP cc_start: 0.7590 (t70) cc_final: 0.7121 (t70) REVERT: B 957 GLN cc_start: 0.8060 (tt0) cc_final: 0.7769 (tt0) REVERT: B 975 SER cc_start: 0.8781 (m) cc_final: 0.8389 (t) REVERT: B 984 LEU cc_start: 0.8324 (tp) cc_final: 0.8111 (tp) REVERT: B 990 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: B 993 ILE cc_start: 0.8488 (tp) cc_final: 0.8279 (tp) REVERT: B 1029 MET cc_start: 0.8557 (tpp) cc_final: 0.8108 (tpp) REVERT: B 1084 ASP cc_start: 0.7743 (t0) cc_final: 0.7532 (t0) REVERT: B 1097 SER cc_start: 0.9020 (t) cc_final: 0.8363 (p) REVERT: C 52 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7591 (tm130) REVERT: C 65 PHE cc_start: 0.8296 (m-10) cc_final: 0.8014 (m-10) REVERT: C 105 ILE cc_start: 0.8060 (mm) cc_final: 0.7721 (mm) REVERT: C 106 PHE cc_start: 0.7749 (m-80) cc_final: 0.7448 (m-80) REVERT: C 177 MET cc_start: 0.6254 (tpp) cc_final: 0.5625 (tpp) REVERT: C 188 ARG cc_start: 0.7747 (ptp-170) cc_final: 0.7410 (ptp-170) REVERT: C 204 LYS cc_start: 0.8383 (tmtt) cc_final: 0.8066 (tttp) REVERT: C 224 GLU cc_start: 0.7415 (pm20) cc_final: 0.6972 (mp0) REVERT: C 265 TYR cc_start: 0.7675 (p90) cc_final: 0.7420 (p90) REVERT: C 347 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.6760 (t80) REVERT: C 349 SER cc_start: 0.8138 (p) cc_final: 0.7908 (t) REVERT: C 398 ASP cc_start: 0.7271 (t70) cc_final: 0.7047 (t70) REVERT: C 414 GLN cc_start: 0.7451 (mp10) cc_final: 0.7073 (mp10) REVERT: C 420 ASP cc_start: 0.7540 (t0) cc_final: 0.7036 (t0) REVERT: C 427 ASP cc_start: 0.7071 (t70) cc_final: 0.6764 (t70) REVERT: C 461 LEU cc_start: 0.7946 (mt) cc_final: 0.7438 (mt) REVERT: C 465 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7436 (tm-30) REVERT: C 641 ASN cc_start: 0.6502 (t0) cc_final: 0.6239 (t0) REVERT: C 656 VAL cc_start: 0.8564 (m) cc_final: 0.8304 (p) REVERT: C 707 TYR cc_start: 0.7895 (t80) cc_final: 0.7019 (t80) REVERT: C 750 SER cc_start: 0.8504 (m) cc_final: 0.8117 (p) REVERT: C 751 ASN cc_start: 0.7978 (m-40) cc_final: 0.7517 (m-40) REVERT: C 755 GLN cc_start: 0.7980 (pp30) cc_final: 0.7648 (pp30) REVERT: C 776 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8233 (tttp) REVERT: C 779 GLN cc_start: 0.7666 (tt0) cc_final: 0.7330 (tm-30) REVERT: C 788 ILE cc_start: 0.8417 (mm) cc_final: 0.8207 (mm) REVERT: C 825 LYS cc_start: 0.8473 (tppt) cc_final: 0.8084 (ttmm) REVERT: C 851 CYS cc_start: 0.7968 (t) cc_final: 0.7535 (m) REVERT: C 868 GLU cc_start: 0.7869 (tp30) cc_final: 0.7429 (tp30) REVERT: C 921 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8487 (mmmm) REVERT: C 933 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7605 (mttp) REVERT: C 984 LEU cc_start: 0.8031 (mp) cc_final: 0.7791 (mt) REVERT: C 1038 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8379 (mtpp) REVERT: C 1073 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8231 (mtpp) outliers start: 147 outliers final: 87 residues processed: 791 average time/residue: 0.1671 time to fit residues: 207.3104 Evaluate side-chains 735 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 634 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 126 optimal weight: 0.0060 chunk 221 optimal weight: 0.2980 chunk 202 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 283 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 239 GLN A 360 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 658 ASN A1002 GLN A1083 HIS B 239 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 751 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.147733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121489 restraints weight = 40259.547| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.71 r_work: 0.3451 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 25107 Z= 0.119 Angle : 0.604 9.793 34257 Z= 0.305 Chirality : 0.046 0.324 3957 Planarity : 0.004 0.055 4379 Dihedral : 7.292 79.932 4011 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 6.04 % Allowed : 17.40 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.14), residues: 3044 helix: 0.96 (0.22), residues: 644 sheet: -2.31 (0.20), residues: 519 loop : -2.97 (0.12), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1107 TYR 0.019 0.001 TYR B 655 PHE 0.027 0.001 PHE C1121 TRP 0.008 0.001 TRP B 104 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00270 (25040) covalent geometry : angle 0.58874 (34095) SS BOND : bond 0.00490 ( 39) SS BOND : angle 2.19655 ( 78) hydrogen bonds : bond 0.03640 ( 695) hydrogen bonds : angle 5.02326 ( 1938) link_NAG-ASN : bond 0.00488 ( 28) link_NAG-ASN : angle 1.85295 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 654 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8064 (t) cc_final: 0.7856 (p) REVERT: A 65 PHE cc_start: 0.7200 (m-10) cc_final: 0.6877 (m-10) REVERT: A 84 LEU cc_start: 0.8491 (pt) cc_final: 0.8284 (pt) REVERT: A 102 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.6843 (mtm-85) REVERT: A 104 TRP cc_start: 0.7798 (OUTLIER) cc_final: 0.7467 (m-90) REVERT: A 129 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7451 (mtmm) REVERT: A 188 ARG cc_start: 0.7867 (ptp-110) cc_final: 0.7433 (ptp90) REVERT: A 189 GLU cc_start: 0.8153 (pm20) cc_final: 0.7800 (pt0) REVERT: A 214 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6310 (mt-10) REVERT: A 267 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8155 (p) REVERT: A 269 TYR cc_start: 0.8270 (m-80) cc_final: 0.7948 (m-10) REVERT: A 281 GLU cc_start: 0.7942 (pp20) cc_final: 0.7668 (pp20) REVERT: A 287 ASP cc_start: 0.7805 (p0) cc_final: 0.7310 (p0) REVERT: A 307 THR cc_start: 0.8265 (m) cc_final: 0.7969 (p) REVERT: A 324 GLU cc_start: 0.7469 (mp0) cc_final: 0.7256 (mp0) REVERT: A 340 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6212 (pm20) REVERT: A 351 TYR cc_start: 0.6659 (p90) cc_final: 0.6178 (p90) REVERT: A 355 ARG cc_start: 0.6938 (ttm170) cc_final: 0.6348 (ttm170) REVERT: A 358 ILE cc_start: 0.6577 (OUTLIER) cc_final: 0.6291 (pt) REVERT: A 380 TYR cc_start: 0.7352 (m-80) cc_final: 0.6784 (m-10) REVERT: A 386 LYS cc_start: 0.8305 (mttp) cc_final: 0.8023 (mttt) REVERT: A 452 LEU cc_start: 0.8091 (tt) cc_final: 0.7499 (mm) REVERT: A 542 ASN cc_start: 0.9000 (t0) cc_final: 0.8788 (t0) REVERT: A 558 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7941 (mtpp) REVERT: A 564 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7426 (tm-30) REVERT: A 569 ILE cc_start: 0.8008 (pt) cc_final: 0.7703 (mp) REVERT: A 588 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8726 (p) REVERT: A 643 PHE cc_start: 0.8145 (t80) cc_final: 0.7941 (t80) REVERT: A 654 GLU cc_start: 0.7350 (pm20) cc_final: 0.7043 (pm20) REVERT: A 662 CYS cc_start: 0.3976 (OUTLIER) cc_final: 0.3471 (p) REVERT: A 670 ILE cc_start: 0.8458 (mm) cc_final: 0.8192 (mp) REVERT: A 675 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7116 (mm-40) REVERT: A 707 TYR cc_start: 0.7918 (t80) cc_final: 0.7669 (t80) REVERT: A 745 ASP cc_start: 0.7257 (m-30) cc_final: 0.6933 (p0) REVERT: A 751 ASN cc_start: 0.8257 (m-40) cc_final: 0.7956 (m-40) REVERT: A 768 THR cc_start: 0.8288 (m) cc_final: 0.8060 (p) REVERT: A 774 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7247 (mp10) REVERT: A 808 ASP cc_start: 0.7984 (t0) cc_final: 0.7702 (t0) REVERT: A 855 PHE cc_start: 0.8056 (m-80) cc_final: 0.7420 (m-80) REVERT: A 868 GLU cc_start: 0.7834 (tp30) cc_final: 0.7588 (tp30) REVERT: A 949 GLN cc_start: 0.7928 (mm110) cc_final: 0.7453 (mm-40) REVERT: A 998 THR cc_start: 0.8027 (m) cc_final: 0.7798 (p) REVERT: A 1030 SER cc_start: 0.8773 (m) cc_final: 0.8260 (t) REVERT: A 1094 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.8039 (t) REVERT: A 1097 SER cc_start: 0.8614 (t) cc_final: 0.8048 (p) REVERT: A 1103 PHE cc_start: 0.8480 (m-10) cc_final: 0.8046 (m-80) REVERT: A 1107 ARG cc_start: 0.7755 (mtt90) cc_final: 0.7507 (mtt90) REVERT: B 52 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7630 (tp-100) REVERT: B 54 LEU cc_start: 0.8205 (mm) cc_final: 0.7956 (mt) REVERT: B 83 VAL cc_start: 0.6199 (OUTLIER) cc_final: 0.5622 (t) REVERT: B 105 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7585 (pt) REVERT: B 106 PHE cc_start: 0.7914 (m-80) cc_final: 0.7584 (m-10) REVERT: B 169 GLU cc_start: 0.7771 (pm20) cc_final: 0.7211 (pm20) REVERT: B 177 MET cc_start: 0.6620 (tmt) cc_final: 0.6009 (tmt) REVERT: B 201 ILE cc_start: 0.8544 (mt) cc_final: 0.8005 (tt) REVERT: B 204 LYS cc_start: 0.8603 (tttp) cc_final: 0.8376 (tttp) REVERT: B 224 GLU cc_start: 0.6774 (pm20) cc_final: 0.6435 (pm20) REVERT: B 273 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.8245 (ttm-80) REVERT: B 290 ASP cc_start: 0.7797 (t70) cc_final: 0.7557 (t0) REVERT: B 362 VAL cc_start: 0.7764 (OUTLIER) cc_final: 0.7346 (p) REVERT: B 528 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8255 (mmmt) REVERT: B 537 LYS cc_start: 0.8145 (tttp) cc_final: 0.7944 (tttm) REVERT: B 547 LYS cc_start: 0.8133 (mttm) cc_final: 0.7663 (mttp) REVERT: B 557 LYS cc_start: 0.8528 (ptpp) cc_final: 0.8233 (ptpt) REVERT: B 558 LYS cc_start: 0.8526 (mppt) cc_final: 0.8042 (mppt) REVERT: B 589 PRO cc_start: 0.8624 (Cg_exo) cc_final: 0.8218 (Cg_endo) REVERT: B 698 SER cc_start: 0.8289 (t) cc_final: 0.7761 (p) REVERT: B 705 VAL cc_start: 0.8624 (t) cc_final: 0.8279 (m) REVERT: B 711 SER cc_start: 0.8654 (t) cc_final: 0.8406 (t) REVERT: B 773 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7115 (tm-30) REVERT: B 774 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7779 (mm-40) REVERT: B 810 SER cc_start: 0.8602 (t) cc_final: 0.8388 (p) REVERT: B 821 LEU cc_start: 0.8804 (tp) cc_final: 0.8321 (tt) REVERT: B 868 GLU cc_start: 0.7343 (tp30) cc_final: 0.6749 (tp30) REVERT: B 914 ASN cc_start: 0.8296 (p0) cc_final: 0.7399 (p0) REVERT: B 918 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7486 (mt-10) REVERT: B 950 ASP cc_start: 0.7550 (t70) cc_final: 0.7121 (t70) REVERT: B 957 GLN cc_start: 0.8068 (tt0) cc_final: 0.7778 (tt0) REVERT: B 975 SER cc_start: 0.8726 (m) cc_final: 0.8322 (t) REVERT: B 984 LEU cc_start: 0.8318 (tp) cc_final: 0.8067 (tp) REVERT: B 990 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: B 993 ILE cc_start: 0.8525 (tp) cc_final: 0.8266 (tp) REVERT: B 1029 MET cc_start: 0.8455 (tpp) cc_final: 0.7761 (tpp) REVERT: B 1033 VAL cc_start: 0.8836 (t) cc_final: 0.8501 (p) REVERT: B 1084 ASP cc_start: 0.7773 (t0) cc_final: 0.7467 (t0) REVERT: B 1097 SER cc_start: 0.8996 (t) cc_final: 0.8312 (p) REVERT: B 1107 ARG cc_start: 0.7973 (ptt-90) cc_final: 0.7152 (ptt180) REVERT: C 53 ASP cc_start: 0.7427 (t0) cc_final: 0.7174 (t0) REVERT: C 105 ILE cc_start: 0.8125 (mm) cc_final: 0.7716 (mp) REVERT: C 106 PHE cc_start: 0.7750 (m-80) cc_final: 0.7383 (m-10) REVERT: C 177 MET cc_start: 0.6479 (tpp) cc_final: 0.6012 (tpp) REVERT: C 188 ARG cc_start: 0.7666 (ptp-170) cc_final: 0.7317 (ptp-170) REVERT: C 204 LYS cc_start: 0.8459 (tmtt) cc_final: 0.8110 (tttp) REVERT: C 224 GLU cc_start: 0.7429 (pm20) cc_final: 0.7059 (mp0) REVERT: C 239 GLN cc_start: 0.7711 (tp40) cc_final: 0.7488 (tp40) REVERT: C 327 VAL cc_start: 0.8666 (m) cc_final: 0.8253 (t) REVERT: C 347 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6807 (t80) REVERT: C 349 SER cc_start: 0.8117 (p) cc_final: 0.7817 (t) REVERT: C 414 GLN cc_start: 0.7403 (mp10) cc_final: 0.7119 (mp10) REVERT: C 420 ASP cc_start: 0.7150 (t0) cc_final: 0.6846 (t0) REVERT: C 427 ASP cc_start: 0.6965 (t70) cc_final: 0.6646 (t70) REVERT: C 439 ASN cc_start: 0.7039 (p0) cc_final: 0.6821 (p0) REVERT: C 465 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7632 (tm-30) REVERT: C 543 PHE cc_start: 0.8162 (m-10) cc_final: 0.7782 (m-80) REVERT: C 565 PHE cc_start: 0.7132 (m-10) cc_final: 0.6799 (m-10) REVERT: C 707 TYR cc_start: 0.7869 (t80) cc_final: 0.7003 (t80) REVERT: C 751 ASN cc_start: 0.7940 (m-40) cc_final: 0.7614 (m-40) REVERT: C 752 LEU cc_start: 0.8917 (mm) cc_final: 0.8698 (mt) REVERT: C 755 GLN cc_start: 0.7996 (pp30) cc_final: 0.7738 (pp30) REVERT: C 776 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8241 (tttp) REVERT: C 779 GLN cc_start: 0.7693 (tt0) cc_final: 0.7287 (tm-30) REVERT: C 819 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 825 LYS cc_start: 0.8435 (tppt) cc_final: 0.8139 (ttmm) REVERT: C 868 GLU cc_start: 0.7859 (tp30) cc_final: 0.7448 (tp30) REVERT: C 904 TYR cc_start: 0.7159 (m-10) cc_final: 0.6842 (m-10) REVERT: C 921 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8334 (mmmm) REVERT: C 933 LYS cc_start: 0.7880 (mtpt) cc_final: 0.7524 (mttp) REVERT: C 984 LEU cc_start: 0.8046 (mp) cc_final: 0.7771 (mt) REVERT: C 1018 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8100 (mt) REVERT: C 1038 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8391 (mtpp) outliers start: 161 outliers final: 84 residues processed: 747 average time/residue: 0.1620 time to fit residues: 190.0240 Evaluate side-chains 726 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 625 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 135 optimal weight: 7.9990 chunk 236 optimal weight: 0.0970 chunk 245 optimal weight: 0.9990 chunk 304 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1101 HIS B 239 GLN B 422 ASN B 895 GLN C 30 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 450 ASN C 505 HIS C 544 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.143066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116828 restraints weight = 40120.415| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.68 r_work: 0.3391 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25107 Z= 0.176 Angle : 0.631 10.681 34257 Z= 0.320 Chirality : 0.047 0.341 3957 Planarity : 0.005 0.062 4379 Dihedral : 7.290 90.889 4007 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 5.62 % Allowed : 19.72 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.14), residues: 3044 helix: 1.00 (0.22), residues: 637 sheet: -1.99 (0.21), residues: 533 loop : -2.87 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 498 TYR 0.021 0.002 TYR B 707 PHE 0.025 0.002 PHE C1121 TRP 0.016 0.001 TRP C 353 HIS 0.006 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00390 (25040) covalent geometry : angle 0.61243 (34095) SS BOND : bond 0.00583 ( 39) SS BOND : angle 2.53120 ( 78) hydrogen bonds : bond 0.03930 ( 695) hydrogen bonds : angle 4.93115 ( 1938) link_NAG-ASN : bond 0.00432 ( 28) link_NAG-ASN : angle 1.98965 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 655 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7285 (m-10) cc_final: 0.7015 (m-10) REVERT: A 91 TYR cc_start: 0.7831 (t80) cc_final: 0.7529 (t80) REVERT: A 102 ARG cc_start: 0.7543 (mtm-85) cc_final: 0.6980 (mtm-85) REVERT: A 104 TRP cc_start: 0.7875 (OUTLIER) cc_final: 0.7331 (m-90) REVERT: A 129 LYS cc_start: 0.7978 (mtmm) cc_final: 0.7366 (mtmm) REVERT: A 188 ARG cc_start: 0.7948 (ptp-110) cc_final: 0.7473 (ptp90) REVERT: A 189 GLU cc_start: 0.8184 (pm20) cc_final: 0.7882 (pt0) REVERT: A 190 PHE cc_start: 0.8369 (m-80) cc_final: 0.8031 (m-10) REVERT: A 214 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6250 (mt-10) REVERT: A 224 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6642 (mm-30) REVERT: A 267 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8154 (p) REVERT: A 269 TYR cc_start: 0.8284 (m-80) cc_final: 0.8040 (m-80) REVERT: A 307 THR cc_start: 0.8372 (m) cc_final: 0.8018 (p) REVERT: A 340 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6394 (pm20) REVERT: A 355 ARG cc_start: 0.6853 (ttm170) cc_final: 0.6605 (ttm-80) REVERT: A 358 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6609 (pt) REVERT: A 380 TYR cc_start: 0.7328 (m-80) cc_final: 0.6800 (m-10) REVERT: A 386 LYS cc_start: 0.8326 (mttp) cc_final: 0.8069 (mttt) REVERT: A 396 TYR cc_start: 0.7702 (m-80) cc_final: 0.7364 (m-80) REVERT: A 436 TRP cc_start: 0.6648 (p90) cc_final: 0.5908 (p90) REVERT: A 542 ASN cc_start: 0.9023 (t0) cc_final: 0.8799 (t0) REVERT: A 558 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7960 (mtpp) REVERT: A 564 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7349 (tm-30) REVERT: A 569 ILE cc_start: 0.8011 (pt) cc_final: 0.7795 (mp) REVERT: A 643 PHE cc_start: 0.8363 (t80) cc_final: 0.8144 (t80) REVERT: A 654 GLU cc_start: 0.7394 (pm20) cc_final: 0.7105 (pm20) REVERT: A 670 ILE cc_start: 0.8442 (mm) cc_final: 0.8239 (mp) REVERT: A 675 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7134 (mm-40) REVERT: A 707 TYR cc_start: 0.8036 (t80) cc_final: 0.7808 (t80) REVERT: A 731 MET cc_start: 0.8225 (mtp) cc_final: 0.7895 (mtm) REVERT: A 745 ASP cc_start: 0.7289 (m-30) cc_final: 0.7013 (p0) REVERT: A 751 ASN cc_start: 0.8312 (m-40) cc_final: 0.8042 (m-40) REVERT: A 768 THR cc_start: 0.8416 (m) cc_final: 0.8153 (p) REVERT: A 820 ASP cc_start: 0.8178 (m-30) cc_final: 0.7923 (m-30) REVERT: A 855 PHE cc_start: 0.8212 (m-80) cc_final: 0.7558 (m-80) REVERT: A 868 GLU cc_start: 0.7890 (tp30) cc_final: 0.7605 (tp30) REVERT: A 869 MET cc_start: 0.8448 (mtt) cc_final: 0.8238 (mtm) REVERT: A 949 GLN cc_start: 0.8078 (mm110) cc_final: 0.7554 (mm-40) REVERT: A 954 HIS cc_start: 0.7582 (m-70) cc_final: 0.7369 (m170) REVERT: A 969 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7961 (mtmm) REVERT: A 970 PHE cc_start: 0.7583 (m-10) cc_final: 0.7333 (m-10) REVERT: A 998 THR cc_start: 0.8151 (m) cc_final: 0.7909 (p) REVERT: A 1017 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7454 (tm-30) REVERT: A 1030 SER cc_start: 0.8649 (m) cc_final: 0.8238 (t) REVERT: A 1097 SER cc_start: 0.8636 (t) cc_final: 0.8141 (p) REVERT: A 1102 TRP cc_start: 0.8760 (m100) cc_final: 0.8089 (m100) REVERT: A 1103 PHE cc_start: 0.8484 (m-10) cc_final: 0.8084 (m-80) REVERT: A 1135 ASN cc_start: 0.8144 (t0) cc_final: 0.7732 (t0) REVERT: B 53 ASP cc_start: 0.7397 (t0) cc_final: 0.7169 (t0) REVERT: B 105 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7574 (pt) REVERT: B 106 PHE cc_start: 0.7960 (m-80) cc_final: 0.7626 (m-10) REVERT: B 169 GLU cc_start: 0.7937 (pm20) cc_final: 0.7377 (pm20) REVERT: B 177 MET cc_start: 0.6827 (tmt) cc_final: 0.6257 (tmt) REVERT: B 188 ARG cc_start: 0.6833 (ttm-80) cc_final: 0.6625 (ttm-80) REVERT: B 201 ILE cc_start: 0.8516 (mt) cc_final: 0.7982 (tt) REVERT: B 204 LYS cc_start: 0.8662 (tttp) cc_final: 0.8425 (tttp) REVERT: B 224 GLU cc_start: 0.6823 (pm20) cc_final: 0.6553 (pm20) REVERT: B 279 TYR cc_start: 0.8334 (m-10) cc_final: 0.8091 (m-10) REVERT: B 290 ASP cc_start: 0.7842 (t70) cc_final: 0.7610 (t0) REVERT: B 319 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7597 (ttm110) REVERT: B 362 VAL cc_start: 0.7757 (OUTLIER) cc_final: 0.7462 (p) REVERT: B 537 LYS cc_start: 0.8328 (tttp) cc_final: 0.7932 (tttm) REVERT: B 557 LYS cc_start: 0.8587 (ptpp) cc_final: 0.8253 (ptpt) REVERT: B 558 LYS cc_start: 0.8560 (mppt) cc_final: 0.8103 (mppt) REVERT: B 564 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8359 (mm110) REVERT: B 589 PRO cc_start: 0.8677 (Cg_exo) cc_final: 0.8247 (Cg_endo) REVERT: B 604 THR cc_start: 0.8601 (p) cc_final: 0.8256 (t) REVERT: B 663 ASP cc_start: 0.7865 (m-30) cc_final: 0.7651 (m-30) REVERT: B 698 SER cc_start: 0.8393 (t) cc_final: 0.7941 (p) REVERT: B 703 ASN cc_start: 0.8619 (t0) cc_final: 0.8104 (m-40) REVERT: B 711 SER cc_start: 0.8653 (t) cc_final: 0.8386 (t) REVERT: B 752 LEU cc_start: 0.8758 (mt) cc_final: 0.8490 (mp) REVERT: B 773 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7125 (tm-30) REVERT: B 810 SER cc_start: 0.8675 (t) cc_final: 0.8463 (p) REVERT: B 821 LEU cc_start: 0.8803 (tp) cc_final: 0.8351 (tt) REVERT: B 904 TYR cc_start: 0.7474 (m-80) cc_final: 0.7064 (m-80) REVERT: B 914 ASN cc_start: 0.8344 (p0) cc_final: 0.7930 (p0) REVERT: B 918 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7501 (mt-10) REVERT: B 933 LYS cc_start: 0.7383 (mtpp) cc_final: 0.7119 (mtpp) REVERT: B 950 ASP cc_start: 0.7668 (t70) cc_final: 0.7337 (t70) REVERT: B 957 GLN cc_start: 0.8226 (tt0) cc_final: 0.7973 (tt0) REVERT: B 975 SER cc_start: 0.8723 (m) cc_final: 0.8298 (t) REVERT: B 984 LEU cc_start: 0.8321 (tp) cc_final: 0.8028 (tp) REVERT: B 990 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: B 993 ILE cc_start: 0.8696 (tp) cc_final: 0.8460 (tp) REVERT: B 1029 MET cc_start: 0.8544 (tpp) cc_final: 0.7731 (tpp) REVERT: B 1033 VAL cc_start: 0.8866 (t) cc_final: 0.8536 (p) REVERT: B 1038 LYS cc_start: 0.8838 (mtpp) cc_final: 0.8613 (mtpp) REVERT: B 1084 ASP cc_start: 0.7904 (t0) cc_final: 0.7599 (t0) REVERT: B 1097 SER cc_start: 0.8942 (t) cc_final: 0.8318 (p) REVERT: B 1107 ARG cc_start: 0.7863 (ptt-90) cc_final: 0.7332 (ptt180) REVERT: C 81 ASN cc_start: 0.8241 (m110) cc_final: 0.7973 (m-40) REVERT: C 105 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7702 (mm) REVERT: C 106 PHE cc_start: 0.7732 (m-80) cc_final: 0.7449 (m-10) REVERT: C 160 TYR cc_start: 0.7323 (p90) cc_final: 0.7084 (p90) REVERT: C 187 LEU cc_start: 0.8232 (tp) cc_final: 0.7938 (tp) REVERT: C 188 ARG cc_start: 0.7706 (ptp-170) cc_final: 0.7346 (ptp-170) REVERT: C 204 LYS cc_start: 0.8527 (tmtt) cc_final: 0.8278 (tttp) REVERT: C 224 GLU cc_start: 0.7453 (pm20) cc_final: 0.7006 (mp0) REVERT: C 327 VAL cc_start: 0.8681 (m) cc_final: 0.8265 (t) REVERT: C 349 SER cc_start: 0.8305 (p) cc_final: 0.7934 (t) REVERT: C 377 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7711 (t80) REVERT: C 427 ASP cc_start: 0.7089 (t70) cc_final: 0.6703 (t70) REVERT: C 461 LEU cc_start: 0.7984 (mt) cc_final: 0.7730 (mm) REVERT: C 465 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7378 (tm-30) REVERT: C 588 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8344 (p) REVERT: C 641 ASN cc_start: 0.6659 (t0) cc_final: 0.6396 (t0) REVERT: C 643 PHE cc_start: 0.8229 (t80) cc_final: 0.7860 (t80) REVERT: C 707 TYR cc_start: 0.7930 (t80) cc_final: 0.7106 (t80) REVERT: C 745 ASP cc_start: 0.7540 (m-30) cc_final: 0.7258 (p0) REVERT: C 751 ASN cc_start: 0.8010 (m-40) cc_final: 0.7660 (m-40) REVERT: C 752 LEU cc_start: 0.8891 (mm) cc_final: 0.8431 (mt) REVERT: C 755 GLN cc_start: 0.8003 (pp30) cc_final: 0.7440 (pp30) REVERT: C 776 LYS cc_start: 0.8586 (ttpt) cc_final: 0.8286 (tttp) REVERT: C 779 GLN cc_start: 0.7857 (tt0) cc_final: 0.7587 (tm-30) REVERT: C 804 GLN cc_start: 0.8111 (mt0) cc_final: 0.7874 (mt0) REVERT: C 819 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7553 (mt-10) REVERT: C 825 LYS cc_start: 0.8486 (tppt) cc_final: 0.8159 (tppt) REVERT: C 868 GLU cc_start: 0.7868 (tp30) cc_final: 0.7517 (tp30) REVERT: C 921 LYS cc_start: 0.8745 (mmmt) cc_final: 0.8438 (mmmm) REVERT: C 984 LEU cc_start: 0.8081 (mp) cc_final: 0.7796 (mt) REVERT: C 1066 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7808 (p) REVERT: C 1073 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8194 (mtmt) REVERT: C 1139 ASP cc_start: 0.8234 (t0) cc_final: 0.8029 (t0) outliers start: 150 outliers final: 96 residues processed: 743 average time/residue: 0.1618 time to fit residues: 188.8637 Evaluate side-chains 723 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 614 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 257 optimal weight: 0.7980 chunk 267 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 218 optimal weight: 0.0970 chunk 281 optimal weight: 0.9980 chunk 94 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 287 optimal weight: 0.3980 chunk 147 optimal weight: 5.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 580 GLN A1011 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B 992 GLN C 30 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** 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 = 0.3897 r_free = 0.3897 target = 0.145408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119141 restraints weight = 39973.625| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.71 r_work: 0.3415 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25107 Z= 0.112 Angle : 0.592 11.245 34257 Z= 0.298 Chirality : 0.046 0.315 3957 Planarity : 0.004 0.067 4379 Dihedral : 6.947 90.581 3999 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.84 % Allowed : 21.15 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.15), residues: 3044 helix: 1.18 (0.21), residues: 645 sheet: -1.84 (0.20), residues: 552 loop : -2.74 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1014 TYR 0.023 0.001 TYR B 707 PHE 0.026 0.001 PHE A 86 TRP 0.008 0.001 TRP C 353 HIS 0.007 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00250 (25040) covalent geometry : angle 0.58083 (34095) SS BOND : bond 0.00378 ( 39) SS BOND : angle 1.57788 ( 78) hydrogen bonds : bond 0.03437 ( 695) hydrogen bonds : angle 4.75935 ( 1938) link_NAG-ASN : bond 0.00418 ( 28) link_NAG-ASN : angle 1.86665 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 639 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7241 (m-10) cc_final: 0.6937 (m-10) REVERT: A 91 TYR cc_start: 0.7786 (t80) cc_final: 0.7241 (t80) REVERT: A 102 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.6932 (mtm-85) REVERT: A 104 TRP cc_start: 0.7897 (OUTLIER) cc_final: 0.7497 (m-90) REVERT: A 129 LYS cc_start: 0.8037 (mtmm) cc_final: 0.7381 (mtmm) REVERT: A 188 ARG cc_start: 0.7912 (ptp-110) cc_final: 0.7437 (ptp90) REVERT: A 189 GLU cc_start: 0.8191 (pm20) cc_final: 0.7894 (pt0) REVERT: A 214 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.5736 (mt-10) REVERT: A 224 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6703 (mm-30) REVERT: A 267 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8188 (p) REVERT: A 269 TYR cc_start: 0.8264 (m-80) cc_final: 0.7922 (m-10) REVERT: A 307 THR cc_start: 0.8353 (m) cc_final: 0.8028 (p) REVERT: A 355 ARG cc_start: 0.6892 (ttm170) cc_final: 0.6664 (ttm-80) REVERT: A 356 LYS cc_start: 0.7459 (ptmm) cc_final: 0.7241 (pttm) REVERT: A 380 TYR cc_start: 0.7325 (m-80) cc_final: 0.6777 (m-10) REVERT: A 386 LYS cc_start: 0.8334 (mttp) cc_final: 0.7753 (mtmm) REVERT: A 409 GLN cc_start: 0.6684 (OUTLIER) cc_final: 0.6115 (pp30) REVERT: A 452 LEU cc_start: 0.7950 (tt) cc_final: 0.7724 (tp) REVERT: A 542 ASN cc_start: 0.8977 (t0) cc_final: 0.8769 (t0) REVERT: A 558 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7969 (mtpp) REVERT: A 564 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7388 (tm-30) REVERT: A 569 ILE cc_start: 0.8005 (pt) cc_final: 0.7791 (mp) REVERT: A 586 ASP cc_start: 0.7546 (t0) cc_final: 0.7220 (m-30) REVERT: A 654 GLU cc_start: 0.7448 (pm20) cc_final: 0.7147 (pm20) REVERT: A 656 VAL cc_start: 0.8617 (p) cc_final: 0.8404 (m) REVERT: A 675 GLN cc_start: 0.7452 (mm-40) cc_final: 0.7071 (mm-40) REVERT: A 707 TYR cc_start: 0.7968 (t80) cc_final: 0.7765 (t80) REVERT: A 745 ASP cc_start: 0.7225 (m-30) cc_final: 0.6927 (p0) REVERT: A 768 THR cc_start: 0.8352 (m) cc_final: 0.8102 (p) REVERT: A 774 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7331 (mp10) REVERT: A 851 CYS cc_start: 0.7945 (t) cc_final: 0.7330 (p) REVERT: A 855 PHE cc_start: 0.8143 (m-80) cc_final: 0.7478 (m-80) REVERT: A 868 GLU cc_start: 0.7805 (tp30) cc_final: 0.7533 (tp30) REVERT: A 905 ARG cc_start: 0.8512 (mtt-85) cc_final: 0.8288 (mtt-85) REVERT: A 949 GLN cc_start: 0.8056 (mm110) cc_final: 0.7565 (mm-40) REVERT: A 969 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7872 (mtmm) REVERT: A 970 PHE cc_start: 0.7442 (m-10) cc_final: 0.7240 (m-10) REVERT: A 997 ILE cc_start: 0.8751 (mm) cc_final: 0.8535 (mt) REVERT: A 998 THR cc_start: 0.8120 (m) cc_final: 0.7892 (p) REVERT: A 1017 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7454 (tm-30) REVERT: A 1030 SER cc_start: 0.8676 (m) cc_final: 0.8405 (p) REVERT: A 1097 SER cc_start: 0.8599 (t) cc_final: 0.8159 (p) REVERT: A 1102 TRP cc_start: 0.8724 (m100) cc_final: 0.8282 (m100) REVERT: B 106 PHE cc_start: 0.7870 (m-80) cc_final: 0.7658 (m-10) REVERT: B 129 LYS cc_start: 0.8094 (tppt) cc_final: 0.7323 (tppt) REVERT: B 169 GLU cc_start: 0.7859 (pm20) cc_final: 0.7269 (pm20) REVERT: B 177 MET cc_start: 0.6830 (tmt) cc_final: 0.6307 (tmt) REVERT: B 190 PHE cc_start: 0.8321 (m-10) cc_final: 0.8087 (m-10) REVERT: B 198 TYR cc_start: 0.6425 (OUTLIER) cc_final: 0.6174 (m-80) REVERT: B 204 LYS cc_start: 0.8592 (tttp) cc_final: 0.8342 (tttp) REVERT: B 224 GLU cc_start: 0.6716 (pm20) cc_final: 0.6454 (pm20) REVERT: B 279 TYR cc_start: 0.8302 (m-10) cc_final: 0.8060 (m-10) REVERT: B 290 ASP cc_start: 0.7803 (t70) cc_final: 0.7475 (t0) REVERT: B 319 ARG cc_start: 0.7829 (ttm110) cc_final: 0.7629 (ttm110) REVERT: B 406 GLU cc_start: 0.7618 (mt-10) cc_final: 0.6578 (tt0) REVERT: B 528 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8321 (mmmt) REVERT: B 537 LYS cc_start: 0.8284 (tttp) cc_final: 0.8021 (tttp) REVERT: B 557 LYS cc_start: 0.8532 (ptpp) cc_final: 0.8227 (ptpt) REVERT: B 558 LYS cc_start: 0.8518 (mppt) cc_final: 0.8079 (mppt) REVERT: B 564 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8330 (mm110) REVERT: B 580 GLN cc_start: 0.8169 (mm110) cc_final: 0.7950 (mm110) REVERT: B 589 PRO cc_start: 0.8618 (Cg_exo) cc_final: 0.8136 (Cg_endo) REVERT: B 604 THR cc_start: 0.8645 (p) cc_final: 0.8303 (t) REVERT: B 703 ASN cc_start: 0.8599 (t0) cc_final: 0.8111 (m-40) REVERT: B 711 SER cc_start: 0.8699 (t) cc_final: 0.8444 (t) REVERT: B 752 LEU cc_start: 0.8720 (mt) cc_final: 0.8432 (mp) REVERT: B 773 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7079 (tm-30) REVERT: B 774 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7543 (mm-40) REVERT: B 810 SER cc_start: 0.8671 (t) cc_final: 0.8460 (p) REVERT: B 821 LEU cc_start: 0.8792 (tp) cc_final: 0.8354 (tt) REVERT: B 904 TYR cc_start: 0.7512 (m-80) cc_final: 0.7234 (m-80) REVERT: B 914 ASN cc_start: 0.8360 (p0) cc_final: 0.7885 (p0) REVERT: B 918 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7506 (mt-10) REVERT: B 950 ASP cc_start: 0.7658 (t70) cc_final: 0.7351 (t70) REVERT: B 957 GLN cc_start: 0.8165 (tt0) cc_final: 0.7899 (tt0) REVERT: B 975 SER cc_start: 0.8683 (m) cc_final: 0.8244 (t) REVERT: B 984 LEU cc_start: 0.8328 (tp) cc_final: 0.7963 (mp) REVERT: B 990 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: B 993 ILE cc_start: 0.8666 (tp) cc_final: 0.8290 (tp) REVERT: B 1033 VAL cc_start: 0.8854 (t) cc_final: 0.8570 (p) REVERT: B 1038 LYS cc_start: 0.8838 (mtpp) cc_final: 0.8562 (mtpp) REVERT: B 1084 ASP cc_start: 0.7975 (t0) cc_final: 0.7595 (t0) REVERT: B 1097 SER cc_start: 0.8912 (t) cc_final: 0.8278 (p) REVERT: B 1107 ARG cc_start: 0.7815 (ptt-90) cc_final: 0.7396 (ptp-170) REVERT: C 53 ASP cc_start: 0.7522 (t0) cc_final: 0.7226 (t0) REVERT: C 81 ASN cc_start: 0.8222 (m110) cc_final: 0.7918 (m-40) REVERT: C 105 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7681 (mm) REVERT: C 106 PHE cc_start: 0.7712 (m-80) cc_final: 0.7423 (m-10) REVERT: C 160 TYR cc_start: 0.7326 (p90) cc_final: 0.7077 (p90) REVERT: C 187 LEU cc_start: 0.8156 (tp) cc_final: 0.7440 (tt) REVERT: C 188 ARG cc_start: 0.7660 (ptp-170) cc_final: 0.7345 (ptp-170) REVERT: C 204 LYS cc_start: 0.8510 (tmtt) cc_final: 0.8210 (tttp) REVERT: C 224 GLU cc_start: 0.7449 (pm20) cc_final: 0.7171 (mp0) REVERT: C 284 THR cc_start: 0.8389 (t) cc_final: 0.8097 (p) REVERT: C 327 VAL cc_start: 0.8629 (m) cc_final: 0.8191 (t) REVERT: C 414 GLN cc_start: 0.7409 (mp10) cc_final: 0.7117 (mp10) REVERT: C 427 ASP cc_start: 0.7004 (t70) cc_final: 0.6646 (t70) REVERT: C 465 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7613 (tm-30) REVERT: C 588 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8304 (p) REVERT: C 643 PHE cc_start: 0.8157 (t80) cc_final: 0.7780 (t80) REVERT: C 656 VAL cc_start: 0.8659 (p) cc_final: 0.8458 (m) REVERT: C 707 TYR cc_start: 0.7927 (t80) cc_final: 0.7028 (t80) REVERT: C 745 ASP cc_start: 0.7486 (m-30) cc_final: 0.7240 (p0) REVERT: C 752 LEU cc_start: 0.8907 (mm) cc_final: 0.8371 (mt) REVERT: C 755 GLN cc_start: 0.7959 (pp30) cc_final: 0.7281 (pp30) REVERT: C 759 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7237 (t80) REVERT: C 776 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8295 (tttp) REVERT: C 779 GLN cc_start: 0.7863 (tt0) cc_final: 0.7639 (tm-30) REVERT: C 819 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7499 (mt-10) REVERT: C 825 LYS cc_start: 0.8427 (tppt) cc_final: 0.8101 (tppt) REVERT: C 868 GLU cc_start: 0.7880 (tp30) cc_final: 0.7569 (tp30) REVERT: C 900 MET cc_start: 0.8291 (mtp) cc_final: 0.8000 (mtp) REVERT: C 921 LYS cc_start: 0.8717 (mmmt) cc_final: 0.8292 (mmmm) REVERT: C 927 PHE cc_start: 0.8739 (t80) cc_final: 0.8280 (t80) REVERT: C 1073 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8073 (mtpp) REVERT: C 1107 ARG cc_start: 0.7283 (tpp80) cc_final: 0.6722 (mmm-85) outliers start: 129 outliers final: 81 residues processed: 724 average time/residue: 0.1741 time to fit residues: 195.4389 Evaluate side-chains 693 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 602 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 196 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 185 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 285 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 580 GLN A 751 ASN A 955 ASN A1083 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 935 GLN B 965 GLN C 30 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.143215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117046 restraints weight = 40035.597| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.71 r_work: 0.3390 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25107 Z= 0.148 Angle : 0.618 9.793 34257 Z= 0.313 Chirality : 0.047 0.335 3957 Planarity : 0.004 0.069 4379 Dihedral : 6.838 90.777 3986 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 5.17 % Allowed : 21.07 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.15), residues: 3044 helix: 1.12 (0.21), residues: 651 sheet: -1.73 (0.21), residues: 547 loop : -2.66 (0.13), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 509 TYR 0.025 0.001 TYR B 707 PHE 0.029 0.001 PHE A 86 TRP 0.011 0.001 TRP C 353 HIS 0.010 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00328 (25040) covalent geometry : angle 0.60597 (34095) SS BOND : bond 0.00376 ( 39) SS BOND : angle 1.85388 ( 78) hydrogen bonds : bond 0.03655 ( 695) hydrogen bonds : angle 4.76935 ( 1938) link_NAG-ASN : bond 0.00400 ( 28) link_NAG-ASN : angle 1.91544 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 630 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7282 (m-10) cc_final: 0.7050 (m-10) REVERT: A 91 TYR cc_start: 0.7491 (t80) cc_final: 0.7137 (t80) REVERT: A 102 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.6975 (mtm-85) REVERT: A 104 TRP cc_start: 0.7906 (OUTLIER) cc_final: 0.7298 (m-90) REVERT: A 129 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7339 (mtmm) REVERT: A 169 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: A 188 ARG cc_start: 0.7962 (ptp-110) cc_final: 0.7545 (ptp90) REVERT: A 189 GLU cc_start: 0.8168 (pm20) cc_final: 0.7869 (pt0) REVERT: A 190 PHE cc_start: 0.8386 (m-80) cc_final: 0.8155 (m-10) REVERT: A 224 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6780 (mm-30) REVERT: A 267 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8165 (p) REVERT: A 269 TYR cc_start: 0.8252 (m-80) cc_final: 0.7899 (m-10) REVERT: A 307 THR cc_start: 0.8410 (m) cc_final: 0.8091 (p) REVERT: A 355 ARG cc_start: 0.7086 (ttm170) cc_final: 0.6824 (ttm-80) REVERT: A 380 TYR cc_start: 0.7345 (m-80) cc_final: 0.7000 (m-10) REVERT: A 386 LYS cc_start: 0.8382 (mttp) cc_final: 0.7809 (mtmm) REVERT: A 537 LYS cc_start: 0.7777 (mtpt) cc_final: 0.7575 (mtpp) REVERT: A 542 ASN cc_start: 0.8991 (t0) cc_final: 0.8750 (t0) REVERT: A 558 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7982 (mtpp) REVERT: A 564 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7372 (tm-30) REVERT: A 586 ASP cc_start: 0.7505 (t0) cc_final: 0.7228 (m-30) REVERT: A 654 GLU cc_start: 0.7513 (pm20) cc_final: 0.7192 (pm20) REVERT: A 656 VAL cc_start: 0.8640 (p) cc_final: 0.8438 (m) REVERT: A 675 GLN cc_start: 0.7446 (mm-40) cc_final: 0.7060 (mm-40) REVERT: A 707 TYR cc_start: 0.8006 (t80) cc_final: 0.7766 (t80) REVERT: A 745 ASP cc_start: 0.7212 (m-30) cc_final: 0.6966 (p0) REVERT: A 768 THR cc_start: 0.8375 (m) cc_final: 0.8132 (p) REVERT: A 774 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7332 (mp10) REVERT: A 855 PHE cc_start: 0.8181 (m-80) cc_final: 0.7527 (m-80) REVERT: A 868 GLU cc_start: 0.7827 (tp30) cc_final: 0.7549 (tp30) REVERT: A 949 GLN cc_start: 0.8115 (mm110) cc_final: 0.7648 (mm-40) REVERT: A 970 PHE cc_start: 0.7604 (m-10) cc_final: 0.7323 (m-10) REVERT: A 995 ARG cc_start: 0.7943 (ttm170) cc_final: 0.7679 (ttm170) REVERT: A 998 THR cc_start: 0.8172 (m) cc_final: 0.7919 (p) REVERT: A 1017 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7460 (tm-30) REVERT: A 1029 MET cc_start: 0.8606 (tpp) cc_final: 0.8335 (ttm) REVERT: A 1030 SER cc_start: 0.8688 (m) cc_final: 0.8332 (t) REVERT: B 106 PHE cc_start: 0.8011 (m-80) cc_final: 0.7768 (m-10) REVERT: B 129 LYS cc_start: 0.8057 (tppt) cc_final: 0.7267 (tppt) REVERT: B 169 GLU cc_start: 0.7919 (pm20) cc_final: 0.7326 (pm20) REVERT: B 177 MET cc_start: 0.6791 (tmt) cc_final: 0.6337 (tmt) REVERT: B 188 ARG cc_start: 0.6888 (ttm-80) cc_final: 0.6626 (ttm-80) REVERT: B 204 LYS cc_start: 0.8644 (tttp) cc_final: 0.8243 (tttp) REVERT: B 224 GLU cc_start: 0.6781 (pm20) cc_final: 0.6421 (pm20) REVERT: B 279 TYR cc_start: 0.8262 (m-10) cc_final: 0.8019 (m-10) REVERT: B 362 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7602 (p) REVERT: B 406 GLU cc_start: 0.7567 (mt-10) cc_final: 0.6648 (tt0) REVERT: B 528 LYS cc_start: 0.8662 (mmmm) cc_final: 0.8432 (mmmt) REVERT: B 537 LYS cc_start: 0.8332 (tttp) cc_final: 0.8072 (tttp) REVERT: B 547 LYS cc_start: 0.8111 (mttp) cc_final: 0.7901 (mmtm) REVERT: B 557 LYS cc_start: 0.8567 (ptpp) cc_final: 0.8257 (ptpt) REVERT: B 558 LYS cc_start: 0.8522 (mppt) cc_final: 0.8096 (mppt) REVERT: B 580 GLN cc_start: 0.8217 (mm110) cc_final: 0.7988 (mm110) REVERT: B 589 PRO cc_start: 0.8556 (Cg_exo) cc_final: 0.7943 (Cg_endo) REVERT: B 604 THR cc_start: 0.8662 (p) cc_final: 0.8337 (t) REVERT: B 643 PHE cc_start: 0.8159 (t80) cc_final: 0.7920 (t80) REVERT: B 703 ASN cc_start: 0.8641 (t0) cc_final: 0.8158 (m-40) REVERT: B 711 SER cc_start: 0.8680 (t) cc_final: 0.8387 (t) REVERT: B 752 LEU cc_start: 0.8732 (mt) cc_final: 0.8452 (mp) REVERT: B 773 GLU cc_start: 0.7749 (tm-30) cc_final: 0.6988 (tm-30) REVERT: B 774 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7525 (mm-40) REVERT: B 810 SER cc_start: 0.8717 (t) cc_final: 0.8494 (p) REVERT: B 821 LEU cc_start: 0.8783 (tp) cc_final: 0.8331 (tt) REVERT: B 904 TYR cc_start: 0.7553 (m-80) cc_final: 0.7178 (m-80) REVERT: B 907 ASN cc_start: 0.8549 (t0) cc_final: 0.8317 (t0) REVERT: B 914 ASN cc_start: 0.8390 (p0) cc_final: 0.7961 (p0) REVERT: B 918 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 935 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7575 (tp-100) REVERT: B 950 ASP cc_start: 0.7685 (t70) cc_final: 0.7381 (t70) REVERT: B 957 GLN cc_start: 0.8197 (tt0) cc_final: 0.7931 (tt0) REVERT: B 975 SER cc_start: 0.8695 (m) cc_final: 0.8253 (t) REVERT: B 984 LEU cc_start: 0.8301 (tp) cc_final: 0.7973 (tp) REVERT: B 988 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7002 (tp30) REVERT: B 990 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: B 991 VAL cc_start: 0.8770 (t) cc_final: 0.8524 (p) REVERT: B 993 ILE cc_start: 0.8752 (tp) cc_final: 0.8475 (tp) REVERT: B 1029 MET cc_start: 0.8573 (tpp) cc_final: 0.7817 (tpp) REVERT: B 1033 VAL cc_start: 0.8870 (t) cc_final: 0.8628 (p) REVERT: B 1038 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8599 (mtpp) REVERT: B 1084 ASP cc_start: 0.7966 (t0) cc_final: 0.7728 (t70) REVERT: B 1097 SER cc_start: 0.8905 (t) cc_final: 0.8297 (p) REVERT: C 53 ASP cc_start: 0.7527 (t0) cc_final: 0.7229 (t0) REVERT: C 105 ILE cc_start: 0.8032 (mm) cc_final: 0.7656 (mm) REVERT: C 106 PHE cc_start: 0.7706 (m-80) cc_final: 0.7405 (m-10) REVERT: C 160 TYR cc_start: 0.7381 (p90) cc_final: 0.7105 (p90) REVERT: C 188 ARG cc_start: 0.7679 (ptp-170) cc_final: 0.7358 (ptp-170) REVERT: C 204 LYS cc_start: 0.8533 (tmtt) cc_final: 0.8300 (tttp) REVERT: C 284 THR cc_start: 0.8407 (t) cc_final: 0.8120 (p) REVERT: C 327 VAL cc_start: 0.8643 (m) cc_final: 0.8220 (t) REVERT: C 414 GLN cc_start: 0.7500 (mp10) cc_final: 0.7023 (mp10) REVERT: C 465 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7570 (tm-30) REVERT: C 537 LYS cc_start: 0.8226 (mmmm) cc_final: 0.8010 (mtpt) REVERT: C 565 PHE cc_start: 0.7173 (m-10) cc_final: 0.6821 (m-10) REVERT: C 588 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8261 (p) REVERT: C 643 PHE cc_start: 0.8192 (t80) cc_final: 0.7956 (t80) REVERT: C 655 TYR cc_start: 0.8065 (t80) cc_final: 0.7862 (t80) REVERT: C 656 VAL cc_start: 0.8661 (p) cc_final: 0.8435 (m) REVERT: C 707 TYR cc_start: 0.7976 (t80) cc_final: 0.7058 (t80) REVERT: C 724 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8507 (p) REVERT: C 752 LEU cc_start: 0.8714 (mm) cc_final: 0.8470 (mt) REVERT: C 755 GLN cc_start: 0.7957 (pp30) cc_final: 0.7309 (pp30) REVERT: C 759 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.7186 (t80) REVERT: C 776 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8335 (tttp) REVERT: C 819 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7539 (mt-10) REVERT: C 825 LYS cc_start: 0.8467 (tppt) cc_final: 0.8149 (tppt) REVERT: C 868 GLU cc_start: 0.7874 (tp30) cc_final: 0.7568 (tp30) REVERT: C 869 MET cc_start: 0.8152 (mmm) cc_final: 0.7931 (mmm) REVERT: C 921 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8427 (mmmm) REVERT: C 927 PHE cc_start: 0.8793 (t80) cc_final: 0.8291 (t80) REVERT: C 1038 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8405 (mmtt) REVERT: C 1066 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7781 (p) REVERT: C 1073 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8089 (mtpp) outliers start: 138 outliers final: 89 residues processed: 717 average time/residue: 0.1637 time to fit residues: 183.2120 Evaluate side-chains 715 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 615 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 111 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 155 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 751 ASN A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 30 ASN C 52 GLN C 81 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.142728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116853 restraints weight = 39817.714| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.66 r_work: 0.3379 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25107 Z= 0.154 Angle : 0.630 10.406 34257 Z= 0.319 Chirality : 0.048 0.333 3957 Planarity : 0.004 0.068 4379 Dihedral : 6.880 91.149 3983 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 4.87 % Allowed : 21.82 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.15), residues: 3044 helix: 1.13 (0.21), residues: 651 sheet: -1.61 (0.21), residues: 559 loop : -2.61 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1014 TYR 0.025 0.001 TYR B 707 PHE 0.032 0.002 PHE A 275 TRP 0.012 0.001 TRP C 353 HIS 0.011 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00346 (25040) covalent geometry : angle 0.61505 (34095) SS BOND : bond 0.00393 ( 39) SS BOND : angle 2.15629 ( 78) hydrogen bonds : bond 0.03678 ( 695) hydrogen bonds : angle 4.79963 ( 1938) link_NAG-ASN : bond 0.00392 ( 28) link_NAG-ASN : angle 1.93618 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 620 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7273 (m-10) cc_final: 0.7052 (m-10) REVERT: A 91 TYR cc_start: 0.7487 (t80) cc_final: 0.7270 (t80) REVERT: A 102 ARG cc_start: 0.7525 (mtm-85) cc_final: 0.6982 (mtm-85) REVERT: A 104 TRP cc_start: 0.7884 (OUTLIER) cc_final: 0.7297 (m-90) REVERT: A 129 LYS cc_start: 0.8012 (mtmm) cc_final: 0.7381 (mtmm) REVERT: A 169 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6957 (pm20) REVERT: A 188 ARG cc_start: 0.7863 (ptp-110) cc_final: 0.7570 (ptp90) REVERT: A 189 GLU cc_start: 0.8136 (pm20) cc_final: 0.7604 (mt-10) REVERT: A 190 PHE cc_start: 0.8393 (m-80) cc_final: 0.8158 (m-10) REVERT: A 224 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6855 (mm-30) REVERT: A 269 TYR cc_start: 0.8256 (m-80) cc_final: 0.7883 (m-10) REVERT: A 307 THR cc_start: 0.8446 (m) cc_final: 0.8135 (p) REVERT: A 340 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6613 (pm20) REVERT: A 380 TYR cc_start: 0.7346 (m-80) cc_final: 0.7008 (m-10) REVERT: A 386 LYS cc_start: 0.8421 (mttp) cc_final: 0.7855 (mtmm) REVERT: A 537 LYS cc_start: 0.7905 (mtpt) cc_final: 0.7702 (mtpp) REVERT: A 542 ASN cc_start: 0.8990 (t0) cc_final: 0.8687 (t0) REVERT: A 543 PHE cc_start: 0.7898 (m-10) cc_final: 0.7440 (m-80) REVERT: A 558 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7994 (mtpp) REVERT: A 564 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7318 (tm-30) REVERT: A 578 ASP cc_start: 0.7935 (t0) cc_final: 0.7633 (t0) REVERT: A 586 ASP cc_start: 0.7531 (t0) cc_final: 0.7178 (m-30) REVERT: A 619 GLU cc_start: 0.7216 (tt0) cc_final: 0.7008 (tt0) REVERT: A 654 GLU cc_start: 0.7502 (pm20) cc_final: 0.7161 (pm20) REVERT: A 656 VAL cc_start: 0.8642 (p) cc_final: 0.8327 (m) REVERT: A 675 GLN cc_start: 0.7430 (mm-40) cc_final: 0.7037 (mm-40) REVERT: A 707 TYR cc_start: 0.8015 (t80) cc_final: 0.7805 (t80) REVERT: A 740 MET cc_start: 0.8017 (ttm) cc_final: 0.7692 (mtp) REVERT: A 745 ASP cc_start: 0.7212 (m-30) cc_final: 0.6945 (p0) REVERT: A 751 ASN cc_start: 0.8134 (m110) cc_final: 0.7890 (m-40) REVERT: A 768 THR cc_start: 0.8400 (m) cc_final: 0.8158 (p) REVERT: A 774 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7215 (mp10) REVERT: A 855 PHE cc_start: 0.8191 (m-80) cc_final: 0.7843 (m-80) REVERT: A 856 LYS cc_start: 0.8891 (tppt) cc_final: 0.8642 (tptt) REVERT: A 868 GLU cc_start: 0.7828 (tp30) cc_final: 0.7545 (tp30) REVERT: A 869 MET cc_start: 0.8438 (mtt) cc_final: 0.8226 (mtm) REVERT: A 949 GLN cc_start: 0.8110 (mm110) cc_final: 0.7687 (mm-40) REVERT: A 995 ARG cc_start: 0.7991 (ttm170) cc_final: 0.7718 (ttm170) REVERT: A 998 THR cc_start: 0.8176 (m) cc_final: 0.7939 (p) REVERT: A 1017 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7460 (tm-30) REVERT: A 1030 SER cc_start: 0.8661 (m) cc_final: 0.8307 (t) REVERT: B 106 PHE cc_start: 0.7988 (m-80) cc_final: 0.7774 (m-10) REVERT: B 119 ILE cc_start: 0.8469 (mt) cc_final: 0.8269 (mm) REVERT: B 129 LYS cc_start: 0.8054 (tppt) cc_final: 0.7296 (tppt) REVERT: B 169 GLU cc_start: 0.7893 (pm20) cc_final: 0.7270 (pm20) REVERT: B 177 MET cc_start: 0.6780 (tmt) cc_final: 0.6305 (tmt) REVERT: B 190 PHE cc_start: 0.8410 (m-10) cc_final: 0.8128 (m-10) REVERT: B 204 LYS cc_start: 0.8706 (tttp) cc_final: 0.8430 (tttp) REVERT: B 224 GLU cc_start: 0.6800 (pm20) cc_final: 0.6477 (pm20) REVERT: B 279 TYR cc_start: 0.8337 (m-10) cc_final: 0.8059 (m-10) REVERT: B 362 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7685 (p) REVERT: B 406 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6682 (tt0) REVERT: B 528 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8512 (mmmt) REVERT: B 537 LYS cc_start: 0.8347 (tttp) cc_final: 0.7953 (tttm) REVERT: B 547 LYS cc_start: 0.8172 (mttp) cc_final: 0.7930 (mmtm) REVERT: B 557 LYS cc_start: 0.8590 (ptpp) cc_final: 0.8265 (ptpt) REVERT: B 558 LYS cc_start: 0.8535 (mppt) cc_final: 0.8100 (mppt) REVERT: B 560 LEU cc_start: 0.8745 (mm) cc_final: 0.8500 (mp) REVERT: B 563 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7409 (mt0) REVERT: B 580 GLN cc_start: 0.8226 (mm110) cc_final: 0.8003 (mm110) REVERT: B 604 THR cc_start: 0.8669 (p) cc_final: 0.8379 (t) REVERT: B 703 ASN cc_start: 0.8655 (t0) cc_final: 0.8173 (m-40) REVERT: B 711 SER cc_start: 0.8669 (t) cc_final: 0.8383 (t) REVERT: B 752 LEU cc_start: 0.8746 (mt) cc_final: 0.8464 (mp) REVERT: B 773 GLU cc_start: 0.7812 (tm-30) cc_final: 0.6694 (tm-30) REVERT: B 774 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7522 (mm110) REVERT: B 821 LEU cc_start: 0.8804 (tp) cc_final: 0.8364 (tt) REVERT: B 860 VAL cc_start: 0.8819 (t) cc_final: 0.8595 (m) REVERT: B 907 ASN cc_start: 0.8524 (t0) cc_final: 0.8283 (t0) REVERT: B 914 ASN cc_start: 0.8407 (p0) cc_final: 0.7965 (p0) REVERT: B 918 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7598 (mt-10) REVERT: B 950 ASP cc_start: 0.7677 (t70) cc_final: 0.7370 (t70) REVERT: B 957 GLN cc_start: 0.8237 (tt0) cc_final: 0.7965 (tt0) REVERT: B 975 SER cc_start: 0.8700 (m) cc_final: 0.8238 (t) REVERT: B 984 LEU cc_start: 0.8277 (tp) cc_final: 0.7965 (tp) REVERT: B 990 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: B 993 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8541 (tp) REVERT: B 1029 MET cc_start: 0.8599 (tpp) cc_final: 0.7655 (ttp) REVERT: B 1033 VAL cc_start: 0.8871 (t) cc_final: 0.8548 (p) REVERT: B 1038 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8577 (mtpp) REVERT: B 1084 ASP cc_start: 0.8016 (t0) cc_final: 0.7775 (t70) REVERT: B 1097 SER cc_start: 0.8891 (t) cc_final: 0.8294 (p) REVERT: C 105 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7831 (mm) REVERT: C 106 PHE cc_start: 0.7738 (m-80) cc_final: 0.7495 (m-80) REVERT: C 160 TYR cc_start: 0.7382 (p90) cc_final: 0.7107 (p90) REVERT: C 177 MET cc_start: 0.6227 (tpp) cc_final: 0.5897 (tpp) REVERT: C 188 ARG cc_start: 0.7561 (ptp-170) cc_final: 0.6920 (ptp-170) REVERT: C 204 LYS cc_start: 0.8555 (tmtt) cc_final: 0.8319 (tttp) REVERT: C 327 VAL cc_start: 0.8636 (m) cc_final: 0.8211 (t) REVERT: C 349 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8214 (t) REVERT: C 414 GLN cc_start: 0.7568 (mp10) cc_final: 0.7090 (mp10) REVERT: C 465 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7573 (tm-30) REVERT: C 537 LYS cc_start: 0.8271 (mmmm) cc_final: 0.8007 (mtpt) REVERT: C 588 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8237 (p) REVERT: C 707 TYR cc_start: 0.7972 (t80) cc_final: 0.6981 (t80) REVERT: C 724 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8513 (p) REVERT: C 729 VAL cc_start: 0.8609 (p) cc_final: 0.8343 (t) REVERT: C 746 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8243 (m) REVERT: C 752 LEU cc_start: 0.8759 (mm) cc_final: 0.8396 (mt) REVERT: C 755 GLN cc_start: 0.7922 (pp30) cc_final: 0.7244 (pp30) REVERT: C 759 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.7117 (t80) REVERT: C 776 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8361 (tttp) REVERT: C 819 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7542 (mt-10) REVERT: C 825 LYS cc_start: 0.8480 (tppt) cc_final: 0.8144 (tppt) REVERT: C 868 GLU cc_start: 0.7854 (tp30) cc_final: 0.7545 (tp30) REVERT: C 869 MET cc_start: 0.8207 (mmm) cc_final: 0.7982 (mmm) REVERT: C 921 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8300 (mmmm) REVERT: C 927 PHE cc_start: 0.8800 (t80) cc_final: 0.8293 (t80) REVERT: C 1038 LYS cc_start: 0.8625 (mtpp) cc_final: 0.8364 (mmtt) REVERT: C 1066 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7777 (p) REVERT: C 1073 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8093 (mtpp) outliers start: 130 outliers final: 91 residues processed: 706 average time/residue: 0.1623 time to fit residues: 179.1738 Evaluate side-chains 710 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 604 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 89 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 290 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 102 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 580 GLN A 690 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1119 ASN C 30 ASN C 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.143082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117071 restraints weight = 39970.401| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.69 r_work: 0.3388 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25107 Z= 0.133 Angle : 0.621 9.795 34257 Z= 0.316 Chirality : 0.047 0.327 3957 Planarity : 0.004 0.068 4379 Dihedral : 6.829 91.885 3982 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 4.54 % Allowed : 22.68 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.15), residues: 3044 helix: 1.29 (0.21), residues: 647 sheet: -1.53 (0.21), residues: 563 loop : -2.53 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 509 TYR 0.022 0.001 TYR B 707 PHE 0.041 0.002 PHE B 643 TRP 0.009 0.001 TRP C 353 HIS 0.012 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00299 (25040) covalent geometry : angle 0.60935 (34095) SS BOND : bond 0.00364 ( 39) SS BOND : angle 1.79952 ( 78) hydrogen bonds : bond 0.03509 ( 695) hydrogen bonds : angle 4.79719 ( 1938) link_NAG-ASN : bond 0.00371 ( 28) link_NAG-ASN : angle 1.90215 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 624 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7249 (m-10) cc_final: 0.6899 (m-10) REVERT: A 91 TYR cc_start: 0.7460 (t80) cc_final: 0.7139 (t80) REVERT: A 102 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.6981 (mtm-85) REVERT: A 104 TRP cc_start: 0.7913 (OUTLIER) cc_final: 0.7290 (m-90) REVERT: A 129 LYS cc_start: 0.8089 (mtmm) cc_final: 0.7472 (mtmm) REVERT: A 169 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6855 (pm20) REVERT: A 188 ARG cc_start: 0.8011 (ptp-110) cc_final: 0.7699 (ptp90) REVERT: A 189 GLU cc_start: 0.8150 (pm20) cc_final: 0.7788 (pt0) REVERT: A 224 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6861 (mm-30) REVERT: A 307 THR cc_start: 0.8460 (m) cc_final: 0.8145 (p) REVERT: A 340 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6621 (pm20) REVERT: A 380 TYR cc_start: 0.7369 (m-80) cc_final: 0.7052 (m-10) REVERT: A 386 LYS cc_start: 0.8412 (mttp) cc_final: 0.7847 (mtmm) REVERT: A 537 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7715 (mtpp) REVERT: A 542 ASN cc_start: 0.8987 (t0) cc_final: 0.8701 (t0) REVERT: A 543 PHE cc_start: 0.7867 (m-10) cc_final: 0.7391 (m-80) REVERT: A 558 LYS cc_start: 0.8292 (mtpp) cc_final: 0.8057 (mtpp) REVERT: A 560 LEU cc_start: 0.8306 (mt) cc_final: 0.8065 (mp) REVERT: A 564 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 578 ASP cc_start: 0.7975 (t0) cc_final: 0.7434 (t0) REVERT: A 586 ASP cc_start: 0.7495 (t0) cc_final: 0.7206 (m-30) REVERT: A 619 GLU cc_start: 0.7200 (tt0) cc_final: 0.6970 (tt0) REVERT: A 643 PHE cc_start: 0.8101 (t80) cc_final: 0.7817 (t80) REVERT: A 654 GLU cc_start: 0.7585 (pm20) cc_final: 0.7263 (pm20) REVERT: A 656 VAL cc_start: 0.8652 (p) cc_final: 0.8426 (m) REVERT: A 675 GLN cc_start: 0.7434 (mm-40) cc_final: 0.7025 (mm-40) REVERT: A 740 MET cc_start: 0.7971 (ttm) cc_final: 0.7605 (mtp) REVERT: A 745 ASP cc_start: 0.7193 (m-30) cc_final: 0.6955 (p0) REVERT: A 768 THR cc_start: 0.8351 (m) cc_final: 0.8117 (p) REVERT: A 854 LYS cc_start: 0.8366 (tptp) cc_final: 0.8139 (tptp) REVERT: A 855 PHE cc_start: 0.8152 (m-80) cc_final: 0.7614 (m-80) REVERT: A 856 LYS cc_start: 0.8893 (tppt) cc_final: 0.8658 (tptt) REVERT: A 868 GLU cc_start: 0.7886 (tp30) cc_final: 0.7597 (tp30) REVERT: A 949 GLN cc_start: 0.8101 (mm110) cc_final: 0.7671 (mm-40) REVERT: A 995 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7576 (ttm170) REVERT: A 997 ILE cc_start: 0.8824 (mm) cc_final: 0.8611 (mt) REVERT: A 998 THR cc_start: 0.8147 (m) cc_final: 0.7914 (p) REVERT: A 1017 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7498 (tm-30) REVERT: B 119 ILE cc_start: 0.8537 (mt) cc_final: 0.8322 (mm) REVERT: B 129 LYS cc_start: 0.8051 (tppt) cc_final: 0.7271 (tppt) REVERT: B 169 GLU cc_start: 0.7841 (pm20) cc_final: 0.7232 (pm20) REVERT: B 177 MET cc_start: 0.6782 (tmt) cc_final: 0.6332 (tmt) REVERT: B 190 PHE cc_start: 0.8407 (m-10) cc_final: 0.8160 (m-10) REVERT: B 204 LYS cc_start: 0.8707 (tttp) cc_final: 0.8443 (tttp) REVERT: B 224 GLU cc_start: 0.6758 (pm20) cc_final: 0.6435 (pm20) REVERT: B 290 ASP cc_start: 0.7714 (t70) cc_final: 0.7316 (t0) REVERT: B 362 VAL cc_start: 0.8008 (OUTLIER) cc_final: 0.7666 (p) REVERT: B 406 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6587 (tt0) REVERT: B 528 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8578 (mmmt) REVERT: B 537 LYS cc_start: 0.8141 (tttp) cc_final: 0.7917 (tttp) REVERT: B 547 LYS cc_start: 0.8145 (mttp) cc_final: 0.7903 (mmtm) REVERT: B 549 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8548 (p) REVERT: B 557 LYS cc_start: 0.8605 (ptpp) cc_final: 0.8251 (ptpt) REVERT: B 558 LYS cc_start: 0.8528 (mppt) cc_final: 0.8091 (mppt) REVERT: B 560 LEU cc_start: 0.8728 (mm) cc_final: 0.8372 (mt) REVERT: B 563 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7479 (mt0) REVERT: B 580 GLN cc_start: 0.8244 (mm110) cc_final: 0.8015 (mm110) REVERT: B 589 PRO cc_start: 0.8621 (Cg_exo) cc_final: 0.8088 (Cg_endo) REVERT: B 604 THR cc_start: 0.8690 (p) cc_final: 0.8417 (t) REVERT: B 703 ASN cc_start: 0.8665 (t0) cc_final: 0.8190 (m-40) REVERT: B 711 SER cc_start: 0.8693 (t) cc_final: 0.8416 (t) REVERT: B 752 LEU cc_start: 0.8758 (mt) cc_final: 0.8489 (mp) REVERT: B 773 GLU cc_start: 0.7787 (tm-30) cc_final: 0.6874 (tm-30) REVERT: B 774 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7465 (mm110) REVERT: B 821 LEU cc_start: 0.8719 (tp) cc_final: 0.8302 (tt) REVERT: B 860 VAL cc_start: 0.8817 (t) cc_final: 0.8597 (m) REVERT: B 904 TYR cc_start: 0.7428 (m-10) cc_final: 0.7211 (m-80) REVERT: B 907 ASN cc_start: 0.8511 (t0) cc_final: 0.8293 (t0) REVERT: B 914 ASN cc_start: 0.8464 (p0) cc_final: 0.8025 (p0) REVERT: B 918 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7573 (mt-10) REVERT: B 950 ASP cc_start: 0.7703 (t70) cc_final: 0.7392 (t70) REVERT: B 957 GLN cc_start: 0.8289 (tt0) cc_final: 0.8039 (tt0) REVERT: B 975 SER cc_start: 0.8673 (m) cc_final: 0.8217 (t) REVERT: B 984 LEU cc_start: 0.8272 (tp) cc_final: 0.7989 (tp) REVERT: B 990 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: B 993 ILE cc_start: 0.8761 (tp) cc_final: 0.8528 (tp) REVERT: B 1029 MET cc_start: 0.8586 (tpp) cc_final: 0.7641 (ttp) REVERT: B 1033 VAL cc_start: 0.8846 (t) cc_final: 0.8632 (p) REVERT: B 1038 LYS cc_start: 0.8857 (mtpp) cc_final: 0.8571 (mtpp) REVERT: B 1084 ASP cc_start: 0.8044 (t0) cc_final: 0.7814 (t70) REVERT: B 1097 SER cc_start: 0.8901 (t) cc_final: 0.8295 (p) REVERT: C 102 ARG cc_start: 0.6949 (mtm110) cc_final: 0.6701 (mtm110) REVERT: C 105 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7796 (mm) REVERT: C 106 PHE cc_start: 0.7698 (m-80) cc_final: 0.7470 (m-80) REVERT: C 160 TYR cc_start: 0.7401 (p90) cc_final: 0.7130 (p90) REVERT: C 188 ARG cc_start: 0.7546 (ptp-170) cc_final: 0.6766 (ptp-170) REVERT: C 204 LYS cc_start: 0.8595 (tmtt) cc_final: 0.8326 (tttp) REVERT: C 289 VAL cc_start: 0.8645 (t) cc_final: 0.8427 (m) REVERT: C 327 VAL cc_start: 0.8615 (m) cc_final: 0.8181 (t) REVERT: C 349 SER cc_start: 0.8581 (m) cc_final: 0.8246 (t) REVERT: C 414 GLN cc_start: 0.7600 (mp10) cc_final: 0.7117 (mp10) REVERT: C 465 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7526 (tm-30) REVERT: C 537 LYS cc_start: 0.8207 (mmmm) cc_final: 0.7924 (mtpt) REVERT: C 565 PHE cc_start: 0.7183 (m-10) cc_final: 0.6839 (m-10) REVERT: C 588 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8165 (p) REVERT: C 656 VAL cc_start: 0.8512 (p) cc_final: 0.8296 (m) REVERT: C 658 ASN cc_start: 0.8535 (m-40) cc_final: 0.8119 (p0) REVERT: C 704 SER cc_start: 0.8544 (p) cc_final: 0.8294 (p) REVERT: C 707 TYR cc_start: 0.7974 (t80) cc_final: 0.7026 (t80) REVERT: C 724 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8500 (p) REVERT: C 746 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8292 (m) REVERT: C 759 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.7090 (t80) REVERT: C 776 LYS cc_start: 0.8660 (ttpt) cc_final: 0.8368 (tttp) REVERT: C 819 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7543 (mt-10) REVERT: C 825 LYS cc_start: 0.8491 (tppt) cc_final: 0.8156 (tppt) REVERT: C 868 GLU cc_start: 0.7854 (tp30) cc_final: 0.7562 (tp30) REVERT: C 869 MET cc_start: 0.8154 (mmm) cc_final: 0.7916 (mmm) REVERT: C 921 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8426 (mmmm) REVERT: C 927 PHE cc_start: 0.8796 (t80) cc_final: 0.8304 (t80) REVERT: C 1038 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8362 (mmtt) REVERT: C 1073 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8118 (mtpp) REVERT: C 1139 ASP cc_start: 0.8029 (t0) cc_final: 0.7773 (t0) outliers start: 121 outliers final: 84 residues processed: 704 average time/residue: 0.1601 time to fit residues: 176.1734 Evaluate side-chains 707 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 611 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 165 optimal weight: 1.9990 chunk 249 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 195 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 301 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 chunk 157 optimal weight: 0.0060 chunk 268 optimal weight: 0.3980 chunk 75 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 334 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN C 30 ASN C 52 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.143122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.116989 restraints weight = 40284.808| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.71 r_work: 0.3391 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25107 Z= 0.129 Angle : 0.632 11.064 34257 Z= 0.321 Chirality : 0.047 0.350 3957 Planarity : 0.004 0.067 4379 Dihedral : 6.692 92.295 3976 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 4.31 % Allowed : 23.40 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.15), residues: 3044 helix: 1.27 (0.21), residues: 653 sheet: -1.41 (0.21), residues: 551 loop : -2.44 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 509 TYR 0.032 0.001 TYR C 904 PHE 0.028 0.001 PHE A 86 TRP 0.008 0.001 TRP C 104 HIS 0.017 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00291 (25040) covalent geometry : angle 0.62092 (34095) SS BOND : bond 0.00343 ( 39) SS BOND : angle 1.78569 ( 78) hydrogen bonds : bond 0.03435 ( 695) hydrogen bonds : angle 4.75156 ( 1938) link_NAG-ASN : bond 0.00377 ( 28) link_NAG-ASN : angle 1.86409 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 614 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7187 (m-10) cc_final: 0.6959 (m-10) REVERT: A 102 ARG cc_start: 0.7562 (mtm-85) cc_final: 0.6917 (mtm-85) REVERT: A 129 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7456 (mtmm) REVERT: A 169 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6836 (pm20) REVERT: A 188 ARG cc_start: 0.8158 (ptp-110) cc_final: 0.7814 (ptp90) REVERT: A 189 GLU cc_start: 0.8222 (pm20) cc_final: 0.8014 (pt0) REVERT: A 203 SER cc_start: 0.8730 (p) cc_final: 0.8274 (m) REVERT: A 224 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6827 (mm-30) REVERT: A 269 TYR cc_start: 0.8191 (m-80) cc_final: 0.7943 (m-10) REVERT: A 275 PHE cc_start: 0.8347 (m-80) cc_final: 0.8065 (m-10) REVERT: A 307 THR cc_start: 0.8467 (m) cc_final: 0.8155 (p) REVERT: A 340 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6616 (pm20) REVERT: A 380 TYR cc_start: 0.7352 (m-80) cc_final: 0.7028 (m-10) REVERT: A 386 LYS cc_start: 0.8392 (mttp) cc_final: 0.7828 (mtmm) REVERT: A 537 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7804 (mtpp) REVERT: A 542 ASN cc_start: 0.8983 (t0) cc_final: 0.8725 (t0) REVERT: A 543 PHE cc_start: 0.7825 (m-10) cc_final: 0.7373 (m-10) REVERT: A 558 LYS cc_start: 0.8329 (mtpp) cc_final: 0.8092 (mtpp) REVERT: A 564 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7302 (tm-30) REVERT: A 586 ASP cc_start: 0.7507 (t0) cc_final: 0.7231 (m-30) REVERT: A 654 GLU cc_start: 0.7603 (pm20) cc_final: 0.7317 (pm20) REVERT: A 656 VAL cc_start: 0.8609 (p) cc_final: 0.8370 (m) REVERT: A 675 GLN cc_start: 0.7402 (mm-40) cc_final: 0.6997 (mm-40) REVERT: A 740 MET cc_start: 0.7932 (ttm) cc_final: 0.7562 (mtp) REVERT: A 745 ASP cc_start: 0.7138 (m-30) cc_final: 0.6877 (p0) REVERT: A 751 ASN cc_start: 0.8248 (m110) cc_final: 0.8031 (m-40) REVERT: A 803 SER cc_start: 0.8461 (t) cc_final: 0.8140 (t) REVERT: A 855 PHE cc_start: 0.8203 (m-80) cc_final: 0.7940 (m-80) REVERT: A 856 LYS cc_start: 0.8895 (tppt) cc_final: 0.8662 (tptt) REVERT: A 868 GLU cc_start: 0.7882 (tp30) cc_final: 0.7597 (tp30) REVERT: A 949 GLN cc_start: 0.8131 (mm110) cc_final: 0.7696 (mm-40) REVERT: A 995 ARG cc_start: 0.7857 (ttm170) cc_final: 0.7598 (ttm170) REVERT: A 997 ILE cc_start: 0.8820 (mm) cc_final: 0.8591 (mt) REVERT: A 998 THR cc_start: 0.8146 (m) cc_final: 0.7926 (p) REVERT: A 1017 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7411 (tm-30) REVERT: A 1136 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8365 (p) REVERT: B 119 ILE cc_start: 0.8521 (mt) cc_final: 0.8312 (mm) REVERT: B 129 LYS cc_start: 0.8010 (tppt) cc_final: 0.7313 (tppt) REVERT: B 169 GLU cc_start: 0.7819 (pm20) cc_final: 0.7178 (pm20) REVERT: B 177 MET cc_start: 0.6707 (tmt) cc_final: 0.6284 (tmt) REVERT: B 190 PHE cc_start: 0.8397 (m-10) cc_final: 0.8143 (m-10) REVERT: B 193 LYS cc_start: 0.8290 (ttpt) cc_final: 0.8068 (ttpt) REVERT: B 204 LYS cc_start: 0.8691 (tttp) cc_final: 0.8338 (tttp) REVERT: B 224 GLU cc_start: 0.6733 (pm20) cc_final: 0.6321 (pm20) REVERT: B 238 PHE cc_start: 0.7958 (t80) cc_final: 0.7702 (t80) REVERT: B 362 VAL cc_start: 0.7963 (OUTLIER) cc_final: 0.7700 (p) REVERT: B 406 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6604 (tt0) REVERT: B 537 LYS cc_start: 0.8064 (tttp) cc_final: 0.7805 (tttm) REVERT: B 547 LYS cc_start: 0.8155 (mttp) cc_final: 0.7942 (mmtm) REVERT: B 557 LYS cc_start: 0.8592 (ptpp) cc_final: 0.8344 (ptpt) REVERT: B 558 LYS cc_start: 0.8553 (mppt) cc_final: 0.8103 (mppt) REVERT: B 559 PHE cc_start: 0.8371 (m-10) cc_final: 0.8143 (m-10) REVERT: B 560 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8399 (mt) REVERT: B 563 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: B 580 GLN cc_start: 0.8233 (mm110) cc_final: 0.8011 (mm110) REVERT: B 604 THR cc_start: 0.8711 (p) cc_final: 0.8440 (t) REVERT: B 711 SER cc_start: 0.8692 (t) cc_final: 0.8416 (t) REVERT: B 752 LEU cc_start: 0.8759 (mt) cc_final: 0.8488 (mp) REVERT: B 773 GLU cc_start: 0.7843 (tm-30) cc_final: 0.6857 (tm-30) REVERT: B 774 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7449 (mm110) REVERT: B 821 LEU cc_start: 0.8720 (tp) cc_final: 0.8245 (tt) REVERT: B 860 VAL cc_start: 0.8820 (t) cc_final: 0.8601 (m) REVERT: B 904 TYR cc_start: 0.7453 (m-10) cc_final: 0.7021 (m-80) REVERT: B 907 ASN cc_start: 0.8520 (t0) cc_final: 0.8308 (t0) REVERT: B 914 ASN cc_start: 0.8495 (p0) cc_final: 0.7687 (p0) REVERT: B 918 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7571 (mt-10) REVERT: B 950 ASP cc_start: 0.7680 (t70) cc_final: 0.7360 (t70) REVERT: B 975 SER cc_start: 0.8664 (m) cc_final: 0.8244 (t) REVERT: B 984 LEU cc_start: 0.8269 (tp) cc_final: 0.7932 (tp) REVERT: B 988 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7051 (tp30) REVERT: B 990 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: B 993 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8521 (tp) REVERT: B 1033 VAL cc_start: 0.8808 (t) cc_final: 0.8605 (p) REVERT: B 1038 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8543 (mtpp) REVERT: B 1084 ASP cc_start: 0.8046 (t0) cc_final: 0.7828 (t70) REVERT: B 1097 SER cc_start: 0.8876 (t) cc_final: 0.8288 (p) REVERT: B 1107 ARG cc_start: 0.7664 (ptp-170) cc_final: 0.7331 (ptp-170) REVERT: B 1111 GLU cc_start: 0.8173 (tt0) cc_final: 0.7891 (tt0) REVERT: C 102 ARG cc_start: 0.6985 (mtm110) cc_final: 0.6747 (mtm110) REVERT: C 105 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7781 (mm) REVERT: C 106 PHE cc_start: 0.7697 (m-80) cc_final: 0.7493 (m-80) REVERT: C 160 TYR cc_start: 0.7373 (p90) cc_final: 0.7113 (p90) REVERT: C 188 ARG cc_start: 0.7419 (ptp-170) cc_final: 0.7083 (ptp-170) REVERT: C 204 LYS cc_start: 0.8607 (tmtt) cc_final: 0.8334 (tttp) REVERT: C 327 VAL cc_start: 0.8589 (m) cc_final: 0.8137 (t) REVERT: C 349 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8259 (t) REVERT: C 414 GLN cc_start: 0.7725 (mp10) cc_final: 0.7348 (mp10) REVERT: C 465 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7533 (tm-30) REVERT: C 508 TYR cc_start: 0.6472 (m-80) cc_final: 0.5873 (m-80) REVERT: C 565 PHE cc_start: 0.7177 (m-10) cc_final: 0.6816 (m-10) REVERT: C 588 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8130 (p) REVERT: C 656 VAL cc_start: 0.8506 (p) cc_final: 0.8284 (m) REVERT: C 658 ASN cc_start: 0.8542 (m-40) cc_final: 0.8106 (p0) REVERT: C 704 SER cc_start: 0.8546 (p) cc_final: 0.8310 (p) REVERT: C 707 TYR cc_start: 0.7999 (t80) cc_final: 0.7027 (t80) REVERT: C 724 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8502 (p) REVERT: C 725 GLU cc_start: 0.7424 (tt0) cc_final: 0.7208 (tt0) REVERT: C 746 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8296 (m) REVERT: C 759 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.7122 (t80) REVERT: C 776 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8361 (tttp) REVERT: C 819 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7538 (mt-10) REVERT: C 825 LYS cc_start: 0.8459 (tppt) cc_final: 0.8136 (tppt) REVERT: C 868 GLU cc_start: 0.7857 (tp30) cc_final: 0.7552 (tp30) REVERT: C 869 MET cc_start: 0.8141 (mmm) cc_final: 0.7903 (mmm) REVERT: C 904 TYR cc_start: 0.6742 (m-10) cc_final: 0.6414 (m-10) REVERT: C 921 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8299 (mmmm) REVERT: C 927 PHE cc_start: 0.8784 (t80) cc_final: 0.8333 (t80) REVERT: C 936 ASP cc_start: 0.8130 (m-30) cc_final: 0.7915 (m-30) REVERT: C 1029 MET cc_start: 0.8211 (ttm) cc_final: 0.7843 (tpp) REVERT: C 1038 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8388 (mmtt) REVERT: C 1073 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8117 (mtpp) REVERT: C 1139 ASP cc_start: 0.8008 (t0) cc_final: 0.7736 (t0) outliers start: 115 outliers final: 82 residues processed: 692 average time/residue: 0.1605 time to fit residues: 174.2724 Evaluate side-chains 693 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 597 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 305 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 chunk 287 optimal weight: 2.9990 chunk 218 optimal weight: 0.5980 chunk 296 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 644 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.140744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114662 restraints weight = 40281.307| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.69 r_work: 0.3359 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25107 Z= 0.192 Angle : 0.677 12.006 34257 Z= 0.345 Chirality : 0.049 0.354 3957 Planarity : 0.005 0.065 4379 Dihedral : 6.885 92.051 3976 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 4.09 % Allowed : 23.85 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.15), residues: 3044 helix: 1.15 (0.21), residues: 653 sheet: -1.35 (0.21), residues: 559 loop : -2.46 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 319 TYR 0.035 0.002 TYR C 904 PHE 0.033 0.002 PHE A 86 TRP 0.017 0.001 TRP C 353 HIS 0.023 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00431 (25040) covalent geometry : angle 0.66425 (34095) SS BOND : bond 0.00393 ( 39) SS BOND : angle 2.03960 ( 78) hydrogen bonds : bond 0.03861 ( 695) hydrogen bonds : angle 4.86093 ( 1938) link_NAG-ASN : bond 0.00383 ( 28) link_NAG-ASN : angle 1.99971 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 627 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 SER cc_start: 0.8528 (m) cc_final: 0.8263 (p) REVERT: A 65 PHE cc_start: 0.7169 (m-10) cc_final: 0.6962 (m-10) REVERT: A 102 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7100 (mtm-85) REVERT: A 104 TRP cc_start: 0.8094 (OUTLIER) cc_final: 0.7761 (m-90) REVERT: A 129 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7412 (mtmm) REVERT: A 169 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6986 (pm20) REVERT: A 188 ARG cc_start: 0.8192 (ptp-110) cc_final: 0.7765 (ptp90) REVERT: A 203 SER cc_start: 0.8754 (p) cc_final: 0.8293 (m) REVERT: A 224 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6875 (mm-30) REVERT: A 275 PHE cc_start: 0.8334 (m-80) cc_final: 0.8091 (m-10) REVERT: A 307 THR cc_start: 0.8489 (m) cc_final: 0.8186 (p) REVERT: A 324 GLU cc_start: 0.7791 (mp0) cc_final: 0.7365 (mp0) REVERT: A 340 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6765 (pm20) REVERT: A 355 ARG cc_start: 0.7473 (ttm-80) cc_final: 0.7036 (tpp80) REVERT: A 380 TYR cc_start: 0.7361 (m-80) cc_final: 0.7025 (m-10) REVERT: A 386 LYS cc_start: 0.8431 (mttp) cc_final: 0.7893 (mtmm) REVERT: A 537 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7989 (mtpp) REVERT: A 542 ASN cc_start: 0.8992 (t0) cc_final: 0.8690 (t0) REVERT: A 558 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8228 (mtpp) REVERT: A 564 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7244 (tm-30) REVERT: A 586 ASP cc_start: 0.7489 (t0) cc_final: 0.7234 (m-30) REVERT: A 619 GLU cc_start: 0.7108 (tt0) cc_final: 0.6518 (tt0) REVERT: A 654 GLU cc_start: 0.7549 (pm20) cc_final: 0.7265 (pm20) REVERT: A 656 VAL cc_start: 0.8539 (p) cc_final: 0.8276 (m) REVERT: A 675 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7027 (mm-40) REVERT: A 740 MET cc_start: 0.8067 (ttm) cc_final: 0.7709 (mtp) REVERT: A 745 ASP cc_start: 0.7184 (m-30) cc_final: 0.6966 (p0) REVERT: A 751 ASN cc_start: 0.8275 (m110) cc_final: 0.8051 (m-40) REVERT: A 855 PHE cc_start: 0.8355 (m-80) cc_final: 0.8047 (m-80) REVERT: A 868 GLU cc_start: 0.7918 (tp30) cc_final: 0.7645 (tp30) REVERT: A 949 GLN cc_start: 0.8264 (mm110) cc_final: 0.7811 (mm-40) REVERT: A 998 THR cc_start: 0.8188 (m) cc_final: 0.7953 (p) REVERT: A 1017 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 1108 ASN cc_start: 0.8647 (m110) cc_final: 0.8425 (m-40) REVERT: A 1136 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8404 (p) REVERT: B 129 LYS cc_start: 0.8072 (tppt) cc_final: 0.7638 (tppt) REVERT: B 169 GLU cc_start: 0.7866 (pm20) cc_final: 0.7213 (pm20) REVERT: B 177 MET cc_start: 0.6736 (tmt) cc_final: 0.6281 (tmt) REVERT: B 190 PHE cc_start: 0.8426 (m-10) cc_final: 0.8106 (m-10) REVERT: B 193 LYS cc_start: 0.8272 (ttpt) cc_final: 0.8027 (ttpp) REVERT: B 204 LYS cc_start: 0.8732 (tttp) cc_final: 0.8386 (tttp) REVERT: B 224 GLU cc_start: 0.6825 (pm20) cc_final: 0.6427 (pm20) REVERT: B 237 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6427 (mtp180) REVERT: B 238 PHE cc_start: 0.8115 (t80) cc_final: 0.7771 (t80) REVERT: B 290 ASP cc_start: 0.7874 (t70) cc_final: 0.7563 (t0) REVERT: B 406 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6647 (tt0) REVERT: B 528 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8244 (mtmt) REVERT: B 547 LYS cc_start: 0.8197 (mttp) cc_final: 0.7973 (mmtm) REVERT: B 549 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8493 (p) REVERT: B 557 LYS cc_start: 0.8627 (ptpp) cc_final: 0.8342 (ptpt) REVERT: B 558 LYS cc_start: 0.8571 (mppt) cc_final: 0.8133 (mppt) REVERT: B 559 PHE cc_start: 0.8402 (m-10) cc_final: 0.8180 (m-10) REVERT: B 560 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8553 (mp) REVERT: B 563 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: B 604 THR cc_start: 0.8700 (p) cc_final: 0.8453 (t) REVERT: B 711 SER cc_start: 0.8664 (t) cc_final: 0.8363 (t) REVERT: B 742 ILE cc_start: 0.8736 (mm) cc_final: 0.8523 (mt) REVERT: B 752 LEU cc_start: 0.8786 (mt) cc_final: 0.8517 (mp) REVERT: B 773 GLU cc_start: 0.7875 (tm-30) cc_final: 0.6805 (tm-30) REVERT: B 774 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7572 (mm110) REVERT: B 821 LEU cc_start: 0.8806 (tp) cc_final: 0.8334 (tt) REVERT: B 860 VAL cc_start: 0.8815 (t) cc_final: 0.8584 (m) REVERT: B 914 ASN cc_start: 0.8519 (p0) cc_final: 0.7716 (p0) REVERT: B 918 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7600 (mt-10) REVERT: B 950 ASP cc_start: 0.7667 (t70) cc_final: 0.7363 (t70) REVERT: B 957 GLN cc_start: 0.8403 (tt0) cc_final: 0.8055 (tt0) REVERT: B 975 SER cc_start: 0.8717 (m) cc_final: 0.8265 (t) REVERT: B 984 LEU cc_start: 0.8310 (tp) cc_final: 0.7984 (tp) REVERT: B 988 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7050 (tp30) REVERT: B 990 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: B 993 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8516 (tp) REVERT: B 1033 VAL cc_start: 0.8852 (t) cc_final: 0.8632 (p) REVERT: B 1038 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8600 (mtpp) REVERT: B 1084 ASP cc_start: 0.8090 (t0) cc_final: 0.7888 (t70) REVERT: B 1097 SER cc_start: 0.8859 (t) cc_final: 0.8318 (p) REVERT: B 1107 ARG cc_start: 0.7883 (ptp-170) cc_final: 0.7626 (ptp-170) REVERT: B 1111 GLU cc_start: 0.8186 (tt0) cc_final: 0.7856 (tt0) REVERT: C 102 ARG cc_start: 0.7093 (mtm110) cc_final: 0.6838 (mtm110) REVERT: C 106 PHE cc_start: 0.7685 (m-80) cc_final: 0.7485 (m-80) REVERT: C 160 TYR cc_start: 0.7472 (p90) cc_final: 0.7169 (p90) REVERT: C 204 LYS cc_start: 0.8640 (tmtt) cc_final: 0.8365 (tttp) REVERT: C 281 GLU cc_start: 0.7890 (pp20) cc_final: 0.7544 (pp20) REVERT: C 289 VAL cc_start: 0.8637 (t) cc_final: 0.8412 (m) REVERT: C 327 VAL cc_start: 0.8601 (m) cc_final: 0.8160 (t) REVERT: C 414 GLN cc_start: 0.7779 (mp10) cc_final: 0.7295 (mp10) REVERT: C 465 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7544 (tm-30) REVERT: C 588 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8186 (p) REVERT: C 656 VAL cc_start: 0.8493 (p) cc_final: 0.8289 (m) REVERT: C 658 ASN cc_start: 0.8545 (m-40) cc_final: 0.8122 (p0) REVERT: C 704 SER cc_start: 0.8561 (p) cc_final: 0.8340 (p) REVERT: C 707 TYR cc_start: 0.8032 (t80) cc_final: 0.7068 (t80) REVERT: C 724 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8504 (p) REVERT: C 725 GLU cc_start: 0.7443 (tt0) cc_final: 0.7204 (tt0) REVERT: C 746 SER cc_start: 0.8647 (OUTLIER) cc_final: 0.8319 (m) REVERT: C 755 GLN cc_start: 0.7945 (pp30) cc_final: 0.7562 (tm-30) REVERT: C 759 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7148 (t80) REVERT: C 761 THR cc_start: 0.8330 (m) cc_final: 0.8017 (p) REVERT: C 776 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8414 (tttp) REVERT: C 825 LYS cc_start: 0.8516 (tppt) cc_final: 0.8207 (tppt) REVERT: C 868 GLU cc_start: 0.7879 (tp30) cc_final: 0.7579 (tp30) REVERT: C 869 MET cc_start: 0.8212 (mmm) cc_final: 0.7981 (mmm) REVERT: C 921 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8324 (mmmm) REVERT: C 927 PHE cc_start: 0.8803 (t80) cc_final: 0.8321 (t80) REVERT: C 1038 LYS cc_start: 0.8697 (mtpp) cc_final: 0.8446 (mmtt) REVERT: C 1066 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7769 (p) REVERT: C 1073 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8128 (mtpp) REVERT: C 1144 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7900 (mm-30) outliers start: 109 outliers final: 82 residues processed: 695 average time/residue: 0.1643 time to fit residues: 178.6449 Evaluate side-chains 712 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 615 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 245 optimal weight: 0.9980 chunk 104 optimal weight: 0.0970 chunk 78 optimal weight: 0.9980 chunk 240 optimal weight: 0.9990 chunk 255 optimal weight: 0.0060 chunk 278 optimal weight: 0.0870 chunk 113 optimal weight: 3.9990 chunk 267 optimal weight: 0.8980 chunk 249 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS C1101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116719 restraints weight = 40252.875| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.71 r_work: 0.3394 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25107 Z= 0.123 Angle : 0.652 10.362 34257 Z= 0.331 Chirality : 0.047 0.329 3957 Planarity : 0.005 0.067 4379 Dihedral : 6.639 91.841 3974 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.67 % Allowed : 24.60 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.15), residues: 3044 helix: 1.35 (0.22), residues: 645 sheet: -1.33 (0.21), residues: 555 loop : -2.37 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 188 TYR 0.039 0.001 TYR C 904 PHE 0.031 0.001 PHE A 86 TRP 0.009 0.001 TRP C 104 HIS 0.021 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00282 (25040) covalent geometry : angle 0.64112 (34095) SS BOND : bond 0.00316 ( 39) SS BOND : angle 1.71793 ( 78) hydrogen bonds : bond 0.03461 ( 695) hydrogen bonds : angle 4.79156 ( 1938) link_NAG-ASN : bond 0.00381 ( 28) link_NAG-ASN : angle 1.90110 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5758.79 seconds wall clock time: 99 minutes 33.55 seconds (5973.55 seconds total)