Starting phenix.real_space_refine on Sat Jun 21 08:10:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wz1_32901/06_2025/7wz1_32901.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wz1_32901/06_2025/7wz1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wz1_32901/06_2025/7wz1_32901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wz1_32901/06_2025/7wz1_32901.map" model { file = "/net/cci-nas-00/data/ceres_data/7wz1_32901/06_2025/7wz1_32901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wz1_32901/06_2025/7wz1_32901.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: 14.92, per 1000 atoms: 0.61 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: 7.23 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 3.75 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: 10.39 Time building geometry restraints manager: 8.01 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 1147 or resid 1301 thr \ ough 1309)) selection = (chain 'B' and (resid 26 through 68 or resid 80 through 1147 or resid 1301 throu \ gh 1309)) selection = (chain 'C' and (resid 26 through 68 or resid 80 through 243 or resid 262 through \ 1147 or resid 1301 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: 2.160 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: 0.010 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 60.070 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.000 TRP A 886 HIS 0.001 0.000 HIS A 505 PHE 0.011 0.001 PHE C 375 TYR 0.008 0.001 TYR A 160 ARG 0.002 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 28) link_NAG-ASN : angle 1.04248 ( 84) hydrogen bonds : bond 0.23227 ( 695) hydrogen bonds : angle 8.01793 ( 1938) SS BOND : bond 0.00130 ( 39) SS BOND : angle 0.46817 ( 78) covalent geometry : bond 0.00283 (25040) covalent geometry : angle 0.65832 (34095) *********************** 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 : 2.607 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: 0.6731 (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: 0.6725 (tm-30) REVERT: A 104 TRP cc_start: 0.7833 (OUTLIER) cc_final: 0.7362 (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: 0.8009 (mm) REVERT: A 237 ARG cc_start: 0.7340 (ttm110) cc_final: 0.7006 (mtp85) REVERT: A 238 PHE cc_start: 0.6719 (t80) cc_final: 0.6505 (t80) REVERT: A 267 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8046 (p) REVERT: A 269 TYR cc_start: 0.7780 (m-80) cc_final: 0.7557 (m-80) REVERT: A 280 ASN cc_start: 0.7510 (t0) cc_final: 0.7263 (t0) REVERT: A 281 GLU cc_start: 0.7475 (pp20) cc_final: 0.6993 (pp20) REVERT: A 340 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5790 (pm20) REVERT: A 351 TYR cc_start: 0.6501 (p90) cc_final: 0.6074 (p90) REVERT: A 380 TYR cc_start: 0.6929 (m-80) cc_final: 0.6492 (m-10) REVERT: A 452 LEU cc_start: 0.7930 (tt) cc_final: 0.7249 (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: 0.7526 (mtpp) REVERT: A 565 PHE cc_start: 0.6229 (m-10) cc_final: 0.5956 (m-10) REVERT: A 574 ASP cc_start: 0.7682 (t70) cc_final: 0.7417 (t0) REVERT: A 578 ASP cc_start: 0.7183 (t0) cc_final: 0.6950 (t0) REVERT: A 586 ASP cc_start: 0.7163 (t0) cc_final: 0.6805 (t0) REVERT: A 599 THR cc_start: 0.8313 (m) cc_final: 0.7922 (t) REVERT: A 654 GLU cc_start: 0.6872 (pm20) cc_final: 0.6591 (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: 0.8065 (mt) REVERT: A 675 GLN cc_start: 0.7193 (mm-40) cc_final: 0.6631 (mm-40) REVERT: A 691 SER cc_start: 0.8092 (t) cc_final: 0.7887 (p) REVERT: A 693 ILE cc_start: 0.8539 (pt) cc_final: 0.8297 (pt) REVERT: A 707 TYR cc_start: 0.7594 (t80) cc_final: 0.7334 (t80) REVERT: A 751 ASN cc_start: 0.7843 (m-40) cc_final: 0.7618 (m110) REVERT: A 768 THR cc_start: 0.8174 (m) cc_final: 0.7897 (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: 0.6511 (mt-10) REVERT: A 825 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8232 (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: 0.7345 (mt-10) REVERT: A 949 GLN cc_start: 0.7550 (mm110) cc_final: 0.7200 (mm-40) REVERT: A 993 ILE cc_start: 0.8343 (tp) cc_final: 0.7783 (tp) REVERT: A 998 THR cc_start: 0.7934 (m) cc_final: 0.7660 (p) REVERT: A 1029 MET cc_start: 0.7863 (ttm) cc_final: 0.7663 (ttm) 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: 0.7956 (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: 0.8082 (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 83 VAL cc_start: 0.5712 (OUTLIER) cc_final: 0.5433 (t) REVERT: B 105 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7639 (pt) REVERT: B 106 PHE cc_start: 0.7818 (m-80) cc_final: 0.7569 (m-10) REVERT: B 169 GLU cc_start: 0.7077 (pm20) cc_final: 0.6810 (pm20) REVERT: B 201 ILE cc_start: 0.8500 (mt) cc_final: 0.7984 (tt) REVERT: B 202 TYR cc_start: 0.7675 (m-80) cc_final: 0.7465 (m-80) REVERT: B 224 GLU cc_start: 0.6684 (pm20) cc_final: 0.6401 (pm20) REVERT: B 289 VAL cc_start: 0.7477 (t) cc_final: 0.7131 (m) REVERT: B 290 ASP cc_start: 0.6967 (p0) cc_final: 0.6660 (p0) 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: 0.8068 (m110) REVERT: B 380 TYR cc_start: 0.7965 (m-80) cc_final: 0.7122 (m-80) REVERT: B 551 VAL cc_start: 0.8694 (t) cc_final: 0.8487 (p) REVERT: B 557 LYS cc_start: 0.8278 (ptpp) cc_final: 0.8037 (ptpt) REVERT: B 558 LYS cc_start: 0.8190 (mppt) cc_final: 0.7660 (mppt) REVERT: B 644 GLN cc_start: 0.8208 (tp40) cc_final: 0.7979 (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: 0.7152 (pm20) REVERT: B 698 SER cc_start: 0.7918 (t) cc_final: 0.7185 (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: 0.8270 (m) REVERT: B 736 VAL cc_start: 0.8582 (m) cc_final: 0.8296 (t) REVERT: B 810 SER cc_start: 0.8275 (t) cc_final: 0.8074 (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: 0.7940 (tt) REVERT: B 850 ILE cc_start: 0.8635 (mm) cc_final: 0.8360 (tp) REVERT: B 868 GLU cc_start: 0.6479 (tp30) cc_final: 0.6012 (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: 0.6537 (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: 0.6694 (tp30) REVERT: B 990 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6201 (mp0) REVERT: B 993 ILE cc_start: 0.8414 (tp) cc_final: 0.8165 (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: 0.8487 (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: 0.6462 (p0) REVERT: C 51 THR cc_start: 0.8419 (p) cc_final: 0.8192 (p) REVERT: C 105 ILE cc_start: 0.7383 (mm) cc_final: 0.7133 (mp) REVERT: C 117 LEU cc_start: 0.7543 (mt) cc_final: 0.7190 (mt) REVERT: C 212 GLU cc_start: 0.5157 (OUTLIER) cc_final: 0.4757 (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: 0.7311 (t80) REVERT: C 269 TYR cc_start: 0.8201 (m-80) cc_final: 0.7835 (m-80) REVERT: C 347 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6040 (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: 0.6401 (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: 0.6566 (t0) REVERT: C 427 ASP cc_start: 0.6600 (t70) cc_final: 0.6332 (t70) REVERT: C 442 ASP cc_start: 0.7161 (m-30) cc_final: 0.6932 (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: 0.6182 (m-10) REVERT: C 675 GLN cc_start: 0.7063 (mm-40) cc_final: 0.6817 (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: 0.6225 (tt0) REVERT: C 750 SER cc_start: 0.8746 (m) cc_final: 0.8254 (p) REVERT: C 751 ASN cc_start: 0.7961 (m-40) cc_final: 0.7516 (m-40) REVERT: C 776 LYS cc_start: 0.8326 (ttpt) cc_final: 0.8057 (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: 0.7907 (ttmm) REVERT: C 868 GLU cc_start: 0.7078 (tp30) cc_final: 0.6739 (tp30) REVERT: C 904 TYR cc_start: 0.6811 (m-10) cc_final: 0.6427 (m-10) REVERT: C 914 ASN cc_start: 0.7475 (p0) cc_final: 0.6940 (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: 0.7886 (ttmm) REVERT: C 975 SER cc_start: 0.8527 (m) cc_final: 0.8304 (t) REVERT: C 983 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7857 (ttm110) REVERT: C 1018 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8016 (mt) REVERT: C 1105 THR cc_start: 0.7596 (t) cc_final: 0.7325 (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: 0.7719 (t0) outliers start: 144 outliers final: 46 residues processed: 909 average time/residue: 0.3610 time to fit residues: 509.0472 Evaluate side-chains 706 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 645 time to evaluate : 2.334 ------------------------------------------------------------------------------- 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 242 LEU 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 260 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 146 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 chunk 279 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 239 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 B1005 GLN 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 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 540 ASN C 563 GLN C 658 ASN C 762 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 853 GLN C 901 GLN C 935 GLN C 957 GLN C 965 GLN C1002 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.145114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118702 restraints weight = 39987.116| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.68 r_work: 0.3412 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 25107 Z= 0.224 Angle : 0.677 11.808 34257 Z= 0.345 Chirality : 0.048 0.316 3957 Planarity : 0.005 0.055 4379 Dihedral : 7.817 81.973 4029 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 5.70 % Allowed : 15.07 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.14), residues: 3044 helix: 0.33 (0.21), residues: 650 sheet: -2.66 (0.20), residues: 509 loop : -3.29 (0.12), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 104 HIS 0.010 0.001 HIS A 519 PHE 0.039 0.002 PHE C1121 TYR 0.023 0.002 TYR C 265 ARG 0.007 0.001 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 28) link_NAG-ASN : angle 1.92672 ( 84) hydrogen bonds : bond 0.04469 ( 695) hydrogen bonds : angle 5.36137 ( 1938) SS BOND : bond 0.00639 ( 39) SS BOND : angle 2.82087 ( 78) covalent geometry : bond 0.00494 (25040) covalent geometry : angle 0.65802 (34095) *********************** 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 874 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 722 time to evaluate : 2.623 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: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7274 (m-10) cc_final: 0.6925 (m-10) REVERT: A 84 LEU cc_start: 0.8458 (pt) cc_final: 0.8105 (pt) REVERT: A 102 ARG cc_start: 0.7580 (mtm-85) cc_final: 0.6960 (mtm-85) REVERT: A 104 TRP cc_start: 0.7798 (OUTLIER) cc_final: 0.7515 (m-90) REVERT: A 129 LYS cc_start: 0.8073 (mtmm) cc_final: 0.7435 (mtmm) REVERT: A 188 ARG cc_start: 0.7936 (ptp-110) cc_final: 0.7475 (ptp90) REVERT: A 189 GLU cc_start: 0.8130 (pm20) cc_final: 0.7818 (pt0) REVERT: A 238 PHE cc_start: 0.7337 (t80) cc_final: 0.7086 (t80) REVERT: A 267 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8113 (p) REVERT: A 269 TYR cc_start: 0.8267 (m-80) cc_final: 0.7891 (m-10) REVERT: A 281 GLU cc_start: 0.7995 (pp20) cc_final: 0.7694 (pp20) REVERT: A 287 ASP cc_start: 0.7911 (p0) cc_final: 0.7621 (p0) REVERT: A 307 THR cc_start: 0.8313 (m) cc_final: 0.8022 (p) REVERT: A 351 TYR cc_start: 0.6642 (p90) cc_final: 0.6158 (p90) REVERT: A 355 ARG cc_start: 0.7155 (ttm170) cc_final: 0.6542 (ttm170) REVERT: A 358 ILE cc_start: 0.6574 (OUTLIER) cc_final: 0.6260 (pt) REVERT: A 380 TYR cc_start: 0.7305 (m-80) cc_final: 0.6786 (m-10) REVERT: A 386 LYS cc_start: 0.8320 (mttp) cc_final: 0.8044 (mttt) REVERT: A 452 LEU cc_start: 0.8096 (tt) cc_final: 0.7527 (mm) REVERT: A 468 ILE cc_start: 0.2456 (OUTLIER) cc_final: 0.2116 (pp) REVERT: A 558 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7979 (mtpp) REVERT: A 562 PHE cc_start: 0.7768 (p90) cc_final: 0.7534 (p90) REVERT: A 569 ILE cc_start: 0.8053 (pt) cc_final: 0.7710 (mp) REVERT: A 586 ASP cc_start: 0.7565 (t0) cc_final: 0.7219 (t0) REVERT: A 599 THR cc_start: 0.8565 (m) cc_final: 0.8234 (t) REVERT: A 643 PHE cc_start: 0.8304 (t80) cc_final: 0.8092 (t80) REVERT: A 654 GLU cc_start: 0.7332 (pm20) cc_final: 0.7075 (pm20) REVERT: A 670 ILE cc_start: 0.8477 (mm) cc_final: 0.8266 (mp) REVERT: A 675 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7416 (mm-40) REVERT: A 707 TYR cc_start: 0.8013 (t80) cc_final: 0.7762 (t80) REVERT: A 740 MET cc_start: 0.7928 (tpp) cc_final: 0.7708 (ttt) REVERT: A 751 ASN cc_start: 0.8243 (m-40) cc_final: 0.7954 (m-40) REVERT: A 774 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7340 (mp10) REVERT: A 787 GLN cc_start: 0.8062 (mt0) cc_final: 0.7731 (mt0) REVERT: A 803 SER cc_start: 0.8491 (m) cc_final: 0.8033 (t) REVERT: A 808 ASP cc_start: 0.7819 (t0) cc_final: 0.7562 (t0) REVERT: A 855 PHE cc_start: 0.8258 (m-80) cc_final: 0.7513 (m-80) REVERT: A 868 GLU cc_start: 0.7863 (tp30) cc_final: 0.7608 (tp30) REVERT: A 949 GLN cc_start: 0.8013 (mm110) cc_final: 0.7545 (mm-40) REVERT: A 970 PHE cc_start: 0.8016 (m-10) cc_final: 0.7802 (m-10) REVERT: A 993 ILE cc_start: 0.8680 (tp) cc_final: 0.8338 (tp) REVERT: A 995 ARG cc_start: 0.8078 (ttp-170) cc_final: 0.7780 (ttm170) REVERT: A 998 THR cc_start: 0.8150 (m) cc_final: 0.7842 (p) REVERT: A 1030 SER cc_start: 0.8734 (m) cc_final: 0.8305 (t) REVERT: A 1094 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8098 (m) REVERT: A 1097 SER cc_start: 0.8599 (t) cc_final: 0.8014 (p) REVERT: B 53 ASP cc_start: 0.7333 (t0) cc_final: 0.7029 (t0) REVERT: B 83 VAL cc_start: 0.6346 (OUTLIER) cc_final: 0.5872 (t) REVERT: B 105 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7612 (pt) REVERT: B 106 PHE cc_start: 0.7957 (m-80) cc_final: 0.7660 (m-10) REVERT: B 169 GLU cc_start: 0.7877 (pm20) cc_final: 0.7452 (pm20) REVERT: B 177 MET cc_start: 0.6640 (tmt) cc_final: 0.6290 (tmt) REVERT: B 189 GLU cc_start: 0.7265 (pm20) cc_final: 0.6705 (mp0) REVERT: B 201 ILE cc_start: 0.8539 (mt) cc_final: 0.8010 (tt) REVERT: B 224 GLU cc_start: 0.6884 (pm20) cc_final: 0.6545 (pm20) REVERT: B 228 ASP cc_start: 0.6639 (t0) cc_final: 0.6215 (t0) REVERT: B 266 TYR cc_start: 0.7200 (m-10) cc_final: 0.7000 (m-10) REVERT: B 290 ASP cc_start: 0.7719 (p0) cc_final: 0.7470 (p0) REVERT: B 319 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7638 (ttm110) REVERT: B 365 TYR cc_start: 0.8026 (m-80) cc_final: 0.7819 (m-10) REVERT: B 547 LYS cc_start: 0.8267 (mttm) cc_final: 0.7846 (mttp) REVERT: B 551 VAL cc_start: 0.9003 (t) cc_final: 0.8600 (p) REVERT: B 557 LYS cc_start: 0.8543 (ptpp) cc_final: 0.8179 (ptpt) REVERT: B 558 LYS cc_start: 0.8588 (mppt) cc_final: 0.8155 (mppt) REVERT: B 580 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7646 (mm-40) REVERT: B 589 PRO cc_start: 0.8854 (Cg_exo) cc_final: 0.8336 (Cg_endo) REVERT: B 698 SER cc_start: 0.8233 (t) cc_final: 0.7857 (p) REVERT: B 703 ASN cc_start: 0.8689 (t0) cc_final: 0.7809 (m-40) REVERT: B 705 VAL cc_start: 0.8718 (t) cc_final: 0.8372 (m) REVERT: B 711 SER cc_start: 0.8628 (t) cc_final: 0.8400 (t) REVERT: B 752 LEU cc_start: 0.8798 (mt) cc_final: 0.8543 (mp) REVERT: B 773 GLU cc_start: 0.7719 (tm-30) cc_final: 0.6819 (tm-30) REVERT: B 774 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7817 (mm-40) REVERT: B 810 SER cc_start: 0.8659 (t) cc_final: 0.8440 (p) REVERT: B 819 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6919 (mt-10) REVERT: B 821 LEU cc_start: 0.8809 (tp) cc_final: 0.8327 (tt) REVERT: B 868 GLU cc_start: 0.7344 (tp30) cc_final: 0.6754 (tp30) REVERT: B 914 ASN cc_start: 0.8287 (p0) cc_final: 0.7852 (p0) REVERT: B 918 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7585 (mt-10) REVERT: B 922 LEU cc_start: 0.8529 (tp) cc_final: 0.8303 (tt) REVERT: B 950 ASP cc_start: 0.7638 (t70) cc_final: 0.7173 (t70) REVERT: B 957 GLN cc_start: 0.8079 (tt0) cc_final: 0.7775 (tt0) REVERT: B 975 SER cc_start: 0.8779 (m) cc_final: 0.8380 (t) REVERT: B 984 LEU cc_start: 0.8329 (tp) cc_final: 0.8025 (tp) REVERT: B 988 GLU cc_start: 0.7782 (mm-30) cc_final: 0.6899 (tp30) REVERT: B 990 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: B 993 ILE cc_start: 0.8580 (tp) cc_final: 0.8202 (tp) REVERT: B 1029 MET cc_start: 0.8574 (tpp) cc_final: 0.8158 (tpp) REVERT: B 1038 LYS cc_start: 0.8819 (mtpp) cc_final: 0.8580 (mtpp) REVERT: B 1090 PRO cc_start: 0.8512 (Cg_exo) cc_final: 0.8266 (Cg_endo) REVERT: B 1097 SER cc_start: 0.9026 (t) cc_final: 0.8391 (p) REVERT: C 52 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7692 (tm130) REVERT: C 105 ILE cc_start: 0.8037 (mm) cc_final: 0.7691 (mm) REVERT: C 106 PHE cc_start: 0.7753 (m-80) cc_final: 0.7456 (m-80) REVERT: C 160 TYR cc_start: 0.7229 (p90) cc_final: 0.6998 (p90) REVERT: C 187 LEU cc_start: 0.8294 (tp) cc_final: 0.7956 (tp) REVERT: C 188 ARG cc_start: 0.7775 (ptp-170) cc_final: 0.7463 (ptp-170) REVERT: C 204 LYS cc_start: 0.8339 (tmtt) cc_final: 0.8072 (tttm) REVERT: C 224 GLU cc_start: 0.7429 (pm20) cc_final: 0.6986 (mp0) REVERT: C 238 PHE cc_start: 0.8115 (t80) cc_final: 0.7904 (t80) REVERT: C 239 GLN cc_start: 0.8032 (tp40) cc_final: 0.7597 (tp40) REVERT: C 269 TYR cc_start: 0.8648 (m-80) cc_final: 0.8245 (m-80) REVERT: C 347 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6860 (t80) REVERT: C 349 SER cc_start: 0.8242 (p) cc_final: 0.8028 (t) REVERT: C 377 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7761 (t80) REVERT: C 398 ASP cc_start: 0.7319 (t70) cc_final: 0.7100 (t0) REVERT: C 414 GLN cc_start: 0.7474 (mp10) cc_final: 0.7105 (mp10) REVERT: C 420 ASP cc_start: 0.7521 (t0) cc_final: 0.7092 (t0) REVERT: C 427 ASP cc_start: 0.7094 (t70) cc_final: 0.6769 (t70) REVERT: C 461 LEU cc_start: 0.8343 (mm) cc_final: 0.8026 (mt) REVERT: C 465 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 516 GLU cc_start: 0.7403 (pt0) cc_final: 0.6265 (pt0) REVERT: C 641 ASN cc_start: 0.6598 (t0) cc_final: 0.6381 (t0) REVERT: C 656 VAL cc_start: 0.8591 (m) cc_final: 0.8343 (p) REVERT: C 707 TYR cc_start: 0.7933 (t80) cc_final: 0.7138 (t80) REVERT: C 711 SER cc_start: 0.8797 (m) cc_final: 0.8474 (p) REVERT: C 750 SER cc_start: 0.8511 (m) cc_final: 0.8157 (p) REVERT: C 751 ASN cc_start: 0.8001 (m-40) cc_final: 0.7571 (m-40) REVERT: C 755 GLN cc_start: 0.8000 (pp30) cc_final: 0.7688 (pp30) REVERT: C 776 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8255 (tttp) REVERT: C 779 GLN cc_start: 0.7736 (tt0) cc_final: 0.7380 (tm-30) REVERT: C 788 ILE cc_start: 0.8407 (mm) cc_final: 0.8200 (mm) REVERT: C 804 GLN cc_start: 0.8069 (mt0) cc_final: 0.7844 (mt0) REVERT: C 825 LYS cc_start: 0.8571 (tppt) cc_final: 0.8158 (ttmm) REVERT: C 851 CYS cc_start: 0.7929 (t) cc_final: 0.7519 (m) REVERT: C 868 GLU cc_start: 0.7876 (tp30) cc_final: 0.7226 (tp30) REVERT: C 921 LYS cc_start: 0.8798 (mmmt) cc_final: 0.8500 (mmmm) REVERT: C 933 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7609 (mttp) REVERT: C 964 LYS cc_start: 0.8511 (ttpp) cc_final: 0.8266 (ttmm) REVERT: C 984 LEU cc_start: 0.8075 (mp) cc_final: 0.7830 (mt) REVERT: C 1014 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7670 (tpp80) REVERT: C 1038 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8398 (mtpp) REVERT: C 1073 LYS cc_start: 0.8569 (mtpt) cc_final: 0.8245 (mtpp) REVERT: C 1139 ASP cc_start: 0.8342 (t70) cc_final: 0.8133 (t0) outliers start: 152 outliers final: 92 residues processed: 816 average time/residue: 0.3819 time to fit residues: 486.8542 Evaluate side-chains 758 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 653 time to evaluate : 2.478 ------------------------------------------------------------------------------- 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 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 468 ILE 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 617 CYS 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 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 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 242 LEU 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 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 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 1005 GLN 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 1081 ILE 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 199 PHE Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 231 ILE 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 453 TYR 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 935 GLN 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 1114 ILE 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 103 optimal weight: 2.9990 chunk 232 optimal weight: 0.3980 chunk 216 optimal weight: 0.7980 chunk 301 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 272 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 212 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 87 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 784 GLN C1010 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 = 0.3902 r_free = 0.3902 target = 0.145860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119700 restraints weight = 39950.547| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.68 r_work: 0.3422 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25107 Z= 0.136 Angle : 0.625 12.637 34257 Z= 0.317 Chirality : 0.046 0.333 3957 Planarity : 0.004 0.057 4379 Dihedral : 7.417 79.846 4011 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 5.77 % Allowed : 17.51 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.14), residues: 3044 helix: 0.78 (0.21), residues: 650 sheet: -2.25 (0.20), residues: 526 loop : -3.05 (0.12), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.007 0.001 HIS A 205 PHE 0.028 0.002 PHE C1121 TYR 0.021 0.001 TYR B 655 ARG 0.010 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 28) link_NAG-ASN : angle 1.95312 ( 84) hydrogen bonds : bond 0.03780 ( 695) hydrogen bonds : angle 5.04264 ( 1938) SS BOND : bond 0.00504 ( 39) SS BOND : angle 2.86215 ( 78) covalent geometry : bond 0.00308 (25040) covalent geometry : angle 0.60347 (34095) *********************** 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 824 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 670 time to evaluate : 2.729 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: A 49 HIS cc_start: 0.7993 (t-90) cc_final: 0.7705 (t-170) REVERT: A 65 PHE cc_start: 0.7199 (m-10) cc_final: 0.6881 (m-10) REVERT: A 102 ARG cc_start: 0.7467 (mtm-85) cc_final: 0.6894 (mtm-85) REVERT: A 104 TRP cc_start: 0.7845 (OUTLIER) cc_final: 0.7491 (m-90) REVERT: A 129 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7378 (mtmm) REVERT: A 188 ARG cc_start: 0.7917 (ptp-110) cc_final: 0.7461 (ptp90) REVERT: A 189 GLU cc_start: 0.8159 (pm20) cc_final: 0.7848 (pt0) REVERT: A 214 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6408 (mt-10) REVERT: A 267 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8150 (p) REVERT: A 269 TYR cc_start: 0.8302 (m-80) cc_final: 0.8031 (m-80) REVERT: A 281 GLU cc_start: 0.7912 (pp20) cc_final: 0.7641 (pp20) REVERT: A 287 ASP cc_start: 0.7812 (p0) cc_final: 0.7288 (p0) REVERT: A 307 THR cc_start: 0.8331 (m) cc_final: 0.7973 (p) REVERT: A 351 TYR cc_start: 0.6741 (p90) cc_final: 0.6258 (p90) REVERT: A 355 ARG cc_start: 0.6747 (ttm170) cc_final: 0.6490 (ttm-80) REVERT: A 358 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6339 (pt) REVERT: A 380 TYR cc_start: 0.7320 (m-80) cc_final: 0.6779 (m-10) REVERT: A 386 LYS cc_start: 0.8308 (mttp) cc_final: 0.8050 (mttt) REVERT: A 436 TRP cc_start: 0.6721 (p90) cc_final: 0.6116 (p90) REVERT: A 452 LEU cc_start: 0.8065 (tt) cc_final: 0.7431 (mm) REVERT: A 468 ILE cc_start: 0.2409 (OUTLIER) cc_final: 0.2032 (pp) REVERT: A 558 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7990 (mtpp) REVERT: A 562 PHE cc_start: 0.7789 (p90) cc_final: 0.7534 (p90) REVERT: A 564 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7454 (tm-30) REVERT: A 569 ILE cc_start: 0.8001 (pt) cc_final: 0.7739 (mp) REVERT: A 588 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8713 (p) REVERT: A 654 GLU cc_start: 0.7346 (pm20) cc_final: 0.7042 (pm20) REVERT: A 670 ILE cc_start: 0.8439 (mm) cc_final: 0.8223 (mp) REVERT: A 675 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7135 (mm-40) REVERT: A 692 ILE cc_start: 0.8108 (mt) cc_final: 0.7546 (mt) REVERT: A 707 TYR cc_start: 0.7962 (t80) cc_final: 0.7702 (t80) REVERT: A 751 ASN cc_start: 0.8249 (m-40) cc_final: 0.7951 (m-40) REVERT: A 768 THR cc_start: 0.8362 (m) cc_final: 0.8106 (p) REVERT: A 774 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7309 (mp10) REVERT: A 787 GLN cc_start: 0.8036 (mt0) cc_final: 0.7799 (mt0) REVERT: A 808 ASP cc_start: 0.7854 (t0) cc_final: 0.7561 (t0) REVERT: A 851 CYS cc_start: 0.7962 (t) cc_final: 0.7333 (p) REVERT: A 855 PHE cc_start: 0.8129 (m-80) cc_final: 0.7507 (m-80) REVERT: A 868 GLU cc_start: 0.7827 (tp30) cc_final: 0.7573 (tp30) REVERT: A 949 GLN cc_start: 0.8019 (mm110) cc_final: 0.7580 (mm-40) REVERT: A 970 PHE cc_start: 0.7874 (m-80) cc_final: 0.7667 (m-10) REVERT: A 993 ILE cc_start: 0.8631 (tp) cc_final: 0.8257 (tp) REVERT: A 995 ARG cc_start: 0.7815 (ttp-170) cc_final: 0.7576 (ttm170) REVERT: A 998 THR cc_start: 0.8107 (m) cc_final: 0.7853 (p) REVERT: A 1029 MET cc_start: 0.8371 (ttm) cc_final: 0.8156 (ttm) REVERT: A 1030 SER cc_start: 0.8730 (m) cc_final: 0.8279 (t) REVERT: A 1094 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.8061 (t) REVERT: A 1097 SER cc_start: 0.8624 (t) cc_final: 0.7925 (p) REVERT: A 1107 ARG cc_start: 0.7759 (mtt90) cc_final: 0.7500 (mtt90) REVERT: A 1139 ASP cc_start: 0.8041 (t70) cc_final: 0.7828 (t70) REVERT: B 83 VAL cc_start: 0.6293 (OUTLIER) cc_final: 0.5671 (t) REVERT: B 105 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7562 (pt) REVERT: B 106 PHE cc_start: 0.7925 (m-80) cc_final: 0.7587 (m-10) REVERT: B 169 GLU cc_start: 0.7872 (pm20) cc_final: 0.7342 (pm20) REVERT: B 177 MET cc_start: 0.6710 (tmt) cc_final: 0.6082 (tmt) REVERT: B 188 ARG cc_start: 0.7251 (ttm-80) cc_final: 0.6901 (ttm-80) REVERT: B 201 ILE cc_start: 0.8529 (mt) cc_final: 0.7996 (tt) REVERT: B 224 GLU cc_start: 0.6695 (pm20) cc_final: 0.6374 (pm20) REVERT: B 266 TYR cc_start: 0.7091 (m-10) cc_final: 0.6886 (m-10) REVERT: B 290 ASP cc_start: 0.7678 (p0) cc_final: 0.7459 (p0) REVERT: B 319 ARG cc_start: 0.7860 (ttm110) cc_final: 0.7645 (ttm110) REVERT: B 537 LYS cc_start: 0.8174 (tttp) cc_final: 0.7906 (tttm) REVERT: B 547 LYS cc_start: 0.8177 (mttm) cc_final: 0.7732 (mttp) REVERT: B 551 VAL cc_start: 0.8943 (t) cc_final: 0.8561 (p) REVERT: B 557 LYS cc_start: 0.8547 (ptpp) cc_final: 0.8235 (ptpt) REVERT: B 558 LYS cc_start: 0.8550 (mppt) cc_final: 0.8097 (mppt) REVERT: B 589 PRO cc_start: 0.8693 (Cg_exo) cc_final: 0.8119 (Cg_endo) REVERT: B 697 MET cc_start: 0.8031 (mtm) cc_final: 0.7802 (mtm) REVERT: B 698 SER cc_start: 0.8354 (t) cc_final: 0.7854 (p) REVERT: B 705 VAL cc_start: 0.8645 (t) cc_final: 0.8309 (m) REVERT: B 711 SER cc_start: 0.8639 (t) cc_final: 0.8402 (t) REVERT: B 752 LEU cc_start: 0.8781 (mt) cc_final: 0.8456 (mp) REVERT: B 773 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7085 (tm-30) REVERT: B 810 SER cc_start: 0.8619 (t) cc_final: 0.8415 (p) REVERT: B 821 LEU cc_start: 0.8813 (tp) cc_final: 0.8324 (tt) REVERT: B 914 ASN cc_start: 0.8260 (p0) cc_final: 0.7829 (p0) REVERT: B 918 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7546 (mt-10) REVERT: B 950 ASP cc_start: 0.7594 (t70) cc_final: 0.7169 (t70) REVERT: B 957 GLN cc_start: 0.8092 (tt0) cc_final: 0.7786 (tt0) REVERT: B 975 SER cc_start: 0.8674 (m) cc_final: 0.8285 (t) REVERT: B 984 LEU cc_start: 0.8323 (tp) cc_final: 0.8059 (tp) REVERT: B 990 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: B 993 ILE cc_start: 0.8599 (tp) cc_final: 0.8352 (tp) REVERT: B 1029 MET cc_start: 0.8516 (tpp) cc_final: 0.8114 (tpp) REVERT: B 1038 LYS cc_start: 0.8791 (mtpp) cc_final: 0.8504 (mtpp) REVERT: B 1084 ASP cc_start: 0.7713 (t0) cc_final: 0.7511 (t0) REVERT: B 1090 PRO cc_start: 0.8503 (Cg_exo) cc_final: 0.8291 (Cg_endo) REVERT: B 1097 SER cc_start: 0.8975 (t) cc_final: 0.8422 (p) REVERT: B 1107 ARG cc_start: 0.7922 (ptt-90) cc_final: 0.7156 (ptt180) REVERT: C 53 ASP cc_start: 0.7434 (t0) cc_final: 0.7182 (t0) REVERT: C 105 ILE cc_start: 0.8035 (mm) cc_final: 0.7621 (mm) REVERT: C 106 PHE cc_start: 0.7714 (m-80) cc_final: 0.7363 (m-10) REVERT: C 160 TYR cc_start: 0.7246 (p90) cc_final: 0.7023 (p90) REVERT: C 187 LEU cc_start: 0.8228 (tp) cc_final: 0.7380 (tt) REVERT: C 188 ARG cc_start: 0.7732 (ptp-170) cc_final: 0.7436 (ptp-170) REVERT: C 204 LYS cc_start: 0.8464 (tmtt) cc_final: 0.8259 (tttp) REVERT: C 224 GLU cc_start: 0.7455 (pm20) cc_final: 0.7037 (mp0) REVERT: C 239 GLN cc_start: 0.8056 (tp40) cc_final: 0.7737 (tp40) REVERT: C 269 TYR cc_start: 0.8644 (m-80) cc_final: 0.8169 (m-80) REVERT: C 347 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6736 (t80) REVERT: C 349 SER cc_start: 0.8258 (p) cc_final: 0.7913 (t) REVERT: C 414 GLN cc_start: 0.7511 (mp10) cc_final: 0.7199 (mp10) REVERT: C 420 ASP cc_start: 0.7378 (t0) cc_final: 0.6924 (t0) REVERT: C 427 ASP cc_start: 0.7025 (t70) cc_final: 0.6672 (t70) REVERT: C 439 ASN cc_start: 0.7074 (p0) cc_final: 0.6852 (p0) REVERT: C 465 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7650 (tm-30) REVERT: C 543 PHE cc_start: 0.8116 (m-10) cc_final: 0.7658 (m-10) REVERT: C 641 ASN cc_start: 0.6686 (t0) cc_final: 0.6375 (t0) REVERT: C 656 VAL cc_start: 0.8561 (m) cc_final: 0.8356 (p) REVERT: C 707 TYR cc_start: 0.7876 (t80) cc_final: 0.7044 (t80) REVERT: C 729 VAL cc_start: 0.8570 (p) cc_final: 0.8349 (t) REVERT: C 750 SER cc_start: 0.8473 (m) cc_final: 0.8033 (p) REVERT: C 751 ASN cc_start: 0.7969 (m-40) cc_final: 0.7391 (m-40) REVERT: C 752 LEU cc_start: 0.8920 (mm) cc_final: 0.8519 (mt) REVERT: C 755 GLN cc_start: 0.7957 (pp30) cc_final: 0.7335 (pp30) REVERT: C 776 LYS cc_start: 0.8553 (ttpt) cc_final: 0.8259 (tttp) REVERT: C 779 GLN cc_start: 0.7793 (tt0) cc_final: 0.7518 (tm-30) REVERT: C 825 LYS cc_start: 0.8447 (tppt) cc_final: 0.8145 (tppt) REVERT: C 868 GLU cc_start: 0.7848 (tp30) cc_final: 0.7456 (tp30) REVERT: C 904 TYR cc_start: 0.7219 (m-10) cc_final: 0.6938 (m-10) REVERT: C 921 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8314 (mmmm) REVERT: C 933 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7613 (mttt) REVERT: C 964 LYS cc_start: 0.8471 (ttpp) cc_final: 0.8228 (ttmm) REVERT: C 984 LEU cc_start: 0.8056 (mp) cc_final: 0.7798 (mt) REVERT: C 1014 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7632 (tpp80) REVERT: C 1018 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8195 (mp) REVERT: C 1038 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8403 (mtpp) REVERT: C 1073 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8122 (mtpp) REVERT: C 1139 ASP cc_start: 0.8332 (t70) cc_final: 0.8102 (t0) outliers start: 154 outliers final: 91 residues processed: 759 average time/residue: 0.3738 time to fit residues: 443.8223 Evaluate side-chains 744 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 639 time to evaluate : 2.485 ------------------------------------------------------------------------------- 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 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 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 468 ILE 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 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 712 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET 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 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 242 LEU 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 453 TYR Chi-restraints excluded: chain B residue 468 ILE 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 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 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 1081 ILE 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 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 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 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 742 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 994 ASP 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 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 80 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 109 optimal weight: 0.0050 chunk 278 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 105 optimal weight: 4.9990 chunk 271 optimal weight: 3.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 955 ASN A1002 GLN A1011 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 239 GLN B 422 ASN B 895 GLN C 30 ASN C 52 GLN C 450 ASN C 564 GLN C1010 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.142710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116492 restraints weight = 40319.256| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.69 r_work: 0.3376 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25107 Z= 0.179 Angle : 0.638 10.101 34257 Z= 0.324 Chirality : 0.047 0.336 3957 Planarity : 0.004 0.061 4379 Dihedral : 7.406 93.489 4006 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 5.55 % Allowed : 19.24 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.14), residues: 3044 helix: 0.95 (0.22), residues: 634 sheet: -1.94 (0.21), residues: 541 loop : -2.94 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 353 HIS 0.006 0.001 HIS C1083 PHE 0.030 0.002 PHE A 86 TYR 0.026 0.002 TYR B 707 ARG 0.008 0.001 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 28) link_NAG-ASN : angle 2.06682 ( 84) hydrogen bonds : bond 0.03965 ( 695) hydrogen bonds : angle 4.94497 ( 1938) SS BOND : bond 0.00526 ( 39) SS BOND : angle 2.44031 ( 78) covalent geometry : bond 0.00397 (25040) covalent geometry : angle 0.62045 (34095) *********************** 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 803 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 655 time to evaluate : 2.766 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: A 49 HIS cc_start: 0.8040 (t-90) cc_final: 0.7695 (t-170) REVERT: A 52 GLN cc_start: 0.7616 (tm-30) cc_final: 0.7324 (tm-30) REVERT: A 65 PHE cc_start: 0.7289 (m-10) cc_final: 0.6998 (m-10) REVERT: A 84 LEU cc_start: 0.8651 (pt) cc_final: 0.8390 (pt) REVERT: A 102 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7006 (mtm-85) REVERT: A 104 TRP cc_start: 0.7852 (OUTLIER) cc_final: 0.7335 (m-10) REVERT: A 129 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7346 (mtmm) REVERT: A 188 ARG cc_start: 0.7998 (ptp-110) cc_final: 0.7503 (ptp90) REVERT: A 189 GLU cc_start: 0.8204 (pm20) cc_final: 0.7930 (pt0) REVERT: A 190 PHE cc_start: 0.8380 (m-80) cc_final: 0.8055 (m-10) REVERT: A 214 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6158 (mt-10) REVERT: A 224 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6770 (mm-30) REVERT: A 267 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8184 (p) REVERT: A 269 TYR cc_start: 0.8281 (m-80) cc_final: 0.8006 (m-80) REVERT: A 307 THR cc_start: 0.8381 (m) cc_final: 0.8072 (p) REVERT: A 340 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6685 (pm20) REVERT: A 356 LYS cc_start: 0.7439 (pttt) cc_final: 0.7148 (pttm) REVERT: A 358 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.7126 (pt) REVERT: A 380 TYR cc_start: 0.7315 (m-80) cc_final: 0.6798 (m-10) REVERT: A 386 LYS cc_start: 0.8377 (mttp) cc_final: 0.8123 (mttt) REVERT: A 436 TRP cc_start: 0.6701 (p90) cc_final: 0.5964 (p90) REVERT: A 558 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8000 (mtpp) REVERT: A 564 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7340 (tm-30) REVERT: A 569 ILE cc_start: 0.8073 (pt) cc_final: 0.7871 (mp) REVERT: A 578 ASP cc_start: 0.7990 (t0) cc_final: 0.7754 (t0) REVERT: A 586 ASP cc_start: 0.7445 (t0) cc_final: 0.7068 (m-30) REVERT: A 654 GLU cc_start: 0.7409 (pm20) cc_final: 0.7085 (pm20) REVERT: A 675 GLN cc_start: 0.7534 (mm-40) cc_final: 0.7137 (mm-40) REVERT: A 707 TYR cc_start: 0.8047 (t80) cc_final: 0.7799 (t80) REVERT: A 730 SER cc_start: 0.8662 (t) cc_final: 0.8455 (t) REVERT: A 731 MET cc_start: 0.8231 (mtp) cc_final: 0.7891 (mtm) REVERT: A 768 THR cc_start: 0.8471 (m) cc_final: 0.8184 (p) REVERT: A 787 GLN cc_start: 0.8019 (mt0) cc_final: 0.7774 (mt0) REVERT: A 808 ASP cc_start: 0.7931 (t0) cc_final: 0.7621 (t0) REVERT: A 851 CYS cc_start: 0.7966 (t) cc_final: 0.7328 (p) REVERT: A 855 PHE cc_start: 0.8265 (m-80) cc_final: 0.7602 (m-80) REVERT: A 868 GLU cc_start: 0.7862 (tp30) cc_final: 0.7574 (tp30) REVERT: A 918 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 949 GLN cc_start: 0.8136 (mm110) cc_final: 0.7660 (mm-40) REVERT: A 969 LYS cc_start: 0.8434 (mtmm) cc_final: 0.8197 (mtmm) REVERT: A 993 ILE cc_start: 0.8653 (tp) cc_final: 0.8442 (tp) REVERT: A 998 THR cc_start: 0.8244 (m) cc_final: 0.7970 (p) REVERT: A 1000 ARG cc_start: 0.8694 (mtt180) cc_final: 0.8470 (mtt180) REVERT: A 1030 SER cc_start: 0.8776 (m) cc_final: 0.8364 (t) REVERT: A 1051 SER cc_start: 0.8174 (m) cc_final: 0.7954 (m) REVERT: A 1094 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8094 (t) REVERT: A 1097 SER cc_start: 0.8653 (t) cc_final: 0.7933 (p) REVERT: A 1135 ASN cc_start: 0.8170 (t0) cc_final: 0.7964 (t0) REVERT: A 1139 ASP cc_start: 0.8087 (t70) cc_final: 0.7731 (t70) REVERT: B 106 PHE cc_start: 0.7994 (m-80) cc_final: 0.7754 (m-10) REVERT: B 119 ILE cc_start: 0.8606 (mp) cc_final: 0.8258 (mt) REVERT: B 129 LYS cc_start: 0.8088 (tppt) cc_final: 0.7690 (tppt) REVERT: B 169 GLU cc_start: 0.7991 (pm20) cc_final: 0.7455 (pm20) REVERT: B 177 MET cc_start: 0.6735 (tmt) cc_final: 0.6249 (tmt) REVERT: B 188 ARG cc_start: 0.7320 (ttm-80) cc_final: 0.6995 (ttm-80) REVERT: B 194 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7109 (p0) REVERT: B 198 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.6101 (m-80) REVERT: B 201 ILE cc_start: 0.8529 (mt) cc_final: 0.8010 (tt) REVERT: B 224 GLU cc_start: 0.6796 (pm20) cc_final: 0.6452 (pm20) REVERT: B 298 GLU cc_start: 0.8137 (tt0) cc_final: 0.7104 (mt-10) REVERT: B 319 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7617 (ttm110) REVERT: B 537 LYS cc_start: 0.8260 (tttp) cc_final: 0.8039 (tttm) REVERT: B 549 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8490 (p) REVERT: B 557 LYS cc_start: 0.8598 (ptpp) cc_final: 0.8256 (ptpt) REVERT: B 558 LYS cc_start: 0.8578 (mppt) cc_final: 0.8127 (mppt) REVERT: B 589 PRO cc_start: 0.8615 (Cg_exo) cc_final: 0.8160 (Cg_endo) REVERT: B 604 THR cc_start: 0.8615 (p) cc_final: 0.8283 (t) REVERT: B 663 ASP cc_start: 0.7825 (m-30) cc_final: 0.7586 (m-30) REVERT: B 698 SER cc_start: 0.8423 (t) cc_final: 0.7982 (p) REVERT: B 711 SER cc_start: 0.8654 (t) cc_final: 0.8399 (t) REVERT: B 752 LEU cc_start: 0.8781 (mt) cc_final: 0.8502 (mp) REVERT: B 773 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7055 (tm-30) REVERT: B 774 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7832 (mm-40) REVERT: B 810 SER cc_start: 0.8692 (t) cc_final: 0.8490 (p) REVERT: B 821 LEU cc_start: 0.8810 (tp) cc_final: 0.8365 (tt) REVERT: B 904 TYR cc_start: 0.7574 (m-80) cc_final: 0.7250 (m-80) REVERT: B 914 ASN cc_start: 0.8350 (p0) cc_final: 0.7943 (p0) REVERT: B 918 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7589 (mt-10) REVERT: B 950 ASP cc_start: 0.7713 (t70) cc_final: 0.7258 (t0) REVERT: B 957 GLN cc_start: 0.8189 (tt0) cc_final: 0.7924 (tt0) REVERT: B 969 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8343 (mtmm) REVERT: B 975 SER cc_start: 0.8651 (m) cc_final: 0.8255 (t) REVERT: B 984 LEU cc_start: 0.8324 (tp) cc_final: 0.8026 (tp) REVERT: B 990 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: B 993 ILE cc_start: 0.8706 (tp) cc_final: 0.8408 (tp) REVERT: B 1029 MET cc_start: 0.8616 (tpp) cc_final: 0.7807 (tpp) REVERT: B 1033 VAL cc_start: 0.8866 (t) cc_final: 0.8534 (p) REVERT: B 1038 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8458 (mtpp) REVERT: B 1084 ASP cc_start: 0.7903 (t0) cc_final: 0.7672 (t0) REVERT: B 1097 SER cc_start: 0.8921 (t) cc_final: 0.8361 (p) REVERT: B 1107 ARG cc_start: 0.7936 (ptt-90) cc_final: 0.7271 (ptt180) REVERT: C 105 ILE cc_start: 0.8068 (mm) cc_final: 0.7688 (mm) REVERT: C 106 PHE cc_start: 0.7715 (m-80) cc_final: 0.7439 (m-10) REVERT: C 160 TYR cc_start: 0.7368 (p90) cc_final: 0.7114 (p90) REVERT: C 187 LEU cc_start: 0.8308 (tp) cc_final: 0.7504 (tt) REVERT: C 188 ARG cc_start: 0.7729 (ptp-170) cc_final: 0.7426 (ptp-170) REVERT: C 204 LYS cc_start: 0.8521 (tmtt) cc_final: 0.8259 (tttp) REVERT: C 224 GLU cc_start: 0.7471 (pm20) cc_final: 0.7209 (mp0) REVERT: C 269 TYR cc_start: 0.8706 (m-80) cc_final: 0.8209 (m-80) REVERT: C 349 SER cc_start: 0.8448 (p) cc_final: 0.8053 (t) REVERT: C 362 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7720 (p) REVERT: C 390 LEU cc_start: 0.7994 (pt) cc_final: 0.7785 (pt) REVERT: C 420 ASP cc_start: 0.7349 (t0) cc_final: 0.6867 (t0) REVERT: C 427 ASP cc_start: 0.7089 (t70) cc_final: 0.6701 (t70) REVERT: C 465 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7577 (tm-30) REVERT: C 588 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8345 (p) REVERT: C 641 ASN cc_start: 0.6720 (t0) cc_final: 0.6495 (t0) REVERT: C 643 PHE cc_start: 0.8311 (t80) cc_final: 0.7974 (t80) REVERT: C 656 VAL cc_start: 0.8587 (m) cc_final: 0.8332 (p) REVERT: C 707 TYR cc_start: 0.7959 (t80) cc_final: 0.7122 (t80) REVERT: C 751 ASN cc_start: 0.8004 (m-40) cc_final: 0.7681 (m-40) REVERT: C 752 LEU cc_start: 0.8939 (mm) cc_final: 0.8507 (mt) REVERT: C 755 GLN cc_start: 0.8057 (pp30) cc_final: 0.7432 (pp30) REVERT: C 776 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8295 (tttp) REVERT: C 779 GLN cc_start: 0.7909 (tt0) cc_final: 0.7625 (tm-30) REVERT: C 797 PHE cc_start: 0.8350 (m-10) cc_final: 0.8067 (m-80) REVERT: C 825 LYS cc_start: 0.8523 (tppt) cc_final: 0.8184 (tppt) REVERT: C 868 GLU cc_start: 0.7885 (tp30) cc_final: 0.7480 (tp30) REVERT: C 894 LEU cc_start: 0.8140 (mt) cc_final: 0.7934 (mp) REVERT: C 921 LYS cc_start: 0.8722 (mmmt) cc_final: 0.8281 (mmmm) REVERT: C 933 LYS cc_start: 0.7866 (mtpt) cc_final: 0.7565 (mttt) REVERT: C 964 LYS cc_start: 0.8505 (ttpp) cc_final: 0.8251 (ttmm) REVERT: C 984 LEU cc_start: 0.8097 (mp) cc_final: 0.7796 (mt) REVERT: C 1002 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7698 (tm-30) REVERT: C 1038 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8437 (mtpp) REVERT: C 1066 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7932 (p) REVERT: C 1073 LYS cc_start: 0.8575 (mtpt) cc_final: 0.8181 (mtmt) REVERT: C 1139 ASP cc_start: 0.8391 (t70) cc_final: 0.8190 (t0) REVERT: C 1144 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7925 (mm-30) outliers start: 148 outliers final: 98 residues processed: 745 average time/residue: 0.3809 time to fit residues: 439.2925 Evaluate side-chains 721 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 607 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR 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 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 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 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 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 1066 THR Chi-restraints excluded: chain A residue 1072 GLU 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 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 205 HIS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU 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 591 SER 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 750 SER Chi-restraints excluded: chain B residue 754 LEU 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 969 LYS 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 1081 ILE 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 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 229 LEU Chi-restraints excluded: chain C residue 231 ILE 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 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 742 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP 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 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 1066 THR Chi-restraints excluded: chain C residue 1104 VAL 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 27 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 295 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 chunk 233 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 751 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 992 GLN C 30 ASN C1010 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.116023 restraints weight = 40291.330| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.70 r_work: 0.3367 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25107 Z= 0.167 Angle : 0.633 10.843 34257 Z= 0.321 Chirality : 0.047 0.335 3957 Planarity : 0.004 0.066 4379 Dihedral : 7.270 93.605 4000 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 5.89 % Allowed : 20.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.15), residues: 3044 helix: 1.01 (0.21), residues: 642 sheet: -1.82 (0.21), residues: 552 loop : -2.83 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.013 0.001 HIS A 205 PHE 0.028 0.002 PHE A 86 TYR 0.027 0.001 TYR C 501 ARG 0.010 0.001 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 28) link_NAG-ASN : angle 2.03225 ( 84) hydrogen bonds : bond 0.03828 ( 695) hydrogen bonds : angle 4.83925 ( 1938) SS BOND : bond 0.00457 ( 39) SS BOND : angle 1.94317 ( 78) covalent geometry : bond 0.00368 (25040) covalent geometry : angle 0.61997 (34095) *********************** 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 788 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 631 time to evaluate : 3.035 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 52 GLN cc_start: 0.7576 (tm-30) cc_final: 0.7236 (tm-30) REVERT: A 65 PHE cc_start: 0.7271 (m-10) cc_final: 0.6934 (m-10) REVERT: A 84 LEU cc_start: 0.8642 (pt) cc_final: 0.8379 (pt) REVERT: A 91 TYR cc_start: 0.7637 (t80) cc_final: 0.7353 (t80) REVERT: A 102 ARG cc_start: 0.7610 (mtm-85) cc_final: 0.6985 (mtm-85) REVERT: A 104 TRP cc_start: 0.7886 (OUTLIER) cc_final: 0.7489 (m-90) REVERT: A 129 LYS cc_start: 0.7991 (mtmm) cc_final: 0.7319 (mtmm) REVERT: A 168 PHE cc_start: 0.7259 (t80) cc_final: 0.6985 (t80) REVERT: A 188 ARG cc_start: 0.8030 (ptp-110) cc_final: 0.7761 (ptp90) REVERT: A 189 GLU cc_start: 0.8198 (pm20) cc_final: 0.7971 (pt0) REVERT: A 214 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.5675 (mt-10) REVERT: A 224 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6845 (mm-30) REVERT: A 267 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8183 (p) REVERT: A 269 TYR cc_start: 0.8253 (m-80) cc_final: 0.7958 (m-80) REVERT: A 307 THR cc_start: 0.8416 (m) cc_final: 0.8098 (p) REVERT: A 358 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7318 (pt) REVERT: A 380 TYR cc_start: 0.7343 (m-80) cc_final: 0.6800 (m-10) REVERT: A 386 LYS cc_start: 0.8407 (mttp) cc_final: 0.7829 (mtmm) REVERT: A 436 TRP cc_start: 0.6715 (p90) cc_final: 0.5914 (p90) REVERT: A 492 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6619 (tp) REVERT: A 558 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8071 (mtpp) REVERT: A 564 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 578 ASP cc_start: 0.7984 (t0) cc_final: 0.7714 (t0) REVERT: A 586 ASP cc_start: 0.7481 (t0) cc_final: 0.7104 (m-30) REVERT: A 654 GLU cc_start: 0.7467 (pm20) cc_final: 0.7140 (pm20) REVERT: A 675 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7121 (mm-40) REVERT: A 740 MET cc_start: 0.8052 (ttm) cc_final: 0.7829 (ttp) REVERT: A 745 ASP cc_start: 0.7195 (m-30) cc_final: 0.6538 (p0) REVERT: A 768 THR cc_start: 0.8423 (m) cc_final: 0.8144 (p) REVERT: A 774 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7284 (mp10) REVERT: A 787 GLN cc_start: 0.8032 (mt0) cc_final: 0.7769 (mt0) REVERT: A 855 PHE cc_start: 0.8238 (m-80) cc_final: 0.7966 (m-80) REVERT: A 868 GLU cc_start: 0.7804 (tp30) cc_final: 0.7548 (tp30) REVERT: A 905 ARG cc_start: 0.8446 (mtt-85) cc_final: 0.8194 (mtt90) REVERT: A 918 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7967 (mt-10) REVERT: A 949 GLN cc_start: 0.8151 (mm110) cc_final: 0.7709 (mm-40) REVERT: A 969 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8135 (mtmm) REVERT: A 970 PHE cc_start: 0.7652 (m-10) cc_final: 0.7447 (m-10) REVERT: A 992 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7775 (mm110) REVERT: A 998 THR cc_start: 0.8178 (m) cc_final: 0.7967 (p) REVERT: A 1017 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7548 (tm-30) REVERT: A 1030 SER cc_start: 0.8769 (m) cc_final: 0.8329 (t) REVERT: A 1094 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.8101 (t) REVERT: A 1097 SER cc_start: 0.8652 (t) cc_final: 0.7957 (p) REVERT: A 1139 ASP cc_start: 0.8122 (t70) cc_final: 0.7758 (t70) REVERT: B 106 PHE cc_start: 0.8030 (m-80) cc_final: 0.7804 (m-10) REVERT: B 119 ILE cc_start: 0.8679 (mp) cc_final: 0.8324 (mt) REVERT: B 129 LYS cc_start: 0.8041 (tppt) cc_final: 0.7656 (tppt) REVERT: B 169 GLU cc_start: 0.8007 (pm20) cc_final: 0.7528 (pm20) REVERT: B 177 MET cc_start: 0.6820 (tmt) cc_final: 0.6300 (tmt) REVERT: B 188 ARG cc_start: 0.7241 (ttm-80) cc_final: 0.6687 (ttm-80) REVERT: B 224 GLU cc_start: 0.6784 (pm20) cc_final: 0.6497 (pm20) REVERT: B 279 TYR cc_start: 0.8304 (m-10) cc_final: 0.8068 (m-10) REVERT: B 537 LYS cc_start: 0.8272 (tttp) cc_final: 0.7930 (tttm) REVERT: B 547 LYS cc_start: 0.8213 (mttm) cc_final: 0.7740 (mttp) REVERT: B 549 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8487 (p) REVERT: B 557 LYS cc_start: 0.8602 (ptpp) cc_final: 0.8339 (ptpp) REVERT: B 558 LYS cc_start: 0.8567 (mppt) cc_final: 0.8144 (mppt) REVERT: B 564 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8374 (mm110) REVERT: B 604 THR cc_start: 0.8623 (p) cc_final: 0.8325 (t) REVERT: B 698 SER cc_start: 0.8428 (t) cc_final: 0.7961 (p) REVERT: B 711 SER cc_start: 0.8670 (t) cc_final: 0.8403 (t) REVERT: B 752 LEU cc_start: 0.8782 (mt) cc_final: 0.8506 (mp) REVERT: B 773 GLU cc_start: 0.7737 (tm-30) cc_final: 0.6742 (tm-30) REVERT: B 774 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7448 (mm110) REVERT: B 821 LEU cc_start: 0.8823 (tp) cc_final: 0.8375 (tt) REVERT: B 914 ASN cc_start: 0.8358 (p0) cc_final: 0.7973 (p0) REVERT: B 918 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7621 (mt-10) REVERT: B 950 ASP cc_start: 0.7690 (t70) cc_final: 0.7363 (t70) REVERT: B 957 GLN cc_start: 0.8240 (tt0) cc_final: 0.7973 (tt0) REVERT: B 975 SER cc_start: 0.8666 (m) cc_final: 0.8237 (t) REVERT: B 984 LEU cc_start: 0.8329 (tp) cc_final: 0.7978 (mp) REVERT: B 990 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: B 993 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8493 (tp) REVERT: B 1029 MET cc_start: 0.8611 (tpp) cc_final: 0.7763 (tpp) REVERT: B 1033 VAL cc_start: 0.8867 (t) cc_final: 0.8531 (p) REVERT: B 1038 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8415 (mtpp) REVERT: B 1084 ASP cc_start: 0.7983 (t0) cc_final: 0.7759 (t0) REVERT: B 1097 SER cc_start: 0.8894 (t) cc_final: 0.8349 (p) REVERT: B 1107 ARG cc_start: 0.7873 (ptt-90) cc_final: 0.7338 (ptt-90) REVERT: C 41 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8113 (pttt) REVERT: C 52 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7955 (tm-30) REVERT: C 53 ASP cc_start: 0.7424 (t0) cc_final: 0.7212 (t0) REVERT: C 105 ILE cc_start: 0.8056 (mm) cc_final: 0.7684 (mm) REVERT: C 106 PHE cc_start: 0.7735 (m-80) cc_final: 0.7475 (m-10) REVERT: C 160 TYR cc_start: 0.7400 (p90) cc_final: 0.7128 (p90) REVERT: C 187 LEU cc_start: 0.8352 (tp) cc_final: 0.7581 (tt) REVERT: C 188 ARG cc_start: 0.7723 (ptp-170) cc_final: 0.7444 (ptp-170) REVERT: C 204 LYS cc_start: 0.8536 (tmtt) cc_final: 0.8252 (tttp) REVERT: C 224 GLU cc_start: 0.7443 (pm20) cc_final: 0.7188 (mp0) REVERT: C 269 TYR cc_start: 0.8737 (m-80) cc_final: 0.8240 (m-80) REVERT: C 327 VAL cc_start: 0.8688 (m) cc_final: 0.8243 (t) REVERT: C 349 SER cc_start: 0.8442 (p) cc_final: 0.8065 (t) REVERT: C 357 ARG cc_start: 0.7579 (mtp180) cc_final: 0.7318 (ttm-80) REVERT: C 362 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7890 (p) REVERT: C 414 GLN cc_start: 0.7555 (mp10) cc_final: 0.7282 (mp10) REVERT: C 427 ASP cc_start: 0.7085 (t70) cc_final: 0.6664 (t70) REVERT: C 465 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7622 (tm-30) REVERT: C 588 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8394 (p) REVERT: C 655 TYR cc_start: 0.8062 (t80) cc_final: 0.7779 (t80) REVERT: C 656 VAL cc_start: 0.8543 (m) cc_final: 0.8285 (p) REVERT: C 707 TYR cc_start: 0.7913 (t80) cc_final: 0.7019 (t80) REVERT: C 724 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8555 (p) REVERT: C 745 ASP cc_start: 0.7611 (m-30) cc_final: 0.7363 (p0) REVERT: C 751 ASN cc_start: 0.7979 (m-40) cc_final: 0.7682 (m-40) REVERT: C 752 LEU cc_start: 0.8876 (mm) cc_final: 0.8386 (mt) REVERT: C 755 GLN cc_start: 0.7998 (pp30) cc_final: 0.7297 (pp30) REVERT: C 759 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.7280 (t80) REVERT: C 776 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8310 (tttp) REVERT: C 779 GLN cc_start: 0.8011 (tt0) cc_final: 0.7792 (tm-30) REVERT: C 797 PHE cc_start: 0.8348 (m-10) cc_final: 0.8051 (m-80) REVERT: C 825 LYS cc_start: 0.8565 (tppt) cc_final: 0.8216 (tppt) REVERT: C 868 GLU cc_start: 0.7870 (tp30) cc_final: 0.7486 (tp30) REVERT: C 921 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8270 (mmmm) REVERT: C 935 GLN cc_start: 0.7959 (mt0) cc_final: 0.7756 (mm-40) REVERT: C 964 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8213 (ttmm) REVERT: C 984 LEU cc_start: 0.8094 (mp) cc_final: 0.7871 (mt) REVERT: C 1002 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7654 (tm-30) REVERT: C 1066 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7926 (p) REVERT: C 1073 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8077 (mtpp) outliers start: 157 outliers final: 96 residues processed: 730 average time/residue: 0.3912 time to fit residues: 439.7886 Evaluate side-chains 725 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 613 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR 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 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 305 SER 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 492 LEU Chi-restraints excluded: chain A residue 519 HIS 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 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 1018 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 67 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 205 HIS 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 242 LEU Chi-restraints excluded: chain B residue 275 PHE 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 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL 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 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 41 LYS 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 172 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 212 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE 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 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 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 743 CYS 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 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP 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 130 optimal weight: 9.9990 chunk 290 optimal weight: 1.9990 chunk 292 optimal weight: 0.1980 chunk 237 optimal weight: 0.9990 chunk 235 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 275 optimal weight: 0.3980 chunk 230 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 245 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 690 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1108 ASN B1119 ASN C 30 ASN C 544 ASN C1010 GLN C1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.142924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116897 restraints weight = 39997.613| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.69 r_work: 0.3384 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25107 Z= 0.130 Angle : 0.617 9.784 34257 Z= 0.312 Chirality : 0.047 0.323 3957 Planarity : 0.004 0.069 4379 Dihedral : 7.030 94.730 3990 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 4.76 % Allowed : 21.71 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.15), residues: 3044 helix: 1.25 (0.22), residues: 642 sheet: -1.71 (0.20), residues: 572 loop : -2.68 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.008 0.001 HIS A 49 PHE 0.026 0.001 PHE A 86 TYR 0.024 0.001 TYR B 707 ARG 0.006 0.000 ARG B1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 28) link_NAG-ASN : angle 1.93453 ( 84) hydrogen bonds : bond 0.03527 ( 695) hydrogen bonds : angle 4.76880 ( 1938) SS BOND : bond 0.00400 ( 39) SS BOND : angle 1.98004 ( 78) covalent geometry : bond 0.00293 (25040) covalent geometry : angle 0.60404 (34095) *********************** 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 750 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 623 time to evaluate : 3.198 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 52 GLN cc_start: 0.7564 (tm-30) cc_final: 0.6776 (tm-30) REVERT: A 65 PHE cc_start: 0.7270 (m-10) cc_final: 0.6982 (m-10) REVERT: A 84 LEU cc_start: 0.8596 (pt) cc_final: 0.8346 (pt) REVERT: A 91 TYR cc_start: 0.7547 (t80) cc_final: 0.7221 (t80) REVERT: A 102 ARG cc_start: 0.7486 (mtm-85) cc_final: 0.6960 (mtm-85) REVERT: A 104 TRP cc_start: 0.7867 (OUTLIER) cc_final: 0.7277 (m-90) REVERT: A 129 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7275 (mtmm) REVERT: A 188 ARG cc_start: 0.7890 (ptp-110) cc_final: 0.7547 (ptp90) REVERT: A 189 GLU cc_start: 0.8155 (pm20) cc_final: 0.7858 (pt0) REVERT: A 190 PHE cc_start: 0.8334 (m-80) cc_final: 0.8031 (m-10) REVERT: A 224 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6866 (mm-30) REVERT: A 269 TYR cc_start: 0.8236 (m-80) cc_final: 0.7950 (m-80) REVERT: A 307 THR cc_start: 0.8439 (m) cc_final: 0.8118 (p) REVERT: A 340 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6596 (pm20) REVERT: A 380 TYR cc_start: 0.7343 (m-80) cc_final: 0.6810 (m-10) REVERT: A 386 LYS cc_start: 0.8413 (mttp) cc_final: 0.7845 (mtmm) REVERT: A 542 ASN cc_start: 0.8982 (t0) cc_final: 0.8766 (t0) REVERT: A 564 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7371 (tm-30) REVERT: A 578 ASP cc_start: 0.7951 (t0) cc_final: 0.7695 (t0) REVERT: A 586 ASP cc_start: 0.7517 (t0) cc_final: 0.7084 (m-30) REVERT: A 619 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6591 (tt0) REVERT: A 654 GLU cc_start: 0.7519 (pm20) cc_final: 0.7189 (pm20) REVERT: A 675 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7070 (mm-40) REVERT: A 740 MET cc_start: 0.7905 (ttm) cc_final: 0.7647 (ttp) REVERT: A 745 ASP cc_start: 0.7441 (m-30) cc_final: 0.6948 (p0) REVERT: A 751 ASN cc_start: 0.8194 (m110) cc_final: 0.7964 (m-40) REVERT: A 768 THR cc_start: 0.8357 (m) cc_final: 0.8115 (p) REVERT: A 787 GLN cc_start: 0.8014 (mt0) cc_final: 0.7790 (mt0) REVERT: A 855 PHE cc_start: 0.8166 (m-80) cc_final: 0.7941 (m-80) REVERT: A 868 GLU cc_start: 0.7775 (tp30) cc_final: 0.7530 (tp30) REVERT: A 949 GLN cc_start: 0.8109 (mm110) cc_final: 0.7669 (mm-40) REVERT: A 970 PHE cc_start: 0.7593 (m-10) cc_final: 0.7323 (m-10) REVERT: A 995 ARG cc_start: 0.7815 (ttp-170) cc_final: 0.7604 (ttm170) REVERT: A 998 THR cc_start: 0.8184 (m) cc_final: 0.7961 (p) REVERT: A 1017 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7531 (tm-30) REVERT: A 1030 SER cc_start: 0.8524 (m) cc_final: 0.8271 (t) REVERT: A 1097 SER cc_start: 0.8645 (t) cc_final: 0.7961 (p) REVERT: A 1139 ASP cc_start: 0.8127 (t70) cc_final: 0.7739 (t70) REVERT: B 129 LYS cc_start: 0.8029 (tppt) cc_final: 0.7637 (tppt) REVERT: B 169 GLU cc_start: 0.7962 (pm20) cc_final: 0.7561 (pm20) REVERT: B 177 MET cc_start: 0.6799 (tmt) cc_final: 0.6318 (tmt) REVERT: B 188 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6759 (ttm-80) REVERT: B 224 GLU cc_start: 0.6720 (pm20) cc_final: 0.6469 (pm20) REVERT: B 279 TYR cc_start: 0.8333 (m-10) cc_final: 0.8066 (m-10) REVERT: B 319 ARG cc_start: 0.7948 (ttm110) cc_final: 0.7589 (ttm110) REVERT: B 324 GLU cc_start: 0.7847 (pm20) cc_final: 0.7630 (pm20) REVERT: B 537 LYS cc_start: 0.8182 (tttp) cc_final: 0.7937 (tttm) REVERT: B 547 LYS cc_start: 0.8194 (mttm) cc_final: 0.7841 (mttm) REVERT: B 549 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8514 (p) REVERT: B 557 LYS cc_start: 0.8602 (ptpp) cc_final: 0.8321 (ptpp) REVERT: B 558 LYS cc_start: 0.8537 (mppt) cc_final: 0.8113 (mppt) REVERT: B 560 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8385 (mt) REVERT: B 563 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7639 (mt0) REVERT: B 580 GLN cc_start: 0.8165 (mm110) cc_final: 0.7932 (mm110) REVERT: B 591 SER cc_start: 0.8393 (p) cc_final: 0.7979 (p) REVERT: B 604 THR cc_start: 0.8665 (p) cc_final: 0.8378 (t) REVERT: B 643 PHE cc_start: 0.7885 (t80) cc_final: 0.7351 (t80) REVERT: B 711 SER cc_start: 0.8681 (t) cc_final: 0.8397 (t) REVERT: B 752 LEU cc_start: 0.8767 (mt) cc_final: 0.8489 (mp) REVERT: B 773 GLU cc_start: 0.7791 (tm-30) cc_final: 0.6578 (tm-30) REVERT: B 774 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7373 (mm110) REVERT: B 821 LEU cc_start: 0.8828 (tp) cc_final: 0.8371 (tt) REVERT: B 907 ASN cc_start: 0.8527 (t0) cc_final: 0.8288 (t0) REVERT: B 914 ASN cc_start: 0.8385 (p0) cc_final: 0.7979 (p0) REVERT: B 918 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7567 (mt-10) REVERT: B 950 ASP cc_start: 0.7674 (t70) cc_final: 0.7349 (t70) REVERT: B 957 GLN cc_start: 0.8232 (tt0) cc_final: 0.7946 (tt0) REVERT: B 975 SER cc_start: 0.8637 (m) cc_final: 0.8225 (t) REVERT: B 977 LEU cc_start: 0.8628 (mm) cc_final: 0.8157 (mt) REVERT: B 984 LEU cc_start: 0.8299 (tp) cc_final: 0.7987 (tp) REVERT: B 990 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: B 993 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8462 (tp) REVERT: B 1029 MET cc_start: 0.8579 (tpp) cc_final: 0.7774 (tpp) REVERT: B 1033 VAL cc_start: 0.8801 (t) cc_final: 0.8519 (p) REVERT: B 1038 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8402 (mtpp) REVERT: B 1084 ASP cc_start: 0.7957 (t0) cc_final: 0.7713 (t0) REVERT: B 1097 SER cc_start: 0.8878 (t) cc_final: 0.8333 (p) REVERT: C 41 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8119 (pttt) REVERT: C 53 ASP cc_start: 0.7530 (t0) cc_final: 0.7224 (t0) REVERT: C 105 ILE cc_start: 0.7989 (mm) cc_final: 0.7675 (mm) REVERT: C 106 PHE cc_start: 0.7729 (m-80) cc_final: 0.7472 (m-10) REVERT: C 160 TYR cc_start: 0.7414 (p90) cc_final: 0.7153 (p90) REVERT: C 177 MET cc_start: 0.6252 (tpp) cc_final: 0.5818 (tpp) REVERT: C 187 LEU cc_start: 0.8374 (tp) cc_final: 0.7595 (tt) REVERT: C 188 ARG cc_start: 0.7592 (ptp-170) cc_final: 0.6942 (ptp-170) REVERT: C 204 LYS cc_start: 0.8544 (tmtt) cc_final: 0.8276 (tttp) REVERT: C 269 TYR cc_start: 0.8676 (m-80) cc_final: 0.8193 (m-80) REVERT: C 327 VAL cc_start: 0.8646 (m) cc_final: 0.8201 (t) REVERT: C 349 SER cc_start: 0.8376 (p) cc_final: 0.8089 (t) REVERT: C 414 GLN cc_start: 0.7570 (mp10) cc_final: 0.7175 (mp10) REVERT: C 427 ASP cc_start: 0.6922 (t70) cc_final: 0.6475 (t70) REVERT: C 465 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7607 (tm-30) REVERT: C 537 LYS cc_start: 0.8244 (mmmm) cc_final: 0.8038 (mtpt) REVERT: C 563 GLN cc_start: 0.7236 (tt0) cc_final: 0.6956 (mt0) REVERT: C 588 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8291 (p) REVERT: C 704 SER cc_start: 0.8530 (p) cc_final: 0.8266 (p) REVERT: C 707 TYR cc_start: 0.7946 (t80) cc_final: 0.6996 (t80) REVERT: C 724 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8499 (p) REVERT: C 752 LEU cc_start: 0.8858 (mm) cc_final: 0.8310 (mt) REVERT: C 755 GLN cc_start: 0.7973 (pp30) cc_final: 0.7353 (pp30) REVERT: C 776 LYS cc_start: 0.8594 (ttpt) cc_final: 0.8312 (tttp) REVERT: C 825 LYS cc_start: 0.8524 (tppt) cc_final: 0.8167 (tppt) REVERT: C 868 GLU cc_start: 0.7872 (tp30) cc_final: 0.7484 (tp30) REVERT: C 869 MET cc_start: 0.8180 (mmm) cc_final: 0.7959 (mmm) REVERT: C 921 LYS cc_start: 0.8702 (mmmt) cc_final: 0.8274 (mmmm) REVERT: C 927 PHE cc_start: 0.8789 (t80) cc_final: 0.8275 (t80) REVERT: C 935 GLN cc_start: 0.7998 (mt0) cc_final: 0.7738 (mt0) REVERT: C 984 LEU cc_start: 0.8082 (mp) cc_final: 0.7869 (mt) REVERT: C 1038 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8380 (mmtt) REVERT: C 1066 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7793 (p) REVERT: C 1073 LYS cc_start: 0.8567 (mtpt) cc_final: 0.8063 (mtpp) REVERT: C 1139 ASP cc_start: 0.8300 (t0) cc_final: 0.8096 (t0) outliers start: 127 outliers final: 86 residues processed: 711 average time/residue: 0.3724 time to fit residues: 411.1918 Evaluate side-chains 700 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 603 time to evaluate : 3.161 ------------------------------------------------------------------------------- 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 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 305 SER 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 524 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 558 LYS 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 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1018 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 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 242 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 GLU 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 551 VAL Chi-restraints excluded: chain B residue 560 LEU 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 754 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 965 GLN 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 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 41 LYS 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 385 THR 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 549 THR Chi-restraints excluded: chain C residue 551 VAL 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 742 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 747 THR 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 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP 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 103 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 294 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 302 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 505 HIS A 544 ASN A 580 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 165 ASN B 239 GLN B 317 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 935 GLN B1108 ASN C 30 ASN C 52 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C1010 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.137938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111866 restraints weight = 40175.256| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.67 r_work: 0.3306 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 25107 Z= 0.304 Angle : 0.736 10.516 34257 Z= 0.376 Chirality : 0.051 0.384 3957 Planarity : 0.005 0.066 4379 Dihedral : 7.510 95.901 3987 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 5.36 % Allowed : 21.71 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.14), residues: 3044 helix: 0.72 (0.21), residues: 654 sheet: -1.64 (0.21), residues: 552 loop : -2.72 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 353 HIS 0.011 0.001 HIS C1048 PHE 0.039 0.002 PHE A 275 TYR 0.028 0.002 TYR B 707 ARG 0.012 0.001 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 28) link_NAG-ASN : angle 2.29994 ( 84) hydrogen bonds : bond 0.04669 ( 695) hydrogen bonds : angle 5.06876 ( 1938) SS BOND : bond 0.00571 ( 39) SS BOND : angle 2.66337 ( 78) covalent geometry : bond 0.00672 (25040) covalent geometry : angle 0.71718 (34095) *********************** 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 785 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 642 time to evaluate : 2.455 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: A 49 HIS cc_start: 0.8282 (t-170) cc_final: 0.7870 (t-170) REVERT: A 52 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7070 (tm-30) REVERT: A 60 SER cc_start: 0.8626 (m) cc_final: 0.8403 (p) REVERT: A 65 PHE cc_start: 0.7476 (m-10) cc_final: 0.7187 (m-10) REVERT: A 91 TYR cc_start: 0.7822 (t80) cc_final: 0.7526 (t80) REVERT: A 102 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7263 (mtm-85) REVERT: A 104 TRP cc_start: 0.8080 (OUTLIER) cc_final: 0.7547 (m-90) REVERT: A 129 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7465 (mtmm) REVERT: A 188 ARG cc_start: 0.8441 (ptp-110) cc_final: 0.8030 (ptp90) REVERT: A 189 GLU cc_start: 0.8413 (pm20) cc_final: 0.8037 (pt0) REVERT: A 190 PHE cc_start: 0.8653 (m-80) cc_final: 0.8353 (m-10) REVERT: A 224 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7369 (mm-30) REVERT: A 231 ILE cc_start: 0.8281 (mm) cc_final: 0.8038 (mm) REVERT: A 269 TYR cc_start: 0.8428 (m-80) cc_final: 0.8140 (m-80) REVERT: A 307 THR cc_start: 0.8635 (m) cc_final: 0.8325 (p) REVERT: A 380 TYR cc_start: 0.7511 (m-80) cc_final: 0.7031 (m-10) REVERT: A 386 LYS cc_start: 0.8555 (mttp) cc_final: 0.8061 (mtmm) REVERT: A 436 TRP cc_start: 0.6870 (p90) cc_final: 0.6079 (p90) REVERT: A 496 SER cc_start: 0.6198 (OUTLIER) cc_final: 0.5743 (t) REVERT: A 542 ASN cc_start: 0.9045 (t0) cc_final: 0.8844 (t0) REVERT: A 558 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8453 (mtpp) REVERT: A 654 GLU cc_start: 0.7831 (pm20) cc_final: 0.7442 (pm20) REVERT: A 675 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7344 (mm-40) REVERT: A 692 ILE cc_start: 0.8231 (mt) cc_final: 0.7745 (mt) REVERT: A 698 SER cc_start: 0.8675 (t) cc_final: 0.8241 (p) REVERT: A 745 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.7008 (p0) REVERT: A 751 ASN cc_start: 0.8416 (m110) cc_final: 0.8157 (m-40) REVERT: A 787 GLN cc_start: 0.8380 (mt0) cc_final: 0.8090 (mt0) REVERT: A 820 ASP cc_start: 0.8317 (m-30) cc_final: 0.8106 (m-30) REVERT: A 868 GLU cc_start: 0.8203 (tp30) cc_final: 0.7913 (tp30) REVERT: A 949 GLN cc_start: 0.8439 (mm110) cc_final: 0.8005 (mm-40) REVERT: A 970 PHE cc_start: 0.7961 (m-10) cc_final: 0.7621 (m-10) REVERT: A 992 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7959 (mm110) REVERT: A 1017 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 1030 SER cc_start: 0.8809 (m) cc_final: 0.8591 (p) REVERT: A 1107 ARG cc_start: 0.8106 (mtt90) cc_final: 0.7645 (mtt90) REVERT: A 1136 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8563 (p) REVERT: A 1139 ASP cc_start: 0.8401 (t70) cc_final: 0.8037 (t70) REVERT: B 169 GLU cc_start: 0.8274 (pm20) cc_final: 0.7722 (pm20) REVERT: B 177 MET cc_start: 0.6956 (tmt) cc_final: 0.6385 (tmt) REVERT: B 188 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.7291 (ttm-80) REVERT: B 224 GLU cc_start: 0.7234 (pm20) cc_final: 0.6831 (pm20) REVERT: B 239 GLN cc_start: 0.7982 (mm110) cc_final: 0.7666 (mm110) REVERT: B 319 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7756 (ttm110) REVERT: B 406 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6868 (tt0) REVERT: B 537 LYS cc_start: 0.8428 (tttp) cc_final: 0.8164 (tttm) REVERT: B 549 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8369 (p) REVERT: B 556 ASN cc_start: 0.8687 (p0) cc_final: 0.8314 (p0) REVERT: B 557 LYS cc_start: 0.8755 (ptpp) cc_final: 0.8438 (ptpp) REVERT: B 558 LYS cc_start: 0.8749 (mppt) cc_final: 0.8337 (mppt) REVERT: B 563 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: B 580 GLN cc_start: 0.8273 (mm110) cc_final: 0.8066 (mm110) REVERT: B 591 SER cc_start: 0.8632 (p) cc_final: 0.8264 (p) REVERT: B 604 THR cc_start: 0.8749 (p) cc_final: 0.8510 (t) REVERT: B 711 SER cc_start: 0.8733 (t) cc_final: 0.8474 (t) REVERT: B 752 LEU cc_start: 0.8952 (mt) cc_final: 0.8717 (mp) REVERT: B 765 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7772 (ttp80) REVERT: B 773 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7176 (tm-30) REVERT: B 774 GLN cc_start: 0.8529 (mm-40) cc_final: 0.7710 (mm110) REVERT: B 821 LEU cc_start: 0.8938 (tp) cc_final: 0.8545 (tt) REVERT: B 884 SER cc_start: 0.7945 (m) cc_final: 0.7608 (p) REVERT: B 918 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7875 (mt-10) REVERT: B 935 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7665 (tp-100) REVERT: B 950 ASP cc_start: 0.7947 (t70) cc_final: 0.7654 (t70) REVERT: B 957 GLN cc_start: 0.8699 (tt0) cc_final: 0.8323 (tt0) REVERT: B 975 SER cc_start: 0.8880 (m) cc_final: 0.8409 (t) REVERT: B 984 LEU cc_start: 0.8477 (tp) cc_final: 0.8161 (tp) REVERT: B 990 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: B 993 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8620 (tp) REVERT: B 1033 VAL cc_start: 0.8898 (t) cc_final: 0.8595 (p) REVERT: B 1038 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8536 (mtpp) REVERT: B 1084 ASP cc_start: 0.8362 (t0) cc_final: 0.8159 (t70) REVERT: B 1097 SER cc_start: 0.8970 (t) cc_final: 0.8506 (p) REVERT: C 41 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8358 (pttt) REVERT: C 52 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7801 (tm130) REVERT: C 53 ASP cc_start: 0.7905 (t0) cc_final: 0.7655 (t0) REVERT: C 99 ASN cc_start: 0.8172 (t0) cc_final: 0.7587 (t0) REVERT: C 160 TYR cc_start: 0.7702 (p90) cc_final: 0.7353 (p90) REVERT: C 177 MET cc_start: 0.6354 (tpp) cc_final: 0.6000 (tpp) REVERT: C 187 LEU cc_start: 0.8493 (tp) cc_final: 0.7789 (tt) REVERT: C 188 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7161 (ptp-170) REVERT: C 204 LYS cc_start: 0.8689 (tmtt) cc_final: 0.8433 (tttp) REVERT: C 281 GLU cc_start: 0.8180 (pp20) cc_final: 0.7891 (pp20) REVERT: C 349 SER cc_start: 0.8735 (p) cc_final: 0.8453 (t) REVERT: C 414 GLN cc_start: 0.7918 (mp10) cc_final: 0.7483 (mp10) REVERT: C 457 ARG cc_start: 0.8096 (ptm-80) cc_final: 0.7785 (ptm-80) REVERT: C 465 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7799 (tm-30) REVERT: C 537 LYS cc_start: 0.8573 (mmmm) cc_final: 0.8364 (mtpt) REVERT: C 588 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8438 (p) REVERT: C 704 SER cc_start: 0.8674 (p) cc_final: 0.8430 (p) REVERT: C 707 TYR cc_start: 0.8169 (t80) cc_final: 0.7297 (t80) REVERT: C 724 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8605 (p) REVERT: C 752 LEU cc_start: 0.8880 (mm) cc_final: 0.8669 (mt) REVERT: C 755 GLN cc_start: 0.8212 (pp30) cc_final: 0.7748 (pp30) REVERT: C 761 THR cc_start: 0.8640 (m) cc_final: 0.8196 (p) REVERT: C 776 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8464 (tttp) REVERT: C 823 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7732 (t80) REVERT: C 825 LYS cc_start: 0.8802 (tppt) cc_final: 0.8464 (tppt) REVERT: C 868 GLU cc_start: 0.8232 (tp30) cc_final: 0.7598 (tp30) REVERT: C 904 TYR cc_start: 0.7299 (m-10) cc_final: 0.6399 (m-10) REVERT: C 921 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8461 (mmmm) REVERT: C 933 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8047 (mttp) REVERT: C 935 GLN cc_start: 0.8273 (mt0) cc_final: 0.7946 (mt0) REVERT: C 985 ASP cc_start: 0.7770 (p0) cc_final: 0.7544 (p0) REVERT: C 1002 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7889 (tm-30) REVERT: C 1066 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8124 (p) REVERT: C 1073 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8281 (mtpp) REVERT: C 1139 ASP cc_start: 0.8445 (t0) cc_final: 0.8195 (t0) REVERT: C 1144 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8363 (mm-30) outliers start: 143 outliers final: 93 residues processed: 735 average time/residue: 0.3765 time to fit residues: 422.3738 Evaluate side-chains 735 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 626 time to evaluate : 2.833 ------------------------------------------------------------------------------- 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 171 VAL 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 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 492 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 505 HIS 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 745 ASP 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 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 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 205 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 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 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER 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 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 1104 VAL Chi-restraints excluded: chain B residue 1105 THR 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 113 LYS Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 188 ARG 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 205 HIS 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 240 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 303 LEU 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 515 PHE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL 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 742 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 823 PHE 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 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE 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 145 optimal weight: 0.0970 chunk 273 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 302 optimal weight: 0.6980 chunk 194 optimal weight: 0.2980 chunk 148 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 245 optimal weight: 0.0770 chunk 264 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 474 GLN A 580 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS B 487 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 935 GLN B1108 ASN C 762 GLN C 935 GLN C1010 GLN C1101 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116146 restraints weight = 40073.564| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.68 r_work: 0.3374 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25107 Z= 0.122 Angle : 0.653 9.761 34257 Z= 0.331 Chirality : 0.047 0.321 3957 Planarity : 0.005 0.069 4379 Dihedral : 6.970 96.036 3977 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 4.50 % Allowed : 23.92 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.15), residues: 3044 helix: 1.04 (0.21), residues: 656 sheet: -1.58 (0.21), residues: 549 loop : -2.53 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.007 0.001 HIS C1048 PHE 0.039 0.002 PHE A 168 TYR 0.024 0.001 TYR B 707 ARG 0.011 0.001 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 28) link_NAG-ASN : angle 1.97134 ( 84) hydrogen bonds : bond 0.03570 ( 695) hydrogen bonds : angle 4.83726 ( 1938) SS BOND : bond 0.00394 ( 39) SS BOND : angle 1.90398 ( 78) covalent geometry : bond 0.00275 (25040) covalent geometry : angle 0.64108 (34095) *********************** 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 748 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 628 time to evaluate : 2.779 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: A 52 GLN cc_start: 0.7563 (tm-30) cc_final: 0.7154 (tm-30) REVERT: A 60 SER cc_start: 0.8467 (m) cc_final: 0.8253 (p) REVERT: A 65 PHE cc_start: 0.7197 (m-10) cc_final: 0.6953 (m-10) REVERT: A 102 ARG cc_start: 0.7536 (mtm-85) cc_final: 0.6929 (mtm-85) REVERT: A 104 TRP cc_start: 0.7818 (OUTLIER) cc_final: 0.7244 (m-90) REVERT: A 129 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7320 (mtmm) REVERT: A 188 ARG cc_start: 0.8125 (ptp-110) cc_final: 0.7744 (ptp90) REVERT: A 189 GLU cc_start: 0.8162 (pm20) cc_final: 0.7837 (pt0) REVERT: A 190 PHE cc_start: 0.8310 (m-80) cc_final: 0.8026 (m-10) REVERT: A 224 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6913 (mm-30) REVERT: A 307 THR cc_start: 0.8508 (m) cc_final: 0.8165 (p) REVERT: A 324 GLU cc_start: 0.7663 (mp0) cc_final: 0.7335 (mp0) REVERT: A 340 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6598 (pm20) REVERT: A 380 TYR cc_start: 0.7336 (m-80) cc_final: 0.6850 (m-10) REVERT: A 386 LYS cc_start: 0.8450 (mttp) cc_final: 0.7858 (mtmm) REVERT: A 390 LEU cc_start: 0.8117 (mt) cc_final: 0.7766 (mt) REVERT: A 409 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6802 (pp30) REVERT: A 496 SER cc_start: 0.6241 (OUTLIER) cc_final: 0.5779 (t) REVERT: A 542 ASN cc_start: 0.9010 (t0) cc_final: 0.8770 (t0) REVERT: A 558 LYS cc_start: 0.8454 (mtpp) cc_final: 0.8207 (mtpp) REVERT: A 564 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7312 (tm-30) REVERT: A 586 ASP cc_start: 0.7451 (t0) cc_final: 0.7100 (m-30) REVERT: A 619 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6726 (tt0) REVERT: A 654 GLU cc_start: 0.7529 (pm20) cc_final: 0.7202 (pm20) REVERT: A 675 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7061 (mm-40) REVERT: A 698 SER cc_start: 0.8476 (t) cc_final: 0.7974 (p) REVERT: A 740 MET cc_start: 0.8039 (ttt) cc_final: 0.7796 (ttp) REVERT: A 745 ASP cc_start: 0.7194 (m-30) cc_final: 0.6960 (p0) REVERT: A 768 THR cc_start: 0.8390 (m) cc_final: 0.8189 (p) REVERT: A 787 GLN cc_start: 0.8137 (mt0) cc_final: 0.7843 (mt0) REVERT: A 820 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7622 (m-30) REVERT: A 868 GLU cc_start: 0.7774 (tp30) cc_final: 0.7532 (tp30) REVERT: A 905 ARG cc_start: 0.8509 (mtt-85) cc_final: 0.8155 (mtt-85) REVERT: A 949 GLN cc_start: 0.8140 (mm110) cc_final: 0.7681 (mm-40) REVERT: A 955 ASN cc_start: 0.8228 (m-40) cc_final: 0.7975 (t0) REVERT: A 998 THR cc_start: 0.8356 (t) cc_final: 0.7999 (p) REVERT: A 1017 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7491 (tm-30) REVERT: A 1107 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7285 (mtt90) REVERT: A 1139 ASP cc_start: 0.8250 (t70) cc_final: 0.7882 (t70) REVERT: B 52 GLN cc_start: 0.8151 (tp40) cc_final: 0.7755 (tp40) REVERT: B 82 PRO cc_start: 0.8624 (Cg_endo) cc_final: 0.8383 (Cg_exo) REVERT: B 129 LYS cc_start: 0.7993 (tppt) cc_final: 0.7609 (tppt) REVERT: B 169 GLU cc_start: 0.7884 (pm20) cc_final: 0.7310 (pm20) REVERT: B 177 MET cc_start: 0.6783 (tmt) cc_final: 0.6242 (tmt) REVERT: B 188 ARG cc_start: 0.7046 (ttm-80) cc_final: 0.6769 (ttm-80) REVERT: B 224 GLU cc_start: 0.6696 (pm20) cc_final: 0.6397 (pm20) REVERT: B 237 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6430 (mtp180) REVERT: B 239 GLN cc_start: 0.7575 (mm110) cc_final: 0.7306 (mm110) REVERT: B 319 ARG cc_start: 0.7820 (ttm110) cc_final: 0.7514 (ttm110) REVERT: B 406 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6831 (tt0) REVERT: B 537 LYS cc_start: 0.8220 (tttp) cc_final: 0.7931 (tttm) REVERT: B 547 LYS cc_start: 0.8246 (mttm) cc_final: 0.7791 (mttp) REVERT: B 549 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8510 (p) REVERT: B 557 LYS cc_start: 0.8663 (ptpp) cc_final: 0.8398 (ptpp) REVERT: B 558 LYS cc_start: 0.8549 (mppt) cc_final: 0.8130 (mppt) REVERT: B 559 PHE cc_start: 0.8462 (m-10) cc_final: 0.8194 (m-10) REVERT: B 563 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7398 (mt0) REVERT: B 580 GLN cc_start: 0.8201 (mm110) cc_final: 0.7972 (mm110) REVERT: B 591 SER cc_start: 0.8515 (p) cc_final: 0.8154 (p) REVERT: B 604 THR cc_start: 0.8672 (p) cc_final: 0.8432 (t) REVERT: B 711 SER cc_start: 0.8682 (t) cc_final: 0.8426 (t) REVERT: B 752 LEU cc_start: 0.8772 (mt) cc_final: 0.8470 (mp) REVERT: B 773 GLU cc_start: 0.7724 (tm-30) cc_final: 0.6728 (tm-30) REVERT: B 774 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7339 (mm-40) REVERT: B 821 LEU cc_start: 0.8844 (tp) cc_final: 0.8337 (tt) REVERT: B 860 VAL cc_start: 0.8816 (t) cc_final: 0.8587 (m) REVERT: B 904 TYR cc_start: 0.7666 (m-10) cc_final: 0.7309 (m-80) REVERT: B 914 ASN cc_start: 0.8402 (p0) cc_final: 0.7634 (p0) REVERT: B 918 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7502 (mt-10) REVERT: B 950 ASP cc_start: 0.7559 (t70) cc_final: 0.7279 (t70) REVERT: B 957 GLN cc_start: 0.8263 (tt0) cc_final: 0.7983 (tt0) REVERT: B 975 SER cc_start: 0.8660 (m) cc_final: 0.8225 (t) REVERT: B 984 LEU cc_start: 0.8313 (tp) cc_final: 0.8016 (tp) REVERT: B 990 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: B 993 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8502 (tp) REVERT: B 1029 MET cc_start: 0.8544 (tpp) cc_final: 0.7894 (tpp) REVERT: B 1033 VAL cc_start: 0.8759 (t) cc_final: 0.8487 (p) REVERT: B 1038 LYS cc_start: 0.8799 (mtpp) cc_final: 0.8350 (mtpp) REVERT: B 1084 ASP cc_start: 0.8044 (t0) cc_final: 0.7832 (t70) REVERT: B 1097 SER cc_start: 0.8814 (t) cc_final: 0.8295 (p) REVERT: B 1111 GLU cc_start: 0.8149 (tt0) cc_final: 0.7934 (tt0) REVERT: C 41 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8182 (pttt) REVERT: C 53 ASP cc_start: 0.7491 (t0) cc_final: 0.7258 (t0) REVERT: C 105 ILE cc_start: 0.7962 (mm) cc_final: 0.7691 (mm) REVERT: C 106 PHE cc_start: 0.7803 (m-80) cc_final: 0.7530 (m-10) REVERT: C 119 ILE cc_start: 0.8548 (mm) cc_final: 0.8252 (mt) REVERT: C 160 TYR cc_start: 0.7477 (p90) cc_final: 0.7204 (p90) REVERT: C 177 MET cc_start: 0.6108 (tpp) cc_final: 0.5825 (tpp) REVERT: C 187 LEU cc_start: 0.8257 (tp) cc_final: 0.7529 (tt) REVERT: C 188 ARG cc_start: 0.7543 (ptp-170) cc_final: 0.6772 (ptp-170) REVERT: C 204 LYS cc_start: 0.8605 (tmtt) cc_final: 0.8341 (tttp) REVERT: C 281 GLU cc_start: 0.7896 (pp20) cc_final: 0.7558 (pp20) REVERT: C 327 VAL cc_start: 0.8522 (m) cc_final: 0.8098 (t) REVERT: C 349 SER cc_start: 0.8535 (p) cc_final: 0.8314 (t) REVERT: C 402 ILE cc_start: 0.7548 (mm) cc_final: 0.7329 (tp) REVERT: C 414 GLN cc_start: 0.7783 (mp10) cc_final: 0.7420 (mp10) REVERT: C 465 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 508 TYR cc_start: 0.6769 (m-80) cc_final: 0.6303 (m-80) REVERT: C 537 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7995 (mtpt) REVERT: C 588 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8211 (p) REVERT: C 658 ASN cc_start: 0.8546 (m-40) cc_final: 0.8135 (p0) REVERT: C 704 SER cc_start: 0.8546 (p) cc_final: 0.8294 (p) REVERT: C 707 TYR cc_start: 0.8066 (t80) cc_final: 0.7172 (t80) REVERT: C 724 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8509 (p) REVERT: C 755 GLN cc_start: 0.7858 (pp30) cc_final: 0.7526 (tm-30) REVERT: C 759 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7162 (t80) REVERT: C 776 LYS cc_start: 0.8650 (ttpt) cc_final: 0.8359 (tttp) REVERT: C 825 LYS cc_start: 0.8600 (tppt) cc_final: 0.8245 (tppt) REVERT: C 868 GLU cc_start: 0.7829 (tp30) cc_final: 0.7453 (tp30) REVERT: C 900 MET cc_start: 0.8196 (mtp) cc_final: 0.7970 (mtp) REVERT: C 904 TYR cc_start: 0.6717 (m-10) cc_final: 0.5826 (m-10) REVERT: C 921 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8287 (mmmm) REVERT: C 927 PHE cc_start: 0.8783 (t80) cc_final: 0.8287 (t80) REVERT: C 935 GLN cc_start: 0.7944 (mt0) cc_final: 0.7592 (mt0) REVERT: C 1073 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8069 (mtpp) REVERT: C 1123 SER cc_start: 0.8662 (t) cc_final: 0.8410 (t) outliers start: 120 outliers final: 80 residues processed: 710 average time/residue: 0.3817 time to fit residues: 416.2660 Evaluate side-chains 699 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 605 time to evaluate : 2.512 ------------------------------------------------------------------------------- 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 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 317 ASN 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 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 492 LEU Chi-restraints excluded: chain A residue 496 SER 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 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET 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 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 235 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 PHE 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 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 913 GLN 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 41 LYS 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 212 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 291 CYS 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 515 PHE Chi-restraints excluded: chain C residue 549 THR 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 604 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 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE 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 271 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 135 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 306 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 580 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 C 30 ASN C 52 GLN C1010 GLN C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.138636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.112059 restraints weight = 40960.078| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.75 r_work: 0.3307 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25107 Z= 0.207 Angle : 0.704 10.143 34257 Z= 0.359 Chirality : 0.050 0.351 3957 Planarity : 0.005 0.067 4379 Dihedral : 7.048 97.051 3975 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 4.24 % Allowed : 24.26 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.15), residues: 3044 helix: 0.90 (0.21), residues: 662 sheet: -1.48 (0.21), residues: 556 loop : -2.52 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.012 0.001 HIS C1048 PHE 0.041 0.002 PHE A 168 TYR 0.026 0.002 TYR B 707 ARG 0.013 0.001 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 28) link_NAG-ASN : angle 2.10998 ( 84) hydrogen bonds : bond 0.04049 ( 695) hydrogen bonds : angle 4.95170 ( 1938) SS BOND : bond 0.00433 ( 39) SS BOND : angle 2.41396 ( 78) covalent geometry : bond 0.00468 (25040) covalent geometry : angle 0.68849 (34095) *********************** 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 726 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 613 time to evaluate : 2.376 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 52 GLN cc_start: 0.7703 (tm-30) cc_final: 0.6850 (tm-30) REVERT: A 60 SER cc_start: 0.8521 (m) cc_final: 0.8305 (p) REVERT: A 65 PHE cc_start: 0.7187 (m-10) cc_final: 0.6970 (m-10) REVERT: A 102 ARG cc_start: 0.7592 (mtm-85) cc_final: 0.6972 (mtm-85) REVERT: A 104 TRP cc_start: 0.7890 (OUTLIER) cc_final: 0.7325 (m-90) REVERT: A 129 LYS cc_start: 0.7991 (mtmm) cc_final: 0.7295 (mtmm) REVERT: A 188 ARG cc_start: 0.8050 (ptp-110) cc_final: 0.7662 (ptp90) REVERT: A 189 GLU cc_start: 0.8166 (pm20) cc_final: 0.7845 (pt0) REVERT: A 190 PHE cc_start: 0.8398 (m-80) cc_final: 0.8078 (m-10) REVERT: A 224 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7049 (mm-30) REVERT: A 227 VAL cc_start: 0.8298 (p) cc_final: 0.8022 (t) REVERT: A 269 TYR cc_start: 0.8430 (m-80) cc_final: 0.8054 (m-80) REVERT: A 275 PHE cc_start: 0.8384 (m-80) cc_final: 0.8097 (m-10) REVERT: A 307 THR cc_start: 0.8540 (m) cc_final: 0.8206 (p) REVERT: A 324 GLU cc_start: 0.7785 (mp0) cc_final: 0.7366 (mp0) REVERT: A 328 ARG cc_start: 0.8100 (mtp85) cc_final: 0.7842 (mtp180) REVERT: A 340 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6726 (pm20) REVERT: A 380 TYR cc_start: 0.7363 (m-80) cc_final: 0.6918 (m-10) REVERT: A 386 LYS cc_start: 0.8537 (mttp) cc_final: 0.7909 (mtmm) REVERT: A 390 LEU cc_start: 0.8184 (mt) cc_final: 0.7866 (mt) REVERT: A 436 TRP cc_start: 0.6718 (p90) cc_final: 0.5868 (p90) REVERT: A 496 SER cc_start: 0.6154 (OUTLIER) cc_final: 0.5704 (t) REVERT: A 537 LYS cc_start: 0.8054 (mtpt) cc_final: 0.7827 (mtpp) REVERT: A 542 ASN cc_start: 0.8966 (t0) cc_final: 0.8736 (t0) REVERT: A 558 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8275 (mtpp) REVERT: A 578 ASP cc_start: 0.7958 (t0) cc_final: 0.7726 (t0) REVERT: A 586 ASP cc_start: 0.7475 (t0) cc_final: 0.7110 (m-30) REVERT: A 619 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7062 (tt0) REVERT: A 654 GLU cc_start: 0.7528 (pm20) cc_final: 0.7235 (pm20) REVERT: A 675 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7085 (mm-40) REVERT: A 698 SER cc_start: 0.8583 (t) cc_final: 0.8122 (p) REVERT: A 745 ASP cc_start: 0.7161 (m-30) cc_final: 0.6872 (p0) REVERT: A 751 ASN cc_start: 0.8314 (m110) cc_final: 0.8107 (m-40) REVERT: A 768 THR cc_start: 0.8444 (m) cc_final: 0.8133 (p) REVERT: A 774 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7290 (mp10) REVERT: A 787 GLN cc_start: 0.8214 (mt0) cc_final: 0.7914 (mt0) REVERT: A 820 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: A 868 GLU cc_start: 0.7826 (tp30) cc_final: 0.7547 (tp30) REVERT: A 949 GLN cc_start: 0.8286 (mm110) cc_final: 0.7835 (mm-40) REVERT: A 955 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.8019 (t0) REVERT: A 970 PHE cc_start: 0.7606 (m-10) cc_final: 0.7323 (m-10) REVERT: A 998 THR cc_start: 0.8409 (t) cc_final: 0.8033 (p) REVERT: A 1017 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 1029 MET cc_start: 0.8668 (tpp) cc_final: 0.8161 (tpp) REVERT: A 1107 ARG cc_start: 0.7994 (mtt90) cc_final: 0.7422 (mtt90) REVERT: A 1136 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8385 (p) REVERT: A 1139 ASP cc_start: 0.8307 (t70) cc_final: 0.7948 (t70) REVERT: B 52 GLN cc_start: 0.8114 (tp40) cc_final: 0.7704 (tp40) REVERT: B 129 LYS cc_start: 0.7997 (tppt) cc_final: 0.7615 (tppt) REVERT: B 169 GLU cc_start: 0.7931 (pm20) cc_final: 0.7292 (pm20) REVERT: B 177 MET cc_start: 0.6652 (tmt) cc_final: 0.6138 (tmt) REVERT: B 188 ARG cc_start: 0.7190 (ttm-80) cc_final: 0.6876 (ttm-80) REVERT: B 224 GLU cc_start: 0.6856 (pm20) cc_final: 0.6435 (pm20) REVERT: B 237 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6404 (mtp180) REVERT: B 239 GLN cc_start: 0.7666 (mm110) cc_final: 0.7374 (mm110) REVERT: B 319 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7693 (ttm110) REVERT: B 406 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6744 (tt0) REVERT: B 537 LYS cc_start: 0.8259 (tttp) cc_final: 0.7990 (tttp) REVERT: B 547 LYS cc_start: 0.8238 (mttm) cc_final: 0.7812 (mttp) REVERT: B 549 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8462 (p) REVERT: B 556 ASN cc_start: 0.8580 (p0) cc_final: 0.8186 (p0) REVERT: B 557 LYS cc_start: 0.8725 (ptpp) cc_final: 0.8333 (ptpt) REVERT: B 558 LYS cc_start: 0.8633 (mppt) cc_final: 0.8194 (mppt) REVERT: B 563 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: B 580 GLN cc_start: 0.8226 (mm110) cc_final: 0.7970 (mm110) REVERT: B 591 SER cc_start: 0.8571 (p) cc_final: 0.8190 (p) REVERT: B 604 THR cc_start: 0.8701 (p) cc_final: 0.8463 (t) REVERT: B 711 SER cc_start: 0.8672 (t) cc_final: 0.8394 (t) REVERT: B 742 ILE cc_start: 0.8751 (mm) cc_final: 0.8531 (mt) REVERT: B 752 LEU cc_start: 0.8823 (mt) cc_final: 0.8549 (mp) REVERT: B 773 GLU cc_start: 0.7908 (tm-30) cc_final: 0.6759 (tm-30) REVERT: B 774 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7484 (mm110) REVERT: B 821 LEU cc_start: 0.8853 (tp) cc_final: 0.8376 (tt) REVERT: B 904 TYR cc_start: 0.7755 (m-10) cc_final: 0.7335 (m-80) REVERT: B 914 ASN cc_start: 0.8455 (p0) cc_final: 0.7699 (p0) REVERT: B 918 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7488 (mt-10) REVERT: B 935 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7634 (tp-100) REVERT: B 950 ASP cc_start: 0.7646 (t70) cc_final: 0.7329 (t70) REVERT: B 957 GLN cc_start: 0.8419 (tt0) cc_final: 0.8023 (tt0) REVERT: B 975 SER cc_start: 0.8731 (m) cc_final: 0.8256 (t) REVERT: B 984 LEU cc_start: 0.8295 (tp) cc_final: 0.7945 (tp) REVERT: B 990 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: B 993 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8537 (tp) REVERT: B 1033 VAL cc_start: 0.8830 (t) cc_final: 0.8552 (p) REVERT: B 1038 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8357 (mtpp) REVERT: B 1084 ASP cc_start: 0.8190 (t0) cc_final: 0.7978 (t70) REVERT: B 1097 SER cc_start: 0.8860 (t) cc_final: 0.8345 (p) REVERT: B 1107 ARG cc_start: 0.7920 (ptt180) cc_final: 0.7602 (ptp90) REVERT: B 1111 GLU cc_start: 0.8198 (tt0) cc_final: 0.7981 (tt0) REVERT: C 105 ILE cc_start: 0.7848 (mm) cc_final: 0.7568 (mm) REVERT: C 106 PHE cc_start: 0.7776 (m-80) cc_final: 0.7516 (m-10) REVERT: C 119 ILE cc_start: 0.8664 (mm) cc_final: 0.8382 (mt) REVERT: C 160 TYR cc_start: 0.7571 (p90) cc_final: 0.7276 (p90) REVERT: C 177 MET cc_start: 0.6125 (tpp) cc_final: 0.5788 (tpp) REVERT: C 187 LEU cc_start: 0.8328 (tp) cc_final: 0.7604 (tt) REVERT: C 188 ARG cc_start: 0.7676 (ptp-170) cc_final: 0.6886 (ptp-170) REVERT: C 204 LYS cc_start: 0.8621 (tmtt) cc_final: 0.8222 (tttp) REVERT: C 224 GLU cc_start: 0.7445 (pm20) cc_final: 0.7099 (pm20) REVERT: C 281 GLU cc_start: 0.7938 (pp20) cc_final: 0.7616 (pp20) REVERT: C 349 SER cc_start: 0.8638 (p) cc_final: 0.8389 (t) REVERT: C 364 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.6720 (p0) REVERT: C 414 GLN cc_start: 0.7898 (mp10) cc_final: 0.7584 (mp10) REVERT: C 465 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7575 (tm-30) REVERT: C 537 LYS cc_start: 0.8277 (mmmm) cc_final: 0.8042 (mtpt) REVERT: C 543 PHE cc_start: 0.8098 (m-10) cc_final: 0.7885 (m-80) REVERT: C 588 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8234 (p) REVERT: C 704 SER cc_start: 0.8598 (p) cc_final: 0.8364 (p) REVERT: C 707 TYR cc_start: 0.8096 (t80) cc_final: 0.7195 (t80) REVERT: C 724 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8514 (p) REVERT: C 742 ILE cc_start: 0.8289 (tt) cc_final: 0.7956 (pt) REVERT: C 759 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7169 (t80) REVERT: C 776 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8386 (tttp) REVERT: C 825 LYS cc_start: 0.8628 (tppt) cc_final: 0.8283 (tppt) REVERT: C 868 GLU cc_start: 0.7939 (tp30) cc_final: 0.7312 (tp30) REVERT: C 904 TYR cc_start: 0.6863 (m-10) cc_final: 0.5919 (m-10) REVERT: C 921 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8330 (mmmm) REVERT: C 927 PHE cc_start: 0.8784 (t80) cc_final: 0.8216 (t80) REVERT: C 933 LYS cc_start: 0.8303 (mtpt) cc_final: 0.7901 (mttp) REVERT: C 935 GLN cc_start: 0.8017 (mt0) cc_final: 0.7789 (mt0) REVERT: C 1002 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7764 (tm-30) REVERT: C 1066 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7874 (p) REVERT: C 1073 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8136 (mtpp) outliers start: 113 outliers final: 81 residues processed: 691 average time/residue: 0.3856 time to fit residues: 409.9373 Evaluate side-chains 705 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 607 time to evaluate : 3.212 ------------------------------------------------------------------------------- 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 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 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 492 LEU Chi-restraints excluded: chain A residue 496 SER 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 553 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU 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 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 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 205 HIS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU 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 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 913 GLN 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 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 52 GLN 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 212 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 425 LEU 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 549 THR 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 604 THR Chi-restraints excluded: chain C residue 724 THR 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 849 LEU 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 1018 ILE 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 220 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 277 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 280 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.137921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111349 restraints weight = 40790.094| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.75 r_work: 0.3301 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 25107 Z= 0.213 Angle : 0.713 10.496 34257 Z= 0.364 Chirality : 0.050 0.375 3957 Planarity : 0.005 0.068 4379 Dihedral : 7.112 97.135 3975 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.51 % Favored : 89.45 % Rotamer: Outliers : 3.86 % Allowed : 24.45 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.15), residues: 3044 helix: 1.00 (0.21), residues: 645 sheet: -1.38 (0.21), residues: 555 loop : -2.51 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.013 0.001 HIS C1048 PHE 0.036 0.002 PHE A 86 TYR 0.027 0.002 TYR B 707 ARG 0.008 0.001 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 28) link_NAG-ASN : angle 2.15568 ( 84) hydrogen bonds : bond 0.04060 ( 695) hydrogen bonds : angle 5.00598 ( 1938) SS BOND : bond 0.00458 ( 39) SS BOND : angle 2.49342 ( 78) covalent geometry : bond 0.00480 (25040) covalent geometry : angle 0.69639 (34095) ********************** 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 712 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 609 time to evaluate : 2.932 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 52 GLN cc_start: 0.7742 (tm-30) cc_final: 0.6883 (tm-30) REVERT: A 60 SER cc_start: 0.8521 (m) cc_final: 0.8304 (p) REVERT: A 102 ARG cc_start: 0.7609 (mtm-85) cc_final: 0.7053 (mtm-85) REVERT: A 104 TRP cc_start: 0.7885 (OUTLIER) cc_final: 0.7330 (m-90) REVERT: A 129 LYS cc_start: 0.8013 (mtmm) cc_final: 0.7307 (mtmm) REVERT: A 188 ARG cc_start: 0.8097 (ptp-110) cc_final: 0.7665 (ptp90) REVERT: A 189 GLU cc_start: 0.8173 (pm20) cc_final: 0.7835 (pt0) REVERT: A 190 PHE cc_start: 0.8392 (m-80) cc_final: 0.8072 (m-10) REVERT: A 224 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7056 (mm-30) REVERT: A 227 VAL cc_start: 0.8316 (p) cc_final: 0.8025 (t) REVERT: A 269 TYR cc_start: 0.8424 (m-80) cc_final: 0.7968 (m-80) REVERT: A 275 PHE cc_start: 0.8375 (m-80) cc_final: 0.8120 (m-10) REVERT: A 307 THR cc_start: 0.8550 (m) cc_final: 0.8227 (p) REVERT: A 324 GLU cc_start: 0.7770 (mp0) cc_final: 0.7372 (mp0) REVERT: A 355 ARG cc_start: 0.7491 (ttm-80) cc_final: 0.7161 (ttt90) REVERT: A 380 TYR cc_start: 0.7362 (m-80) cc_final: 0.6907 (m-10) REVERT: A 386 LYS cc_start: 0.8548 (mttp) cc_final: 0.7947 (mtmm) REVERT: A 390 LEU cc_start: 0.8269 (mt) cc_final: 0.7919 (mt) REVERT: A 436 TRP cc_start: 0.6727 (p90) cc_final: 0.5832 (p90) REVERT: A 496 SER cc_start: 0.6090 (OUTLIER) cc_final: 0.5696 (t) REVERT: A 537 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7972 (mtpp) REVERT: A 542 ASN cc_start: 0.8967 (t0) cc_final: 0.8715 (t0) REVERT: A 558 LYS cc_start: 0.8506 (mtpp) cc_final: 0.8276 (mtpp) REVERT: A 586 ASP cc_start: 0.7467 (t0) cc_final: 0.7100 (m-30) REVERT: A 619 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7049 (tt0) REVERT: A 675 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7100 (mm-40) REVERT: A 698 SER cc_start: 0.8595 (t) cc_final: 0.8134 (p) REVERT: A 745 ASP cc_start: 0.7137 (m-30) cc_final: 0.6882 (p0) REVERT: A 774 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7229 (mp10) REVERT: A 787 GLN cc_start: 0.8194 (mt0) cc_final: 0.7897 (mt0) REVERT: A 820 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: A 854 LYS cc_start: 0.8468 (tptp) cc_final: 0.8178 (tptp) REVERT: A 868 GLU cc_start: 0.7829 (tp30) cc_final: 0.7557 (tp30) REVERT: A 949 GLN cc_start: 0.8287 (mm110) cc_final: 0.7844 (mm-40) REVERT: A 955 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7990 (t0) REVERT: A 970 PHE cc_start: 0.7553 (m-10) cc_final: 0.7257 (m-10) REVERT: A 992 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7810 (mm110) REVERT: A 998 THR cc_start: 0.8406 (t) cc_final: 0.8044 (p) REVERT: A 1017 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7505 (tm-30) REVERT: A 1136 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8453 (p) REVERT: A 1139 ASP cc_start: 0.8292 (t70) cc_final: 0.7916 (t0) REVERT: B 52 GLN cc_start: 0.8119 (tp40) cc_final: 0.7687 (tp40) REVERT: B 129 LYS cc_start: 0.8026 (tppt) cc_final: 0.7636 (tppt) REVERT: B 169 GLU cc_start: 0.7917 (pm20) cc_final: 0.7285 (pm20) REVERT: B 177 MET cc_start: 0.6590 (tmt) cc_final: 0.6090 (tmt) REVERT: B 188 ARG cc_start: 0.7230 (ttm-80) cc_final: 0.6926 (ttm-80) REVERT: B 224 GLU cc_start: 0.6865 (pm20) cc_final: 0.6456 (pm20) REVERT: B 239 GLN cc_start: 0.7753 (mm110) cc_final: 0.7460 (mm110) REVERT: B 319 ARG cc_start: 0.7922 (ttm110) cc_final: 0.7662 (ttm110) REVERT: B 335 LEU cc_start: 0.8367 (mm) cc_final: 0.8160 (mm) REVERT: B 406 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6825 (tt0) REVERT: B 547 LYS cc_start: 0.8244 (mttm) cc_final: 0.7818 (mttp) REVERT: B 549 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8452 (p) REVERT: B 556 ASN cc_start: 0.8593 (p0) cc_final: 0.8262 (p0) REVERT: B 557 LYS cc_start: 0.8724 (ptpp) cc_final: 0.8504 (ptpp) REVERT: B 558 LYS cc_start: 0.8645 (mppt) cc_final: 0.8245 (mppt) REVERT: B 563 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: B 580 GLN cc_start: 0.8219 (mm110) cc_final: 0.7975 (mm110) REVERT: B 591 SER cc_start: 0.8596 (p) cc_final: 0.8216 (p) REVERT: B 604 THR cc_start: 0.8664 (p) cc_final: 0.8427 (t) REVERT: B 711 SER cc_start: 0.8668 (t) cc_final: 0.8376 (t) REVERT: B 752 LEU cc_start: 0.8820 (mt) cc_final: 0.8550 (mp) REVERT: B 773 GLU cc_start: 0.7904 (tm-30) cc_final: 0.6763 (tm-30) REVERT: B 774 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7484 (mm110) REVERT: B 821 LEU cc_start: 0.8871 (tp) cc_final: 0.8449 (tt) REVERT: B 904 TYR cc_start: 0.7759 (m-10) cc_final: 0.7326 (m-80) REVERT: B 914 ASN cc_start: 0.8479 (p0) cc_final: 0.7666 (p0) REVERT: B 918 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7507 (mt-10) REVERT: B 950 ASP cc_start: 0.7607 (t70) cc_final: 0.7316 (t70) REVERT: B 957 GLN cc_start: 0.8425 (tt0) cc_final: 0.8031 (tt0) REVERT: B 975 SER cc_start: 0.8780 (m) cc_final: 0.8270 (t) REVERT: B 984 LEU cc_start: 0.8287 (tp) cc_final: 0.7943 (tp) REVERT: B 990 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: B 993 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8552 (tp) REVERT: B 1033 VAL cc_start: 0.8815 (t) cc_final: 0.8537 (p) REVERT: B 1038 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8356 (mtpp) REVERT: B 1084 ASP cc_start: 0.8203 (t0) cc_final: 0.7994 (t70) REVERT: B 1097 SER cc_start: 0.8812 (t) cc_final: 0.8305 (p) REVERT: B 1107 ARG cc_start: 0.7971 (ptt180) cc_final: 0.7548 (ptp90) REVERT: B 1111 GLU cc_start: 0.8198 (tt0) cc_final: 0.7915 (tt0) REVERT: C 52 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: C 105 ILE cc_start: 0.7844 (mm) cc_final: 0.7567 (mm) REVERT: C 106 PHE cc_start: 0.7763 (m-80) cc_final: 0.7508 (m-10) REVERT: C 119 ILE cc_start: 0.8687 (mm) cc_final: 0.8442 (mt) REVERT: C 160 TYR cc_start: 0.7575 (p90) cc_final: 0.7289 (p90) REVERT: C 177 MET cc_start: 0.6085 (tpp) cc_final: 0.5788 (tpp) REVERT: C 187 LEU cc_start: 0.8326 (tp) cc_final: 0.7615 (tt) REVERT: C 188 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6853 (ptp-170) REVERT: C 204 LYS cc_start: 0.8617 (tmtt) cc_final: 0.8184 (tttp) REVERT: C 224 GLU cc_start: 0.7447 (pm20) cc_final: 0.7108 (pm20) REVERT: C 281 GLU cc_start: 0.7957 (pp20) cc_final: 0.7626 (pp20) REVERT: C 289 VAL cc_start: 0.8647 (t) cc_final: 0.8399 (m) REVERT: C 327 VAL cc_start: 0.8557 (m) cc_final: 0.8099 (t) REVERT: C 349 SER cc_start: 0.8714 (p) cc_final: 0.8433 (t) REVERT: C 364 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.6907 (p0) REVERT: C 414 GLN cc_start: 0.7861 (mp10) cc_final: 0.7546 (mp10) REVERT: C 457 ARG cc_start: 0.8001 (ptt90) cc_final: 0.7638 (ptt90) REVERT: C 465 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7588 (tm-30) REVERT: C 537 LYS cc_start: 0.8296 (mmmm) cc_final: 0.8072 (mmtm) REVERT: C 543 PHE cc_start: 0.8120 (m-10) cc_final: 0.7812 (m-10) REVERT: C 588 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8210 (p) REVERT: C 704 SER cc_start: 0.8613 (p) cc_final: 0.8373 (p) REVERT: C 759 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7203 (t80) REVERT: C 776 LYS cc_start: 0.8687 (ttpt) cc_final: 0.8386 (tttp) REVERT: C 825 LYS cc_start: 0.8629 (tppt) cc_final: 0.8285 (tppt) REVERT: C 868 GLU cc_start: 0.7923 (tp30) cc_final: 0.7471 (tp30) REVERT: C 921 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8336 (mmmm) REVERT: C 927 PHE cc_start: 0.8782 (t80) cc_final: 0.8215 (t80) REVERT: C 933 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7893 (mttp) REVERT: C 935 GLN cc_start: 0.8018 (mt0) cc_final: 0.7779 (mt0) REVERT: C 985 ASP cc_start: 0.7553 (p0) cc_final: 0.7288 (p0) REVERT: C 1002 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7578 (tm-30) REVERT: C 1066 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7967 (p) REVERT: C 1073 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8150 (mtpp) outliers start: 103 outliers final: 85 residues processed: 680 average time/residue: 0.5039 time to fit residues: 536.9860 Evaluate side-chains 707 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 607 time to evaluate : 4.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU 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 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 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 492 LEU Chi-restraints excluded: chain A residue 496 SER 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 730 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU 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 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 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 206 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 PHE 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 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 913 GLN 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 52 GLN Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 188 ARG 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 291 CYS Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 425 LEU 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 549 THR 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 604 THR Chi-restraints excluded: chain C residue 724 THR 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 849 LEU 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 1018 ILE 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 264 optimal weight: 0.7980 chunk 255 optimal weight: 0.0570 chunk 245 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 168 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 283 optimal weight: 0.6980 chunk 247 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 751 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 52 GLN C1010 GLN C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.140735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114113 restraints weight = 40611.125| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.77 r_work: 0.3343 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25107 Z= 0.130 Angle : 0.660 10.319 34257 Z= 0.336 Chirality : 0.047 0.337 3957 Planarity : 0.005 0.068 4379 Dihedral : 6.918 97.709 3975 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 3.71 % Allowed : 24.93 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.15), residues: 3044 helix: 1.23 (0.21), residues: 646 sheet: -1.30 (0.21), residues: 560 loop : -2.40 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.010 0.001 HIS C1048 PHE 0.029 0.002 PHE A 86 TYR 0.025 0.001 TYR B 707 ARG 0.008 0.001 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 28) link_NAG-ASN : angle 1.94225 ( 84) hydrogen bonds : bond 0.03548 ( 695) hydrogen bonds : angle 4.92637 ( 1938) SS BOND : bond 0.00368 ( 39) SS BOND : angle 1.85754 ( 78) covalent geometry : bond 0.00296 (25040) covalent geometry : angle 0.64884 (34095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14530.27 seconds wall clock time: 255 minutes 39.01 seconds (15339.01 seconds total)