Starting phenix.real_space_refine on Fri Mar 6 22:01:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wov_32660/03_2026/7wov_32660.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wov_32660/03_2026/7wov_32660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wov_32660/03_2026/7wov_32660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wov_32660/03_2026/7wov_32660.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wov_32660/03_2026/7wov_32660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wov_32660/03_2026/7wov_32660.map" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 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 156 5.16 5 C 22148 2.51 5 N 5802 2.21 5 O 6778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34884 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7989 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "E" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "F" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "G" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "H" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "I" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 8.45, per 1000 atoms: 0.24 Number of scatterers: 34884 At special positions: 0 Unit cell: (144.704, 164.92, 212.8, 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 156 16.00 O 6778 8.00 N 5802 7.00 C 22148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, 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=2.04 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 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 221 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 146 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 221 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 146 " - pdb=" SG CYS G 220 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 221 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 146 " - pdb=" SG CYS I 220 " 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 331 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A 717 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 717 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B1134 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C1098 " " NAG C1307 " - " ASN C1134 " Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8268 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 72 sheets defined 16.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.749A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.781A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.627A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.819A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 783 removed outlier: 3.514A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.800A 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 886 through 891 removed outlier: 4.060A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.866A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 910 " --> pdb=" O PHE A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 930 through 941 removed outlier: 3.928A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.674A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.272A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.952A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.711A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.712A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.590A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.527A 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 756 Processing helix chain 'B' and resid 761 through 782 removed outlier: 3.528A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 906 Processing helix chain 'B' and resid 907 through 909 No H-bonds generated for 'chain 'B' and resid 907 through 909' Processing helix chain 'B' and resid 912 through 939 removed outlier: 4.404A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.615A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.206A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B1001 " --> pdb=" O ILE B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 removed outlier: 3.864A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1143 through 1147' Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.792A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.605A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 755 removed outlier: 4.018A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 778 removed outlier: 3.586A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.628A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 882 Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.610A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 removed outlier: 3.594A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.597A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.517A pdb=" N ASP C 979 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE C 980 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N PHE C 981 " --> pdb=" O ASN C 978 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 982 " --> pdb=" O ASP C 979 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 983 " --> pdb=" O ILE C 980 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 983' Processing helix chain 'C' and resid 985 through 993 removed outlier: 4.178A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1033 removed outlier: 3.664A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.971A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'G' and resid 152 through 156 Processing helix chain 'I' and resid 80 through 84 Processing helix chain 'I' and resid 152 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 3.933A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (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: 7.799A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.812A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 93 removed outlier: 3.596A pdb=" N VAL A 191 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 203 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 224 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.514A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.674A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.443A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.461A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 removed outlier: 5.738A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.721A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.533A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.906A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 90 through 94 removed outlier: 3.523A pdb=" N VAL B 191 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B 198 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 229 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 201 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 227 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER B 203 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 120 through 122 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.763A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.820A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.478A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.674A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.821A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 712 through 718 removed outlier: 6.945A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 721 through 728 removed outlier: 7.248A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (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: 5.724A 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 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.335A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 224 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.759A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.873A pdb=" N SER C 94 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.979A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.656A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.404A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.697A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.780A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AE9, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AF1, first strand: chain 'C' and resid 721 through 728 removed outlier: 3.693A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.592A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF5, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.208A pdb=" N LEU D 48 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN D 39 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D 88 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR D 106 " --> pdb=" O TYR D 88 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 64 through 69 removed outlier: 5.278A pdb=" N SER D 65 " --> pdb=" O THR D 76 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER D 67 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 172 through 176 removed outlier: 6.007A pdb=" N TRP D 173 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG D 164 " --> pdb=" O TRP D 173 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 21 through 23 Processing sheet with id=AF9, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.025A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.025A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR E 87 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 143 through 144 Processing sheet with id=AG3, first strand: chain 'E' and resid 182 through 184 removed outlier: 6.610A pdb=" N TRP E 160 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL E 174 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N MET E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 47 through 50 removed outlier: 6.836A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR F 88 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR F 106 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 66 through 69 removed outlier: 3.707A pdb=" N SER F 67 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 172 through 176 removed outlier: 6.023A pdb=" N TRP F 173 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG F 164 " --> pdb=" O TRP F 173 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 21 through 23 Processing sheet with id=AG8, first strand: chain 'G' and resid 46 through 49 removed outlier: 5.031A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN G 97 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 130 through 131 Processing sheet with id=AH1, first strand: chain 'G' and resid 182 through 184 removed outlier: 6.589A pdb=" N TRP G 160 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL G 174 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N MET G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 47 through 50 removed outlier: 6.210A pdb=" N LEU H 48 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN H 39 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR H 88 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR H 106 " --> pdb=" O TYR H 88 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 66 through 69 removed outlier: 3.706A pdb=" N SER H 67 " --> pdb=" O SER H 74 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 172 through 177 removed outlier: 5.992A pdb=" N TRP H 173 " --> pdb=" O ARG H 164 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG H 164 " --> pdb=" O TRP H 173 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE H 177 " --> pdb=" O MET H 160 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET H 160 " --> pdb=" O ILE H 177 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 21 through 23 Processing sheet with id=AH6, first strand: chain 'I' and resid 46 through 49 removed outlier: 5.019A pdb=" N LEU I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLN I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN I 97 " --> pdb=" O ASP I 93 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 46 through 49 removed outlier: 5.019A pdb=" N LEU I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLN I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR I 87 " --> pdb=" O THR I 104 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 143 through 144 Processing sheet with id=AH9, first strand: chain 'I' and resid 182 through 184 removed outlier: 6.618A pdb=" N TRP I 160 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL I 174 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET I 158 " --> pdb=" O VAL I 174 " (cutoff:3.500A) 915 hydrogen bonds defined for protein. 2379 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: 8.28 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6382 1.33 - 1.45: 9725 1.45 - 1.57: 19390 1.57 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 35701 Sorted by residual: bond pdb=" CA THR A 33 " pdb=" C THR A 33 " ideal model delta sigma weight residual 1.524 1.450 0.075 8.80e-03 1.29e+04 7.19e+01 bond pdb=" CA ARG A 34 " pdb=" C ARG A 34 " ideal model delta sigma weight residual 1.527 1.429 0.098 1.41e-02 5.03e+03 4.86e+01 bond pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 1.526 1.453 0.073 1.28e-02 6.10e+03 3.24e+01 bond pdb=" CA ASN A 801 " pdb=" C ASN A 801 " ideal model delta sigma weight residual 1.526 1.458 0.068 1.30e-02 5.92e+03 2.74e+01 bond pdb=" CA ASN A 717 " pdb=" C ASN A 717 " ideal model delta sigma weight residual 1.522 1.461 0.062 1.20e-02 6.94e+03 2.64e+01 ... (remaining 35696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 47472 1.51 - 3.03: 909 3.03 - 4.54: 162 4.54 - 6.06: 22 6.06 - 7.57: 15 Bond angle restraints: 48580 Sorted by residual: angle pdb=" O SER A 708 " pdb=" C SER A 708 " pdb=" N ASN A 709 " ideal model delta sigma weight residual 122.81 115.24 7.57 1.23e+00 6.61e-01 3.79e+01 angle pdb=" CA SER A 708 " pdb=" C SER A 708 " pdb=" N ASN A 709 " ideal model delta sigma weight residual 115.56 123.05 -7.49 1.30e+00 5.92e-01 3.32e+01 angle pdb=" C ILE B 233 " pdb=" N ASN B 234 " pdb=" CA ASN B 234 " ideal model delta sigma weight residual 122.30 116.06 6.24 1.35e+00 5.49e-01 2.14e+01 angle pdb=" C SER A 708 " pdb=" N ASN A 709 " pdb=" CA ASN A 709 " ideal model delta sigma weight residual 120.31 113.29 7.02 1.52e+00 4.33e-01 2.13e+01 angle pdb=" C ASN A 709 " pdb=" N ASN A 710 " pdb=" CA ASN A 710 " ideal model delta sigma weight residual 123.33 116.28 7.05 1.64e+00 3.72e-01 1.85e+01 ... (remaining 48575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 20249 16.34 - 32.69: 915 32.69 - 49.03: 159 49.03 - 65.38: 42 65.38 - 81.72: 6 Dihedral angle restraints: 21371 sinusoidal: 8409 harmonic: 12962 Sorted by residual: dihedral pdb=" CA ALA C 570 " pdb=" C ALA C 570 " pdb=" N ASP C 571 " pdb=" CA ASP C 571 " ideal model delta harmonic sigma weight residual 180.00 164.36 15.64 0 5.00e+00 4.00e-02 9.79e+00 dihedral pdb=" N CYS F 90 " pdb=" CA CYS F 90 " pdb=" CB CYS F 90 " pdb=" SG CYS F 90 " ideal model delta sinusoidal sigma weight residual 180.00 120.57 59.43 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ASP A1041 " pdb=" CA ASP A1041 " pdb=" CB ASP A1041 " pdb=" CG ASP A1041 " ideal model delta sinusoidal sigma weight residual 60.00 119.34 -59.34 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 21368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 5004 0.079 - 0.158: 454 0.158 - 0.238: 5 0.238 - 0.317: 2 0.317 - 0.396: 2 Chirality restraints: 5467 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 5464 not shown) Planarity restraints: 6310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.352 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG A1301 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.086 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " 0.325 2.00e-02 2.50e+03 2.83e-01 9.98e+02 pdb=" C7 NAG A1303 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " 0.056 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " -0.499 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " 0.189 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1306 " -0.324 2.00e-02 2.50e+03 2.82e-01 9.96e+02 pdb=" C7 NAG B1306 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG B1306 " -0.058 2.00e-02 2.50e+03 pdb=" N2 NAG B1306 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG B1306 " -0.188 2.00e-02 2.50e+03 ... (remaining 6307 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 941 2.69 - 3.24: 33795 3.24 - 3.79: 53437 3.79 - 4.35: 69937 4.35 - 4.90: 115385 Nonbonded interactions: 273495 Sorted by model distance: nonbonded pdb=" O4 NAG B1304 " pdb=" O6 NAG B1304 " model vdw 2.137 3.040 nonbonded pdb=" OG SER D 91 " pdb=" OE1 GLN D 227 " model vdw 2.209 3.040 nonbonded pdb=" OG SER F 91 " pdb=" OE1 GLN F 227 " model vdw 2.212 3.040 nonbonded pdb=" OG SER H 91 " pdb=" OE1 GLN H 227 " model vdw 2.219 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.223 3.040 ... (remaining 273490 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 1305)) selection = (chain 'B' and (resid 26 through 243 or resid 262 through 1305)) selection = (chain 'C' and resid 26 through 1305) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.250 Find NCS groups from input model: 0.880 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 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 0.098 35770 Z= 0.191 Angle : 0.553 9.444 48736 Z= 0.314 Chirality : 0.042 0.396 5467 Planarity : 0.010 0.303 6292 Dihedral : 9.471 81.723 12950 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.03 % Favored : 91.81 % Rotamer: Outliers : 5.98 % Allowed : 8.00 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.10), residues: 4433 helix: -0.96 (0.19), residues: 632 sheet: -2.54 (0.16), residues: 829 loop : -3.58 (0.09), residues: 2972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 34 TYR 0.011 0.001 TYR A1067 PHE 0.006 0.001 PHE C 318 TRP 0.008 0.001 TRP G 98 HIS 0.004 0.000 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00294 (35701) covalent geometry : angle 0.54400 (48580) SS BOND : bond 0.00161 ( 51) SS BOND : angle 0.57090 ( 102) hydrogen bonds : bond 0.17232 ( 899) hydrogen bonds : angle 6.42232 ( 2379) link_NAG-ASN : bond 0.01006 ( 18) link_NAG-ASN : angle 2.96380 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 781 time to evaluate : 1.170 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: 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 34 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7736 (mtp85) REVERT: A 48 LEU cc_start: 0.8575 (mp) cc_final: 0.8330 (mt) REVERT: A 52 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7546 (tp40) REVERT: A 54 LEU cc_start: 0.8351 (mt) cc_final: 0.7992 (mm) REVERT: A 274 THR cc_start: 0.8426 (m) cc_final: 0.7921 (m) REVERT: A 290 ASP cc_start: 0.7167 (t70) cc_final: 0.6042 (p0) REVERT: A 720 ILE cc_start: 0.8762 (mp) cc_final: 0.8553 (mm) REVERT: A 776 LYS cc_start: 0.7958 (tmmt) cc_final: 0.7612 (tttm) REVERT: A 777 ASN cc_start: 0.7827 (m-40) cc_final: 0.7490 (m-40) REVERT: A 895 GLN cc_start: 0.7584 (pt0) cc_final: 0.7154 (mt0) REVERT: A 913 GLN cc_start: 0.7292 (pt0) cc_final: 0.6988 (pt0) REVERT: A 921 LYS cc_start: 0.7573 (mmmt) cc_final: 0.7183 (mppt) REVERT: A 925 ASN cc_start: 0.7773 (m-40) cc_final: 0.7138 (m-40) REVERT: A 976 VAL cc_start: 0.8668 (t) cc_final: 0.8405 (p) REVERT: A 993 ILE cc_start: 0.8238 (tp) cc_final: 0.7887 (tt) REVERT: A 1000 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7367 (mmt90) REVERT: A 1002 GLN cc_start: 0.7275 (tp-100) cc_final: 0.6946 (tp-100) REVERT: A 1019 ARG cc_start: 0.6665 (ttm110) cc_final: 0.6222 (ttm110) REVERT: A 1031 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6911 (mt-10) REVERT: A 1038 LYS cc_start: 0.7601 (mtmp) cc_final: 0.7351 (mtmm) REVERT: B 41 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7135 (mttt) REVERT: B 46 SER cc_start: 0.8082 (m) cc_final: 0.7504 (p) REVERT: B 119 ILE cc_start: 0.7511 (mt) cc_final: 0.7213 (tt) REVERT: B 126 VAL cc_start: 0.8106 (t) cc_final: 0.7803 (m) REVERT: B 194 ASN cc_start: 0.8447 (t0) cc_final: 0.8228 (t0) REVERT: B 200 LYS cc_start: 0.7971 (mttt) cc_final: 0.7547 (mttm) REVERT: B 205 HIS cc_start: 0.7139 (t-170) cc_final: 0.6867 (t-170) REVERT: B 276 LEU cc_start: 0.8428 (tp) cc_final: 0.8074 (tt) REVERT: B 278 LYS cc_start: 0.8185 (ttmp) cc_final: 0.7777 (tttm) REVERT: B 298 GLU cc_start: 0.7044 (tt0) cc_final: 0.6825 (tt0) REVERT: B 306 PHE cc_start: 0.7282 (m-10) cc_final: 0.6995 (m-10) REVERT: B 315 THR cc_start: 0.7773 (p) cc_final: 0.7546 (p) REVERT: B 425 LEU cc_start: 0.8693 (mp) cc_final: 0.8203 (pp) REVERT: B 542 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7649 (t0) REVERT: B 584 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7829 (pt) REVERT: B 587 ILE cc_start: 0.8059 (mt) cc_final: 0.7801 (mm) REVERT: B 616 ASN cc_start: 0.5695 (t0) cc_final: 0.5201 (t0) REVERT: B 619 GLU cc_start: 0.5957 (tt0) cc_final: 0.5710 (tt0) REVERT: B 663 ASP cc_start: 0.6883 (t70) cc_final: 0.6662 (t0) REVERT: B 698 SER cc_start: 0.8022 (t) cc_final: 0.7398 (p) REVERT: B 740 MET cc_start: 0.5868 (ttp) cc_final: 0.5642 (ttp) REVERT: B 773 GLU cc_start: 0.6310 (tm-30) cc_final: 0.4975 (tm-30) REVERT: B 774 GLN cc_start: 0.7206 (mm-40) cc_final: 0.5466 (mm-40) REVERT: B 790 LYS cc_start: 0.7732 (mppt) cc_final: 0.7361 (mtmm) REVERT: B 804 GLN cc_start: 0.7728 (mt0) cc_final: 0.7304 (mt0) REVERT: B 895 GLN cc_start: 0.7277 (pt0) cc_final: 0.7054 (mt0) REVERT: B 922 LEU cc_start: 0.7922 (tp) cc_final: 0.7719 (tp) REVERT: B 933 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7012 (mtpp) REVERT: B 974 SER cc_start: 0.6196 (p) cc_final: 0.5544 (m) REVERT: B 1000 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7472 (mtt180) REVERT: B 1010 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.6892 (mp-120) REVERT: B 1019 ARG cc_start: 0.6696 (ttm110) cc_final: 0.6406 (tmm-80) REVERT: B 1074 ASN cc_start: 0.8014 (m-40) cc_final: 0.7800 (m110) REVERT: B 1081 ILE cc_start: 0.8291 (pt) cc_final: 0.7924 (mm) REVERT: B 1118 ASP cc_start: 0.6423 (t70) cc_final: 0.6223 (t0) REVERT: C 33 THR cc_start: 0.7680 (OUTLIER) cc_final: 0.7446 (p) REVERT: C 65 PHE cc_start: 0.6923 (m-10) cc_final: 0.6499 (m-10) REVERT: C 106 PHE cc_start: 0.6687 (m-80) cc_final: 0.6202 (m-80) REVERT: C 126 VAL cc_start: 0.7097 (OUTLIER) cc_final: 0.6789 (t) REVERT: C 190 PHE cc_start: 0.6103 (m-80) cc_final: 0.5774 (m-80) REVERT: C 326 ILE cc_start: 0.8164 (mp) cc_final: 0.7807 (tt) REVERT: C 362 VAL cc_start: 0.7104 (OUTLIER) cc_final: 0.6543 (p) REVERT: C 542 ASN cc_start: 0.7489 (t0) cc_final: 0.7190 (t0) REVERT: C 551 VAL cc_start: 0.8078 (t) cc_final: 0.7845 (t) REVERT: C 644 GLN cc_start: 0.8313 (tp40) cc_final: 0.7439 (tp40) REVERT: C 659 SER cc_start: 0.8692 (t) cc_final: 0.8492 (p) REVERT: C 707 TYR cc_start: 0.7631 (t80) cc_final: 0.7356 (t80) REVERT: C 765 ARG cc_start: 0.7016 (ttp-110) cc_final: 0.6718 (ttp-110) REVERT: C 780 GLU cc_start: 0.7036 (pt0) cc_final: 0.6435 (pt0) REVERT: C 790 LYS cc_start: 0.7791 (mtmm) cc_final: 0.7557 (mtmm) REVERT: C 808 ASP cc_start: 0.7283 (t70) cc_final: 0.6967 (t70) REVERT: C 819 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6845 (mt-10) REVERT: C 820 ASP cc_start: 0.7554 (m-30) cc_final: 0.7300 (m-30) REVERT: C 901 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: C 914 ASN cc_start: 0.7346 (p0) cc_final: 0.6985 (p0) REVERT: C 960 ASN cc_start: 0.6554 (m110) cc_final: 0.6139 (m110) REVERT: C 973 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6696 (pp) REVERT: C 993 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7631 (mm) REVERT: C 994 ASP cc_start: 0.7583 (m-30) cc_final: 0.6682 (p0) REVERT: C 998 THR cc_start: 0.7873 (m) cc_final: 0.7506 (p) REVERT: C 1129 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7906 (p) REVERT: E 67 LYS cc_start: 0.0561 (OUTLIER) cc_final: 0.0290 (tmmm) REVERT: F 144 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.5842 (tm) REVERT: G 210 LEU cc_start: 0.0009 (OUTLIER) cc_final: -0.0479 (tm) REVERT: H 83 GLU cc_start: 0.3006 (OUTLIER) cc_final: 0.2568 (pp20) REVERT: I 67 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6758 (tmmm) outliers start: 228 outliers final: 96 residues processed: 977 average time/residue: 0.2098 time to fit residues: 332.4087 Evaluate side-chains 722 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 609 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 378 LYS 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 558 LYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.0870 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 4.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 52 GLN A 121 ASN A 173 GLN A 354 ASN A 370 ASN A 388 ASN A 409 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 487 ASN A 563 GLN A 690 GLN A 853 GLN A 901 GLN A1002 GLN A1011 GLN A1048 HIS B 173 GLN B 181 GLN B 186 ASN B 239 GLN B 245 HIS B 354 ASN B 388 ASN B 409 GLN B 422 ASN B 448 ASN B 477 ASN B 487 ASN B 540 ASN B 563 GLN B 762 GLN B 784 GLN B 853 GLN B 901 GLN B 914 ASN B1002 GLN B1010 GLN B1011 GLN B1048 HIS B1119 ASN C 30 ASN C 81 ASN C 164 ASN C 183 ASN C 205 HIS C 218 GLN C 354 ASN C 370 ASN C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 477 ASN C 487 ASN C 540 ASN C 580 GLN C 755 GLN C 774 GLN C 784 GLN C 853 GLN C 895 GLN C 913 GLN C 914 ASN C 955 ASN C1011 GLN C1048 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 39 GLN D 40 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 165 GLN D 202 ASN E 52 ASN E 80 GLN E 97 ASN E 127 GLN E 137 GLN E 159 HIS E 201 ASN E 206 GLN F 33 ASN F 39 GLN F 40 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN F 165 GLN F 202 ASN F 207 GLN G 35 ASN G 52 ASN G 80 GLN G 97 ASN G 137 GLN G 159 HIS G 201 ASN G 206 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 39 GLN H 40 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 GLN H 202 ASN I 32 ASN I 52 ASN I 80 GLN I 97 ASN I 127 GLN I 137 GLN I 159 HIS I 201 ASN I 206 GLN Total number of N/Q/H flips: 108 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.224185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.177170 restraints weight = 63776.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.173834 restraints weight = 52318.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.175544 restraints weight = 39390.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.175483 restraints weight = 29080.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.175686 restraints weight = 25138.733| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35770 Z= 0.146 Angle : 0.591 10.668 48736 Z= 0.297 Chirality : 0.045 0.255 5467 Planarity : 0.005 0.054 6292 Dihedral : 7.269 80.352 5506 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 6.01 % Allowed : 13.22 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.11), residues: 4433 helix: -0.02 (0.21), residues: 673 sheet: -2.12 (0.16), residues: 829 loop : -3.29 (0.09), residues: 2931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 567 TYR 0.022 0.001 TYR B1067 PHE 0.028 0.002 PHE C 643 TRP 0.040 0.001 TRP A 64 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00318 (35701) covalent geometry : angle 0.57850 (48580) SS BOND : bond 0.00287 ( 51) SS BOND : angle 1.74375 ( 102) hydrogen bonds : bond 0.03882 ( 899) hydrogen bonds : angle 4.86841 ( 2379) link_NAG-ASN : bond 0.00212 ( 18) link_NAG-ASN : angle 2.96237 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 642 time to evaluate : 1.042 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: 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 36 VAL cc_start: 0.8135 (t) cc_final: 0.7908 (t) REVERT: A 52 GLN cc_start: 0.8245 (tp40) cc_final: 0.7699 (tp-100) REVERT: A 54 LEU cc_start: 0.8359 (mt) cc_final: 0.8074 (mp) REVERT: A 92 PHE cc_start: 0.7525 (t80) cc_final: 0.7318 (t80) REVERT: A 318 PHE cc_start: 0.7713 (t80) cc_final: 0.7492 (t80) REVERT: A 537 LYS cc_start: 0.7262 (tmtt) cc_final: 0.6694 (tmtt) REVERT: A 581 THR cc_start: 0.7066 (OUTLIER) cc_final: 0.6588 (t) REVERT: A 586 ASP cc_start: 0.7599 (t0) cc_final: 0.7285 (t0) REVERT: A 649 CYS cc_start: 0.5206 (t) cc_final: 0.4857 (t) REVERT: A 675 GLN cc_start: 0.6642 (pp30) cc_final: 0.6274 (tm-30) REVERT: A 720 ILE cc_start: 0.8677 (mp) cc_final: 0.8407 (mm) REVERT: A 733 LYS cc_start: 0.8258 (mtmt) cc_final: 0.8049 (mtpt) REVERT: A 761 THR cc_start: 0.7569 (OUTLIER) cc_final: 0.7328 (p) REVERT: A 776 LYS cc_start: 0.8177 (tmmt) cc_final: 0.7799 (tttm) REVERT: A 777 ASN cc_start: 0.8184 (m-40) cc_final: 0.7661 (m-40) REVERT: A 821 LEU cc_start: 0.8615 (tp) cc_final: 0.8206 (tp) REVERT: A 825 LYS cc_start: 0.7884 (mmtp) cc_final: 0.7630 (ttmt) REVERT: A 869 MET cc_start: 0.8445 (mtp) cc_final: 0.8177 (mtp) REVERT: A 895 GLN cc_start: 0.7682 (pt0) cc_final: 0.7278 (pt0) REVERT: A 913 GLN cc_start: 0.7728 (pt0) cc_final: 0.7424 (pt0) REVERT: A 921 LYS cc_start: 0.7741 (mmmt) cc_final: 0.7119 (mppt) REVERT: A 925 ASN cc_start: 0.7745 (m-40) cc_final: 0.7433 (m-40) REVERT: A 933 LYS cc_start: 0.8055 (mtmm) cc_final: 0.7782 (mtmm) REVERT: A 957 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: A 976 VAL cc_start: 0.8505 (t) cc_final: 0.8142 (p) REVERT: A 1002 GLN cc_start: 0.7317 (tp40) cc_final: 0.6728 (tp-100) REVERT: A 1038 LYS cc_start: 0.7677 (mtmp) cc_final: 0.7433 (mtmm) REVERT: A 1073 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8033 (mtpp) REVERT: A 1088 HIS cc_start: 0.7859 (m90) cc_final: 0.7210 (m90) REVERT: A 1103 PHE cc_start: 0.8121 (m-80) cc_final: 0.7429 (m-10) REVERT: B 40 ASP cc_start: 0.7834 (p0) cc_final: 0.7533 (p0) REVERT: B 41 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7085 (mttt) REVERT: B 46 SER cc_start: 0.8238 (m) cc_final: 0.7660 (p) REVERT: B 52 GLN cc_start: 0.7577 (tm-30) cc_final: 0.6899 (tm-30) REVERT: B 62 VAL cc_start: 0.8090 (m) cc_final: 0.7800 (p) REVERT: B 65 PHE cc_start: 0.6891 (m-80) cc_final: 0.6612 (m-10) REVERT: B 95 ILE cc_start: 0.6503 (tp) cc_final: 0.6164 (mm) REVERT: B 200 LYS cc_start: 0.8060 (mttt) cc_final: 0.7690 (mttm) REVERT: B 276 LEU cc_start: 0.8489 (tp) cc_final: 0.8190 (tt) REVERT: B 278 LYS cc_start: 0.8240 (ttmp) cc_final: 0.7811 (tttm) REVERT: B 293 LEU cc_start: 0.8106 (tp) cc_final: 0.7869 (tp) REVERT: B 306 PHE cc_start: 0.7569 (m-10) cc_final: 0.7265 (m-10) REVERT: B 308 VAL cc_start: 0.8816 (t) cc_final: 0.8526 (m) REVERT: B 542 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.7331 (t0) REVERT: B 562 PHE cc_start: 0.8106 (p90) cc_final: 0.7893 (p90) REVERT: B 584 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7831 (tt) REVERT: B 587 ILE cc_start: 0.8272 (mt) cc_final: 0.8054 (mm) REVERT: B 606 ASN cc_start: 0.8309 (m-40) cc_final: 0.8065 (m-40) REVERT: B 616 ASN cc_start: 0.6349 (t0) cc_final: 0.5921 (t0) REVERT: B 698 SER cc_start: 0.8177 (t) cc_final: 0.7506 (p) REVERT: B 703 ASN cc_start: 0.6673 (t0) cc_final: 0.6133 (t0) REVERT: B 710 ASN cc_start: 0.7810 (p0) cc_final: 0.7552 (p0) REVERT: B 726 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7816 (mm) REVERT: B 774 GLN cc_start: 0.7383 (mm-40) cc_final: 0.6842 (mm-40) REVERT: B 790 LYS cc_start: 0.7917 (mppt) cc_final: 0.7615 (mtmm) REVERT: B 808 ASP cc_start: 0.7728 (t0) cc_final: 0.7202 (p0) REVERT: B 895 GLN cc_start: 0.7444 (pt0) cc_final: 0.7175 (pt0) REVERT: B 931 ILE cc_start: 0.7409 (mm) cc_final: 0.6701 (mt) REVERT: B 933 LYS cc_start: 0.8039 (mtmt) cc_final: 0.7183 (mtpp) REVERT: B 964 LYS cc_start: 0.8045 (ttpp) cc_final: 0.7713 (ttmm) REVERT: B 974 SER cc_start: 0.6184 (p) cc_final: 0.5713 (m) REVERT: B 977 LEU cc_start: 0.7775 (mp) cc_final: 0.7419 (mt) REVERT: B 990 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6301 (mt-10) REVERT: B 1081 ILE cc_start: 0.8436 (pt) cc_final: 0.8126 (pt) REVERT: C 33 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7591 (p) REVERT: C 92 PHE cc_start: 0.7530 (t80) cc_final: 0.7163 (t80) REVERT: C 192 PHE cc_start: 0.7725 (m-80) cc_final: 0.6921 (m-80) REVERT: C 204 LYS cc_start: 0.7863 (tptp) cc_final: 0.7292 (tptp) REVERT: C 224 GLU cc_start: 0.7595 (mp0) cc_final: 0.7224 (mp0) REVERT: C 326 ILE cc_start: 0.8069 (mp) cc_final: 0.7489 (tt) REVERT: C 537 LYS cc_start: 0.8372 (tttt) cc_final: 0.8011 (ptmt) REVERT: C 551 VAL cc_start: 0.8176 (t) cc_final: 0.7929 (t) REVERT: C 707 TYR cc_start: 0.7906 (t80) cc_final: 0.7571 (t80) REVERT: C 725 GLU cc_start: 0.7243 (pt0) cc_final: 0.7031 (pt0) REVERT: C 765 ARG cc_start: 0.7234 (ttp-110) cc_final: 0.6884 (ttp-110) REVERT: C 780 GLU cc_start: 0.7128 (pt0) cc_final: 0.6798 (pt0) REVERT: C 790 LYS cc_start: 0.7976 (mtmm) cc_final: 0.7681 (mtmm) REVERT: C 808 ASP cc_start: 0.7329 (t70) cc_final: 0.7033 (t0) REVERT: C 819 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6831 (mt-10) REVERT: C 901 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: C 902 MET cc_start: 0.7705 (tpp) cc_final: 0.7495 (tpp) REVERT: C 914 ASN cc_start: 0.7527 (p0) cc_final: 0.7144 (p0) REVERT: C 973 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6688 (pp) REVERT: C 993 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7650 (mm) REVERT: C 994 ASP cc_start: 0.7332 (m-30) cc_final: 0.6664 (p0) REVERT: C 1028 LYS cc_start: 0.8190 (ttmm) cc_final: 0.7954 (ttmt) REVERT: C 1097 SER cc_start: 0.8970 (t) cc_final: 0.8764 (t) REVERT: C 1129 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7957 (p) REVERT: C 1136 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8044 (p) REVERT: E 67 LYS cc_start: 0.0460 (OUTLIER) cc_final: 0.0214 (tmmm) REVERT: F 90 CYS cc_start: -0.0599 (OUTLIER) cc_final: -0.2725 (t) REVERT: G 158 MET cc_start: 0.5381 (mmm) cc_final: 0.5029 (mmm) REVERT: G 207 MET cc_start: 0.2815 (mpp) cc_final: 0.0832 (ptp) REVERT: H 83 GLU cc_start: 0.2623 (OUTLIER) cc_final: 0.2388 (pp20) REVERT: I 67 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6718 (tmmm) outliers start: 229 outliers final: 139 residues processed: 822 average time/residue: 0.2094 time to fit residues: 281.5186 Evaluate side-chains 764 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 607 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 378 LYS 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 552 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 288 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 275 optimal weight: 0.0470 chunk 157 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 319 optimal weight: 40.0000 chunk 217 optimal weight: 10.0000 chunk 354 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 340 optimal weight: 20.0000 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 205 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 913 GLN C 955 ASN C1048 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 GLN G 201 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.218647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.169953 restraints weight = 62749.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163685 restraints weight = 52166.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.165719 restraints weight = 41236.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165827 restraints weight = 35025.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.166419 restraints weight = 26003.966| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 35770 Z= 0.231 Angle : 0.665 14.200 48736 Z= 0.337 Chirality : 0.047 0.277 5467 Planarity : 0.005 0.061 6292 Dihedral : 7.421 80.914 5472 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 6.48 % Allowed : 14.40 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.11), residues: 4433 helix: 0.12 (0.20), residues: 667 sheet: -1.86 (0.16), residues: 904 loop : -3.11 (0.10), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 328 TYR 0.027 0.002 TYR B 904 PHE 0.037 0.002 PHE B 981 TRP 0.048 0.002 TRP A 64 HIS 0.017 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00504 (35701) covalent geometry : angle 0.65383 (48580) SS BOND : bond 0.00663 ( 51) SS BOND : angle 2.06660 ( 102) hydrogen bonds : bond 0.04290 ( 899) hydrogen bonds : angle 4.99553 ( 2379) link_NAG-ASN : bond 0.00424 ( 18) link_NAG-ASN : angle 2.61824 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 622 time to evaluate : 1.245 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: 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 34 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7429 (mtp180) REVERT: A 38 TYR cc_start: 0.8503 (m-80) cc_final: 0.8252 (m-10) REVERT: A 54 LEU cc_start: 0.8513 (mt) cc_final: 0.8109 (mp) REVERT: A 104 TRP cc_start: 0.7264 (m-90) cc_final: 0.7041 (m-90) REVERT: A 130 VAL cc_start: 0.6121 (OUTLIER) cc_final: 0.5851 (t) REVERT: A 303 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7673 (tt) REVERT: A 334 ASN cc_start: 0.8081 (p0) cc_final: 0.7826 (p0) REVERT: A 586 ASP cc_start: 0.7652 (t0) cc_final: 0.7290 (t0) REVERT: A 607 GLN cc_start: 0.7352 (mt0) cc_final: 0.7102 (mt0) REVERT: A 644 GLN cc_start: 0.7501 (tp-100) cc_final: 0.6880 (tp-100) REVERT: A 675 GLN cc_start: 0.6571 (pp30) cc_final: 0.6351 (tm-30) REVERT: A 702 GLU cc_start: 0.7103 (mp0) cc_final: 0.6896 (mp0) REVERT: A 720 ILE cc_start: 0.8796 (mp) cc_final: 0.8579 (mm) REVERT: A 776 LYS cc_start: 0.8357 (tmmt) cc_final: 0.7977 (tttp) REVERT: A 777 ASN cc_start: 0.8381 (m-40) cc_final: 0.7813 (m-40) REVERT: A 813 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.8020 (t) REVERT: A 821 LEU cc_start: 0.8677 (tp) cc_final: 0.8383 (tp) REVERT: A 825 LYS cc_start: 0.7889 (mmtp) cc_final: 0.7637 (mmmm) REVERT: A 868 GLU cc_start: 0.7099 (tp30) cc_final: 0.6887 (tp30) REVERT: A 913 GLN cc_start: 0.7938 (pt0) cc_final: 0.7704 (pt0) REVERT: A 922 LEU cc_start: 0.8336 (tp) cc_final: 0.8078 (tt) REVERT: A 925 ASN cc_start: 0.7902 (m-40) cc_final: 0.7589 (m-40) REVERT: A 933 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7835 (mtmm) REVERT: A 957 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: A 976 VAL cc_start: 0.8474 (t) cc_final: 0.8010 (p) REVERT: A 1072 GLU cc_start: 0.8164 (pm20) cc_final: 0.7740 (pm20) REVERT: A 1073 LYS cc_start: 0.8498 (ttmt) cc_final: 0.8074 (mtpp) REVERT: A 1091 ARG cc_start: 0.7618 (ttm170) cc_final: 0.7286 (ttm-80) REVERT: B 40 ASP cc_start: 0.8072 (p0) cc_final: 0.7813 (p0) REVERT: B 46 SER cc_start: 0.8435 (m) cc_final: 0.7951 (p) REVERT: B 52 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7554 (tm-30) REVERT: B 62 VAL cc_start: 0.8172 (m) cc_final: 0.7954 (p) REVERT: B 65 PHE cc_start: 0.7568 (m-80) cc_final: 0.7008 (m-10) REVERT: B 84 LEU cc_start: 0.8368 (mt) cc_final: 0.8167 (mt) REVERT: B 85 PRO cc_start: 0.7597 (Cg_exo) cc_final: 0.7357 (Cg_endo) REVERT: B 120 VAL cc_start: 0.8346 (m) cc_final: 0.7926 (p) REVERT: B 169 GLU cc_start: 0.6447 (pm20) cc_final: 0.6139 (pm20) REVERT: B 199 PHE cc_start: 0.8063 (t80) cc_final: 0.7836 (t80) REVERT: B 200 LYS cc_start: 0.8264 (mttt) cc_final: 0.7694 (mttm) REVERT: B 238 PHE cc_start: 0.7770 (t80) cc_final: 0.7493 (t80) REVERT: B 276 LEU cc_start: 0.8573 (tp) cc_final: 0.8034 (tt) REVERT: B 278 LYS cc_start: 0.8332 (ttmp) cc_final: 0.7999 (tttm) REVERT: B 281 GLU cc_start: 0.7412 (pp20) cc_final: 0.7150 (pp20) REVERT: B 297 SER cc_start: 0.8112 (m) cc_final: 0.7749 (p) REVERT: B 306 PHE cc_start: 0.7980 (m-10) cc_final: 0.7579 (m-10) REVERT: B 308 VAL cc_start: 0.8902 (t) cc_final: 0.8502 (m) REVERT: B 319 ARG cc_start: 0.6663 (ttm110) cc_final: 0.6420 (ttp-110) REVERT: B 542 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7422 (t0) REVERT: B 562 PHE cc_start: 0.8232 (p90) cc_final: 0.7739 (p90) REVERT: B 563 GLN cc_start: 0.7567 (mt0) cc_final: 0.7034 (mt0) REVERT: B 569 ILE cc_start: 0.8116 (pt) cc_final: 0.7844 (mp) REVERT: B 573 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8431 (p) REVERT: B 587 ILE cc_start: 0.8548 (mt) cc_final: 0.8343 (mm) REVERT: B 606 ASN cc_start: 0.8413 (m-40) cc_final: 0.8151 (m-40) REVERT: B 644 GLN cc_start: 0.8045 (tp40) cc_final: 0.7834 (tp40) REVERT: B 649 CYS cc_start: 0.5506 (OUTLIER) cc_final: 0.5198 (p) REVERT: B 703 ASN cc_start: 0.7129 (t0) cc_final: 0.6573 (t0) REVERT: B 765 ARG cc_start: 0.7106 (ttp-170) cc_final: 0.6607 (ttp-170) REVERT: B 774 GLN cc_start: 0.7408 (mm-40) cc_final: 0.7016 (mm-40) REVERT: B 790 LYS cc_start: 0.8039 (mppt) cc_final: 0.7826 (mtmm) REVERT: B 804 GLN cc_start: 0.8076 (mt0) cc_final: 0.7811 (mm-40) REVERT: B 808 ASP cc_start: 0.7804 (t0) cc_final: 0.7078 (p0) REVERT: B 819 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7226 (mt-10) REVERT: B 895 GLN cc_start: 0.7758 (pt0) cc_final: 0.7263 (pt0) REVERT: B 933 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7261 (mtpp) REVERT: B 935 GLN cc_start: 0.7369 (tt0) cc_final: 0.6739 (tt0) REVERT: B 957 GLN cc_start: 0.6707 (tm130) cc_final: 0.6013 (tm130) REVERT: B 964 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7760 (ttmm) REVERT: B 974 SER cc_start: 0.6972 (p) cc_final: 0.6525 (m) REVERT: B 977 LEU cc_start: 0.7944 (mp) cc_final: 0.7739 (mt) REVERT: B 990 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: B 1006 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8138 (t) REVERT: B 1081 ILE cc_start: 0.8424 (pt) cc_final: 0.8211 (pt) REVERT: C 104 TRP cc_start: 0.6468 (m-10) cc_final: 0.6190 (m-10) REVERT: C 129 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7673 (tptt) REVERT: C 177 MET cc_start: -0.0516 (tmt) cc_final: -0.0879 (tmt) REVERT: C 189 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7435 (mt-10) REVERT: C 201 ILE cc_start: 0.8499 (mp) cc_final: 0.8069 (tt) REVERT: C 203 SER cc_start: 0.8398 (t) cc_final: 0.8004 (m) REVERT: C 279 TYR cc_start: 0.8448 (m-80) cc_final: 0.8190 (m-10) REVERT: C 326 ILE cc_start: 0.8152 (mp) cc_final: 0.7558 (tt) REVERT: C 537 LYS cc_start: 0.8482 (tttt) cc_final: 0.8144 (tttp) REVERT: C 602 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7711 (p) REVERT: C 615 VAL cc_start: 0.8124 (m) cc_final: 0.7748 (t) REVERT: C 734 THR cc_start: 0.8323 (p) cc_final: 0.8065 (m) REVERT: C 740 MET cc_start: 0.7724 (mmm) cc_final: 0.7360 (mmm) REVERT: C 765 ARG cc_start: 0.7509 (ttp-110) cc_final: 0.6945 (ttp-170) REVERT: C 773 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6556 (tm-30) REVERT: C 780 GLU cc_start: 0.7378 (pt0) cc_final: 0.7004 (pt0) REVERT: C 790 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7661 (mtmm) REVERT: C 819 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6886 (mt-10) REVERT: C 901 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: C 902 MET cc_start: 0.8042 (tpp) cc_final: 0.7692 (tpp) REVERT: C 914 ASN cc_start: 0.7795 (p0) cc_final: 0.7490 (p0) REVERT: C 945 LEU cc_start: 0.8034 (mm) cc_final: 0.7777 (mt) REVERT: C 973 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7261 (pp) REVERT: C 993 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7763 (mm) REVERT: C 994 ASP cc_start: 0.7454 (m-30) cc_final: 0.6984 (p0) REVERT: C 998 THR cc_start: 0.8103 (m) cc_final: 0.7778 (p) REVERT: C 1019 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7421 (tpp-160) REVERT: C 1097 SER cc_start: 0.9000 (t) cc_final: 0.8650 (t) REVERT: C 1129 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.8013 (p) REVERT: C 1136 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8218 (p) REVERT: D 155 VAL cc_start: 0.6110 (OUTLIER) cc_final: 0.5733 (t) REVERT: E 67 LYS cc_start: 0.0557 (OUTLIER) cc_final: 0.0288 (tmmm) REVERT: F 144 LEU cc_start: 0.5641 (OUTLIER) cc_final: 0.5241 (tm) REVERT: F 148 CYS cc_start: 0.4567 (OUTLIER) cc_final: 0.4232 (m) REVERT: F 208 MET cc_start: 0.1448 (mtt) cc_final: 0.1227 (mtp) REVERT: F 226 ILE cc_start: -0.3606 (OUTLIER) cc_final: -0.4177 (pt) REVERT: G 158 MET cc_start: 0.5371 (mmm) cc_final: 0.4962 (mmm) REVERT: G 207 MET cc_start: 0.2785 (mpp) cc_final: 0.1005 (ptp) REVERT: H 49 MET cc_start: 0.6003 (mmm) cc_final: 0.5529 (mmm) REVERT: H 83 GLU cc_start: 0.2736 (OUTLIER) cc_final: 0.2484 (pp20) REVERT: H 208 MET cc_start: 0.4006 (mmm) cc_final: 0.2533 (tpt) REVERT: I 67 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6845 (tmmm) outliers start: 247 outliers final: 162 residues processed: 814 average time/residue: 0.2071 time to fit residues: 275.6275 Evaluate side-chains 768 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 582 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 361 CYS 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 558 LYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1048 HIS Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 221 CYS Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 226 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 chunk 243 optimal weight: 10.0000 chunk 420 optimal weight: 7.9990 chunk 293 optimal weight: 0.9990 chunk 288 optimal weight: 0.0070 chunk 208 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 356 optimal weight: 8.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN B 271 GLN B 556 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN E 201 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.220093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.172136 restraints weight = 62636.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.168425 restraints weight = 55828.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.169892 restraints weight = 45231.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.170292 restraints weight = 31377.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.170735 restraints weight = 25804.401| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35770 Z= 0.125 Angle : 0.587 13.107 48736 Z= 0.295 Chirality : 0.045 0.466 5467 Planarity : 0.004 0.052 6292 Dihedral : 7.147 82.166 5459 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 5.93 % Allowed : 16.29 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.12), residues: 4433 helix: 0.51 (0.21), residues: 667 sheet: -1.61 (0.17), residues: 869 loop : -2.99 (0.10), residues: 2897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 765 TYR 0.026 0.001 TYR B 674 PHE 0.041 0.001 PHE B 981 TRP 0.045 0.001 TRP A 64 HIS 0.017 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00278 (35701) covalent geometry : angle 0.57231 (48580) SS BOND : bond 0.00392 ( 51) SS BOND : angle 1.94299 ( 102) hydrogen bonds : bond 0.03441 ( 899) hydrogen bonds : angle 4.77249 ( 2379) link_NAG-ASN : bond 0.00201 ( 18) link_NAG-ASN : angle 3.07963 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 599 time to evaluate : 1.244 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: 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 34 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7401 (mtp180) REVERT: A 38 TYR cc_start: 0.8447 (m-80) cc_final: 0.8225 (m-10) REVERT: A 52 GLN cc_start: 0.7981 (tp40) cc_final: 0.7514 (tp-100) REVERT: A 54 LEU cc_start: 0.8537 (mt) cc_final: 0.8217 (mp) REVERT: A 118 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8091 (tp) REVERT: A 128 ILE cc_start: 0.8550 (mp) cc_final: 0.8349 (mp) REVERT: A 130 VAL cc_start: 0.6143 (OUTLIER) cc_final: 0.5860 (t) REVERT: A 586 ASP cc_start: 0.7492 (t0) cc_final: 0.7178 (t0) REVERT: A 619 GLU cc_start: 0.7057 (mp0) cc_final: 0.6749 (mp0) REVERT: A 643 PHE cc_start: 0.6026 (t80) cc_final: 0.5818 (t80) REVERT: A 655 TYR cc_start: 0.7310 (t80) cc_final: 0.6910 (t80) REVERT: A 675 GLN cc_start: 0.6611 (pp30) cc_final: 0.6184 (tm-30) REVERT: A 720 ILE cc_start: 0.8709 (mp) cc_final: 0.8477 (mm) REVERT: A 776 LYS cc_start: 0.8346 (tmmt) cc_final: 0.7953 (tttp) REVERT: A 777 ASN cc_start: 0.8309 (m-40) cc_final: 0.7675 (m-40) REVERT: A 821 LEU cc_start: 0.8641 (tp) cc_final: 0.8349 (tp) REVERT: A 825 LYS cc_start: 0.7850 (mmtp) cc_final: 0.7577 (mmmm) REVERT: A 868 GLU cc_start: 0.6941 (tp30) cc_final: 0.6525 (tp30) REVERT: A 869 MET cc_start: 0.8636 (mtp) cc_final: 0.8419 (mtp) REVERT: A 922 LEU cc_start: 0.8309 (tp) cc_final: 0.7963 (tt) REVERT: A 925 ASN cc_start: 0.7927 (m-40) cc_final: 0.7464 (m-40) REVERT: A 933 LYS cc_start: 0.8053 (mtmm) cc_final: 0.7760 (mtmm) REVERT: A 957 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: A 962 LEU cc_start: 0.8791 (tp) cc_final: 0.8571 (tp) REVERT: A 976 VAL cc_start: 0.8502 (t) cc_final: 0.8096 (p) REVERT: A 1031 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6834 (mt-10) REVERT: A 1072 GLU cc_start: 0.8093 (pm20) cc_final: 0.7686 (pm20) REVERT: A 1073 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8025 (mtpp) REVERT: A 1091 ARG cc_start: 0.7602 (ttm170) cc_final: 0.7293 (ttm-80) REVERT: A 1098 ASN cc_start: 0.5329 (p0) cc_final: 0.5116 (p0) REVERT: A 1103 PHE cc_start: 0.8194 (m-80) cc_final: 0.7908 (m-10) REVERT: B 46 SER cc_start: 0.8406 (m) cc_final: 0.7930 (p) REVERT: B 52 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7485 (tm-30) REVERT: B 62 VAL cc_start: 0.8148 (m) cc_final: 0.7945 (p) REVERT: B 65 PHE cc_start: 0.7401 (m-80) cc_final: 0.6787 (m-10) REVERT: B 120 VAL cc_start: 0.8320 (m) cc_final: 0.7941 (p) REVERT: B 169 GLU cc_start: 0.6239 (pm20) cc_final: 0.5911 (pm20) REVERT: B 170 TYR cc_start: 0.6944 (t80) cc_final: 0.6683 (t80) REVERT: B 200 LYS cc_start: 0.8224 (mttt) cc_final: 0.7671 (mttm) REVERT: B 228 ASP cc_start: 0.6456 (t70) cc_final: 0.6070 (t70) REVERT: B 238 PHE cc_start: 0.7710 (t80) cc_final: 0.7487 (t80) REVERT: B 276 LEU cc_start: 0.8544 (tp) cc_final: 0.8049 (tt) REVERT: B 278 LYS cc_start: 0.8253 (ttmp) cc_final: 0.7923 (tttm) REVERT: B 281 GLU cc_start: 0.7406 (pp20) cc_final: 0.7105 (pp20) REVERT: B 306 PHE cc_start: 0.7920 (m-10) cc_final: 0.7549 (m-10) REVERT: B 308 VAL cc_start: 0.8906 (t) cc_final: 0.8522 (m) REVERT: B 319 ARG cc_start: 0.6553 (ttm110) cc_final: 0.6319 (ttp-110) REVERT: B 542 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7431 (t0) REVERT: B 562 PHE cc_start: 0.8064 (p90) cc_final: 0.7589 (p90) REVERT: B 563 GLN cc_start: 0.7452 (mt0) cc_final: 0.7200 (mt0) REVERT: B 587 ILE cc_start: 0.8468 (mt) cc_final: 0.8260 (mm) REVERT: B 606 ASN cc_start: 0.8313 (m-40) cc_final: 0.8053 (m-40) REVERT: B 774 GLN cc_start: 0.7448 (mm-40) cc_final: 0.6967 (mm-40) REVERT: B 790 LYS cc_start: 0.8233 (mppt) cc_final: 0.7941 (mtmm) REVERT: B 819 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6919 (mt-10) REVERT: B 822 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8584 (mt) REVERT: B 895 GLN cc_start: 0.7444 (pt0) cc_final: 0.7024 (pt0) REVERT: B 906 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7339 (m-10) REVERT: B 921 LYS cc_start: 0.7854 (mmmt) cc_final: 0.7648 (mppt) REVERT: B 933 LYS cc_start: 0.8062 (mtmt) cc_final: 0.7149 (mtpp) REVERT: B 957 GLN cc_start: 0.6493 (tm130) cc_final: 0.5889 (tm130) REVERT: B 964 LYS cc_start: 0.8116 (ttpp) cc_final: 0.7734 (ttmm) REVERT: B 974 SER cc_start: 0.7090 (p) cc_final: 0.6664 (m) REVERT: B 990 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: B 1018 ILE cc_start: 0.8120 (mt) cc_final: 0.7880 (mm) REVERT: B 1081 ILE cc_start: 0.8412 (pt) cc_final: 0.8199 (pt) REVERT: C 129 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7794 (tptt) REVERT: C 177 MET cc_start: -0.0360 (tmt) cc_final: -0.0686 (tmt) REVERT: C 203 SER cc_start: 0.8445 (t) cc_final: 0.7792 (m) REVERT: C 224 GLU cc_start: 0.7518 (mp0) cc_final: 0.6988 (mp0) REVERT: C 326 ILE cc_start: 0.8125 (mp) cc_final: 0.7587 (tt) REVERT: C 328 ARG cc_start: 0.7267 (mtp85) cc_final: 0.6943 (mtp85) REVERT: C 537 LYS cc_start: 0.8417 (tttt) cc_final: 0.8055 (tttp) REVERT: C 542 ASN cc_start: 0.7509 (t0) cc_final: 0.7237 (t0) REVERT: C 551 VAL cc_start: 0.8382 (t) cc_final: 0.8158 (t) REVERT: C 657 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.7820 (t0) REVERT: C 707 TYR cc_start: 0.7962 (t80) cc_final: 0.7648 (t80) REVERT: C 734 THR cc_start: 0.8219 (p) cc_final: 0.7964 (m) REVERT: C 740 MET cc_start: 0.7624 (mmm) cc_final: 0.7212 (mmm) REVERT: C 765 ARG cc_start: 0.7539 (ttp-110) cc_final: 0.7008 (ttp-170) REVERT: C 780 GLU cc_start: 0.7256 (pt0) cc_final: 0.6914 (pt0) REVERT: C 790 LYS cc_start: 0.7919 (mtmm) cc_final: 0.7591 (mtmm) REVERT: C 819 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6791 (mt-10) REVERT: C 823 PHE cc_start: 0.7101 (m-80) cc_final: 0.6815 (t80) REVERT: C 901 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: C 902 MET cc_start: 0.7901 (tpp) cc_final: 0.7583 (tpp) REVERT: C 914 ASN cc_start: 0.7613 (p0) cc_final: 0.7358 (p0) REVERT: C 945 LEU cc_start: 0.7944 (mm) cc_final: 0.7693 (mt) REVERT: C 973 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7213 (pp) REVERT: C 993 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7687 (mm) REVERT: C 994 ASP cc_start: 0.7336 (m-30) cc_final: 0.6902 (p0) REVERT: C 998 THR cc_start: 0.7997 (m) cc_final: 0.7690 (p) REVERT: C 1019 ARG cc_start: 0.7579 (tpt90) cc_final: 0.7256 (tpp-160) REVERT: C 1129 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7906 (p) REVERT: C 1136 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8191 (p) REVERT: D 155 VAL cc_start: 0.6034 (OUTLIER) cc_final: 0.5696 (t) REVERT: E 67 LYS cc_start: 0.0527 (OUTLIER) cc_final: 0.0219 (tmmm) REVERT: F 144 LEU cc_start: 0.5591 (OUTLIER) cc_final: 0.5090 (tm) REVERT: F 148 CYS cc_start: 0.4784 (OUTLIER) cc_final: 0.4552 (m) REVERT: F 226 ILE cc_start: -0.3506 (OUTLIER) cc_final: -0.4172 (pt) REVERT: G 158 MET cc_start: 0.5219 (mmm) cc_final: 0.4798 (mmm) REVERT: H 49 MET cc_start: 0.6120 (mmm) cc_final: 0.5723 (mmm) REVERT: H 83 GLU cc_start: 0.2576 (OUTLIER) cc_final: 0.2366 (pp20) REVERT: H 129 GLN cc_start: 0.3690 (OUTLIER) cc_final: 0.3269 (pm20) REVERT: H 160 MET cc_start: 0.2926 (mmt) cc_final: 0.2613 (mmt) REVERT: H 234 MET cc_start: 0.4576 (tmm) cc_final: 0.4275 (tmm) REVERT: I 67 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6825 (tmmm) outliers start: 226 outliers final: 158 residues processed: 771 average time/residue: 0.2132 time to fit residues: 268.0400 Evaluate side-chains 756 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 576 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 361 CYS 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 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1048 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 221 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 163 optimal weight: 0.9990 chunk 418 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 400 optimal weight: 50.0000 chunk 60 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN A 895 GLN B 87 ASN B 556 ASN B 675 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.216038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.160224 restraints weight = 61660.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.158734 restraints weight = 38458.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.159680 restraints weight = 25062.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.160597 restraints weight = 22140.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.161386 restraints weight = 17198.614| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 35770 Z= 0.232 Angle : 0.641 10.345 48736 Z= 0.327 Chirality : 0.047 0.290 5467 Planarity : 0.005 0.050 6292 Dihedral : 7.382 82.616 5455 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 6.45 % Allowed : 16.42 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.12), residues: 4433 helix: 0.34 (0.20), residues: 673 sheet: -1.67 (0.16), residues: 942 loop : -2.91 (0.10), residues: 2818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 328 TYR 0.026 0.001 TYR A1067 PHE 0.039 0.002 PHE B 981 TRP 0.036 0.002 TRP A 64 HIS 0.017 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00507 (35701) covalent geometry : angle 0.63000 (48580) SS BOND : bond 0.00490 ( 51) SS BOND : angle 2.02533 ( 102) hydrogen bonds : bond 0.04132 ( 899) hydrogen bonds : angle 4.96290 ( 2379) link_NAG-ASN : bond 0.00417 ( 18) link_NAG-ASN : angle 2.51132 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 590 time to evaluate : 1.237 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: 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 34 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7317 (mtp180) REVERT: A 118 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8051 (tp) REVERT: A 334 ASN cc_start: 0.7853 (p0) cc_final: 0.7632 (p0) REVERT: A 537 LYS cc_start: 0.7486 (tmtt) cc_final: 0.6671 (tmtt) REVERT: A 643 PHE cc_start: 0.6308 (t80) cc_final: 0.6034 (t80) REVERT: A 675 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.6129 (tm-30) REVERT: A 720 ILE cc_start: 0.8893 (mp) cc_final: 0.8653 (mm) REVERT: A 776 LYS cc_start: 0.8376 (tmmt) cc_final: 0.8101 (tttm) REVERT: A 777 ASN cc_start: 0.8411 (m-40) cc_final: 0.7848 (m-40) REVERT: A 803 SER cc_start: 0.8208 (m) cc_final: 0.7924 (p) REVERT: A 813 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8234 (t) REVERT: A 868 GLU cc_start: 0.7015 (tp30) cc_final: 0.6557 (tp30) REVERT: A 895 GLN cc_start: 0.7908 (pt0) cc_final: 0.7420 (pt0) REVERT: A 921 LYS cc_start: 0.7779 (mmmt) cc_final: 0.7273 (mtmm) REVERT: A 922 LEU cc_start: 0.8319 (tp) cc_final: 0.7983 (tt) REVERT: A 925 ASN cc_start: 0.7979 (m-40) cc_final: 0.7600 (m-40) REVERT: A 933 LYS cc_start: 0.8045 (mtmm) cc_final: 0.7800 (mtmm) REVERT: A 957 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: A 962 LEU cc_start: 0.8878 (tp) cc_final: 0.8604 (tp) REVERT: A 976 VAL cc_start: 0.8509 (t) cc_final: 0.8115 (p) REVERT: A 1068 VAL cc_start: 0.8057 (t) cc_final: 0.7758 (m) REVERT: A 1072 GLU cc_start: 0.8064 (pm20) cc_final: 0.7685 (pm20) REVERT: A 1091 ARG cc_start: 0.7678 (ttm170) cc_final: 0.7393 (ttm-80) REVERT: A 1098 ASN cc_start: 0.5255 (p0) cc_final: 0.5028 (p0) REVERT: A 1103 PHE cc_start: 0.8186 (m-80) cc_final: 0.7933 (m-10) REVERT: B 46 SER cc_start: 0.8411 (m) cc_final: 0.7950 (p) REVERT: B 56 LEU cc_start: 0.8805 (tp) cc_final: 0.8496 (tt) REVERT: B 62 VAL cc_start: 0.8105 (m) cc_final: 0.7895 (p) REVERT: B 65 PHE cc_start: 0.7556 (m-80) cc_final: 0.6888 (m-10) REVERT: B 169 GLU cc_start: 0.6428 (pm20) cc_final: 0.6078 (pm20) REVERT: B 170 TYR cc_start: 0.7082 (t80) cc_final: 0.6768 (t80) REVERT: B 200 LYS cc_start: 0.8238 (mttt) cc_final: 0.7689 (mttm) REVERT: B 228 ASP cc_start: 0.6575 (t70) cc_final: 0.6204 (t70) REVERT: B 238 PHE cc_start: 0.7890 (t80) cc_final: 0.7604 (t80) REVERT: B 278 LYS cc_start: 0.8303 (ttmp) cc_final: 0.7988 (tttm) REVERT: B 281 GLU cc_start: 0.7484 (pp20) cc_final: 0.7259 (pp20) REVERT: B 297 SER cc_start: 0.8221 (m) cc_final: 0.7911 (p) REVERT: B 308 VAL cc_start: 0.8998 (t) cc_final: 0.8595 (m) REVERT: B 319 ARG cc_start: 0.6601 (ttm110) cc_final: 0.6276 (ttp-110) REVERT: B 542 ASN cc_start: 0.7722 (OUTLIER) cc_final: 0.7387 (t0) REVERT: B 562 PHE cc_start: 0.8186 (p90) cc_final: 0.7951 (p90) REVERT: B 563 GLN cc_start: 0.7453 (mt0) cc_final: 0.7083 (mt0) REVERT: B 569 ILE cc_start: 0.8078 (pt) cc_final: 0.7814 (mp) REVERT: B 674 TYR cc_start: 0.7674 (t80) cc_final: 0.7456 (t80) REVERT: B 774 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7075 (mm-40) REVERT: B 790 LYS cc_start: 0.8266 (mppt) cc_final: 0.7999 (mtmm) REVERT: B 819 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7118 (mt-10) REVERT: B 933 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7100 (mtpp) REVERT: B 936 ASP cc_start: 0.6768 (m-30) cc_final: 0.6281 (m-30) REVERT: B 957 GLN cc_start: 0.6620 (tm130) cc_final: 0.6234 (tm130) REVERT: B 964 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7866 (ttmm) REVERT: B 974 SER cc_start: 0.7407 (p) cc_final: 0.7034 (m) REVERT: B 1006 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8185 (t) REVERT: B 1018 ILE cc_start: 0.8142 (mt) cc_final: 0.7901 (mm) REVERT: B 1081 ILE cc_start: 0.8492 (pt) cc_final: 0.8241 (pt) REVERT: B 1084 ASP cc_start: 0.7020 (p0) cc_final: 0.6696 (p0) REVERT: C 129 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7726 (tptt) REVERT: C 190 PHE cc_start: 0.6744 (m-80) cc_final: 0.6444 (m-80) REVERT: C 201 ILE cc_start: 0.8280 (mp) cc_final: 0.7959 (tt) REVERT: C 203 SER cc_start: 0.8424 (t) cc_final: 0.7989 (m) REVERT: C 224 GLU cc_start: 0.7523 (mp0) cc_final: 0.7310 (mp0) REVERT: C 237 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7530 (mtp180) REVERT: C 279 TYR cc_start: 0.8399 (m-80) cc_final: 0.8183 (m-10) REVERT: C 326 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7649 (tt) REVERT: C 537 LYS cc_start: 0.8404 (tttt) cc_final: 0.7934 (tttp) REVERT: C 542 ASN cc_start: 0.7555 (t0) cc_final: 0.7293 (t0) REVERT: C 592 PHE cc_start: 0.7150 (p90) cc_final: 0.6884 (p90) REVERT: C 602 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7765 (p) REVERT: C 657 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.7780 (t0) REVERT: C 734 THR cc_start: 0.8400 (p) cc_final: 0.8101 (m) REVERT: C 765 ARG cc_start: 0.7689 (ttp-110) cc_final: 0.6846 (ttp-170) REVERT: C 780 GLU cc_start: 0.7308 (pt0) cc_final: 0.6940 (pt0) REVERT: C 790 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7576 (mtmm) REVERT: C 819 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6834 (mt-10) REVERT: C 882 ILE cc_start: 0.8574 (pt) cc_final: 0.8008 (mt) REVERT: C 901 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: C 902 MET cc_start: 0.7922 (tpp) cc_final: 0.7682 (tpp) REVERT: C 904 TYR cc_start: 0.7902 (m-10) cc_final: 0.7567 (m-10) REVERT: C 945 LEU cc_start: 0.8011 (mm) cc_final: 0.7762 (mt) REVERT: C 973 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7497 (pp) REVERT: C 994 ASP cc_start: 0.7493 (m-30) cc_final: 0.7270 (p0) REVERT: C 998 THR cc_start: 0.8096 (m) cc_final: 0.7874 (p) REVERT: C 1019 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7185 (tpp-160) REVERT: C 1083 HIS cc_start: 0.7432 (t70) cc_final: 0.7126 (t70) REVERT: C 1129 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8092 (p) REVERT: D 176 VAL cc_start: 0.6000 (OUTLIER) cc_final: 0.5775 (t) REVERT: E 67 LYS cc_start: 0.0651 (OUTLIER) cc_final: 0.0440 (tmmm) REVERT: F 148 CYS cc_start: 0.5051 (OUTLIER) cc_final: 0.4796 (m) REVERT: G 158 MET cc_start: 0.5182 (mmm) cc_final: 0.4901 (mmm) REVERT: G 207 MET cc_start: 0.3383 (mpp) cc_final: 0.1210 (ptp) REVERT: H 83 GLU cc_start: 0.2859 (OUTLIER) cc_final: 0.2588 (pp20) REVERT: H 208 MET cc_start: 0.3851 (mmm) cc_final: 0.2169 (tpt) REVERT: I 67 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6996 (tmmm) outliers start: 246 outliers final: 182 residues processed: 771 average time/residue: 0.2073 time to fit residues: 262.0429 Evaluate side-chains 769 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 568 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 361 CYS 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 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1048 HIS Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 221 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 221 CYS Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 97 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 406 optimal weight: 50.0000 chunk 341 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 313 optimal weight: 0.0060 chunk 64 optimal weight: 0.5980 chunk 227 optimal weight: 0.1980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 824 ASN B 703 ASN B 913 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 955 ASN C1048 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.219045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.163856 restraints weight = 62160.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.162595 restraints weight = 42228.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.164145 restraints weight = 23776.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.164651 restraints weight = 22925.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.165695 restraints weight = 16967.978| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35770 Z= 0.111 Angle : 0.582 13.744 48736 Z= 0.291 Chirality : 0.044 0.272 5467 Planarity : 0.004 0.054 6292 Dihedral : 7.119 83.142 5449 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 5.82 % Allowed : 17.13 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.12), residues: 4433 helix: 0.80 (0.21), residues: 669 sheet: -1.52 (0.16), residues: 931 loop : -2.79 (0.10), residues: 2833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 328 TYR 0.024 0.001 TYR A 170 PHE 0.042 0.001 PHE B 981 TRP 0.062 0.001 TRP A 64 HIS 0.017 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00252 (35701) covalent geometry : angle 0.57419 (48580) SS BOND : bond 0.00367 ( 51) SS BOND : angle 1.51623 ( 102) hydrogen bonds : bond 0.03287 ( 899) hydrogen bonds : angle 4.72445 ( 2379) link_NAG-ASN : bond 0.00192 ( 18) link_NAG-ASN : angle 2.14914 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 590 time to evaluate : 1.044 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7507 (mmt90) REVERT: A 64 TRP cc_start: 0.6070 (t60) cc_final: 0.5786 (t60) REVERT: A 130 VAL cc_start: 0.6274 (t) cc_final: 0.5958 (t) REVERT: A 334 ASN cc_start: 0.8045 (p0) cc_final: 0.7748 (p0) REVERT: A 537 LYS cc_start: 0.7551 (tmtt) cc_final: 0.6665 (tmtt) REVERT: A 586 ASP cc_start: 0.7400 (t0) cc_final: 0.7155 (t0) REVERT: A 675 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.6252 (tm-30) REVERT: A 720 ILE cc_start: 0.8893 (mp) cc_final: 0.8662 (mm) REVERT: A 776 LYS cc_start: 0.8325 (tmmt) cc_final: 0.7973 (tttp) REVERT: A 777 ASN cc_start: 0.8267 (m-40) cc_final: 0.7674 (m-40) REVERT: A 803 SER cc_start: 0.7903 (m) cc_final: 0.7649 (p) REVERT: A 868 GLU cc_start: 0.6962 (tp30) cc_final: 0.6503 (tp30) REVERT: A 895 GLN cc_start: 0.7837 (pt0) cc_final: 0.7301 (pt0) REVERT: A 921 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7264 (mtmm) REVERT: A 922 LEU cc_start: 0.8300 (tp) cc_final: 0.7973 (tt) REVERT: A 925 ASN cc_start: 0.7969 (m-40) cc_final: 0.7600 (m-40) REVERT: A 933 LYS cc_start: 0.8009 (mtmm) cc_final: 0.7709 (mtmm) REVERT: A 945 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8147 (mp) REVERT: A 955 ASN cc_start: 0.7345 (m-40) cc_final: 0.7127 (m-40) REVERT: A 957 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: A 976 VAL cc_start: 0.8487 (t) cc_final: 0.8062 (p) REVERT: A 1072 GLU cc_start: 0.8034 (pm20) cc_final: 0.7701 (pm20) REVERT: A 1091 ARG cc_start: 0.7568 (ttm170) cc_final: 0.7284 (ttm-80) REVERT: A 1103 PHE cc_start: 0.8198 (m-80) cc_final: 0.7910 (m-10) REVERT: A 1107 ARG cc_start: 0.7543 (mtt90) cc_final: 0.6663 (mtt90) REVERT: B 44 ARG cc_start: 0.8142 (mtt180) cc_final: 0.7940 (mtt90) REVERT: B 46 SER cc_start: 0.8448 (m) cc_final: 0.7906 (p) REVERT: B 56 LEU cc_start: 0.8743 (tp) cc_final: 0.8517 (tt) REVERT: B 62 VAL cc_start: 0.8111 (m) cc_final: 0.7885 (p) REVERT: B 65 PHE cc_start: 0.7462 (m-80) cc_final: 0.6858 (m-10) REVERT: B 169 GLU cc_start: 0.6288 (pm20) cc_final: 0.5929 (pm20) REVERT: B 170 TYR cc_start: 0.7064 (t80) cc_final: 0.6771 (t80) REVERT: B 200 LYS cc_start: 0.8209 (mttt) cc_final: 0.7660 (mttm) REVERT: B 218 GLN cc_start: 0.7741 (mm110) cc_final: 0.7464 (mm110) REVERT: B 276 LEU cc_start: 0.8579 (tp) cc_final: 0.8336 (tp) REVERT: B 278 LYS cc_start: 0.8249 (ttmp) cc_final: 0.7973 (tttm) REVERT: B 297 SER cc_start: 0.8230 (m) cc_final: 0.7908 (p) REVERT: B 308 VAL cc_start: 0.8910 (t) cc_final: 0.8527 (m) REVERT: B 319 ARG cc_start: 0.6519 (ttm110) cc_final: 0.6218 (ttp-110) REVERT: B 465 GLU cc_start: 0.7029 (pt0) cc_final: 0.6653 (pt0) REVERT: B 542 ASN cc_start: 0.7628 (OUTLIER) cc_final: 0.7345 (t0) REVERT: B 562 PHE cc_start: 0.8138 (p90) cc_final: 0.7893 (p90) REVERT: B 563 GLN cc_start: 0.7410 (mt0) cc_final: 0.7070 (mt0) REVERT: B 674 TYR cc_start: 0.7626 (t80) cc_final: 0.7402 (t80) REVERT: B 774 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7108 (mm-40) REVERT: B 790 LYS cc_start: 0.8216 (mppt) cc_final: 0.7823 (mtmm) REVERT: B 819 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6854 (mt-10) REVERT: B 822 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8606 (mt) REVERT: B 856 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8161 (tppt) REVERT: B 895 GLN cc_start: 0.7425 (pt0) cc_final: 0.7026 (pt0) REVERT: B 921 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7655 (mppt) REVERT: B 933 LYS cc_start: 0.7898 (mtmt) cc_final: 0.7040 (mtpp) REVERT: B 957 GLN cc_start: 0.6458 (tm130) cc_final: 0.5994 (tm130) REVERT: B 964 LYS cc_start: 0.8163 (ttpp) cc_final: 0.7815 (ttmm) REVERT: B 974 SER cc_start: 0.7350 (p) cc_final: 0.7082 (m) REVERT: B 1018 ILE cc_start: 0.8142 (mt) cc_final: 0.7907 (mm) REVERT: B 1081 ILE cc_start: 0.8415 (pt) cc_final: 0.8137 (pt) REVERT: B 1084 ASP cc_start: 0.6949 (p0) cc_final: 0.6605 (p0) REVERT: B 1121 PHE cc_start: 0.8085 (p90) cc_final: 0.7825 (p90) REVERT: C 59 PHE cc_start: 0.8041 (m-10) cc_final: 0.7823 (m-80) REVERT: C 106 PHE cc_start: 0.6659 (m-80) cc_final: 0.6411 (m-80) REVERT: C 129 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7800 (tptt) REVERT: C 190 PHE cc_start: 0.6701 (m-80) cc_final: 0.6433 (m-80) REVERT: C 201 ILE cc_start: 0.8256 (mp) cc_final: 0.7936 (tt) REVERT: C 203 SER cc_start: 0.8231 (t) cc_final: 0.7742 (m) REVERT: C 224 GLU cc_start: 0.7395 (mp0) cc_final: 0.6958 (mp0) REVERT: C 237 ARG cc_start: 0.7761 (mtp85) cc_final: 0.7529 (mtp180) REVERT: C 321 GLN cc_start: 0.7937 (pm20) cc_final: 0.7684 (pm20) REVERT: C 326 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7634 (tt) REVERT: C 537 LYS cc_start: 0.8384 (tttt) cc_final: 0.7989 (tttp) REVERT: C 542 ASN cc_start: 0.7645 (t0) cc_final: 0.7386 (t0) REVERT: C 592 PHE cc_start: 0.7003 (p90) cc_final: 0.6802 (p90) REVERT: C 602 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7688 (p) REVERT: C 707 TYR cc_start: 0.7913 (t80) cc_final: 0.7547 (t80) REVERT: C 734 THR cc_start: 0.8280 (p) cc_final: 0.8030 (m) REVERT: C 740 MET cc_start: 0.7345 (mmm) cc_final: 0.6977 (mmm) REVERT: C 765 ARG cc_start: 0.7647 (ttp-110) cc_final: 0.6924 (ttp-170) REVERT: C 780 GLU cc_start: 0.7245 (pt0) cc_final: 0.6852 (pt0) REVERT: C 790 LYS cc_start: 0.7787 (mtmm) cc_final: 0.7516 (mtmm) REVERT: C 819 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6780 (mt-10) REVERT: C 820 ASP cc_start: 0.7500 (t0) cc_final: 0.7256 (t0) REVERT: C 823 PHE cc_start: 0.7131 (m-80) cc_final: 0.6849 (t80) REVERT: C 882 ILE cc_start: 0.8559 (pt) cc_final: 0.8154 (mt) REVERT: C 901 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: C 902 MET cc_start: 0.7867 (tpp) cc_final: 0.7641 (tpp) REVERT: C 904 TYR cc_start: 0.7757 (m-10) cc_final: 0.7454 (m-10) REVERT: C 973 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7413 (pp) REVERT: C 994 ASP cc_start: 0.7494 (m-30) cc_final: 0.7097 (p0) REVERT: C 998 THR cc_start: 0.8060 (m) cc_final: 0.7738 (p) REVERT: C 1019 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7407 (tpp-160) REVERT: C 1129 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7981 (p) REVERT: D 176 VAL cc_start: 0.6070 (OUTLIER) cc_final: 0.5861 (t) REVERT: E 67 LYS cc_start: 0.0672 (OUTLIER) cc_final: 0.0470 (tmmm) REVERT: F 148 CYS cc_start: 0.4995 (OUTLIER) cc_final: 0.4751 (m) REVERT: F 153 PHE cc_start: -0.1177 (OUTLIER) cc_final: -0.2614 (m-80) REVERT: G 158 MET cc_start: 0.5103 (mmm) cc_final: 0.4775 (mmm) REVERT: G 207 MET cc_start: 0.3228 (mpp) cc_final: 0.1084 (ptp) REVERT: H 49 MET cc_start: 0.5908 (mmm) cc_final: 0.5554 (mmm) REVERT: H 83 GLU cc_start: 0.2647 (OUTLIER) cc_final: 0.2403 (pp20) REVERT: H 129 GLN cc_start: 0.2830 (OUTLIER) cc_final: 0.2526 (pm20) REVERT: H 160 MET cc_start: 0.3057 (mmt) cc_final: -0.0640 (mtp) REVERT: H 234 MET cc_start: 0.4178 (tmm) cc_final: 0.3806 (tmm) REVERT: I 67 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7006 (tmmm) outliers start: 222 outliers final: 166 residues processed: 752 average time/residue: 0.2035 time to fit residues: 251.0629 Evaluate side-chains 755 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 569 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 361 CYS 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 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1048 HIS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 221 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 289 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 246 optimal weight: 10.0000 chunk 268 optimal weight: 0.7980 chunk 219 optimal weight: 2.9990 chunk 233 optimal weight: 0.7980 chunk 284 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 441 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 641 ASN B 644 GLN B 920 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 ASN H 6 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.217534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.161536 restraints weight = 62028.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159964 restraints weight = 41195.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.161459 restraints weight = 24306.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.161994 restraints weight = 20471.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.164851 restraints weight = 16875.157| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 35770 Z= 0.147 Angle : 0.620 19.566 48736 Z= 0.305 Chirality : 0.045 0.277 5467 Planarity : 0.004 0.053 6292 Dihedral : 7.196 82.458 5443 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 5.93 % Allowed : 17.47 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.12), residues: 4433 helix: 0.82 (0.21), residues: 676 sheet: -1.39 (0.17), residues: 914 loop : -2.77 (0.10), residues: 2843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 328 TYR 0.020 0.001 TYR B1067 PHE 0.039 0.002 PHE B 981 TRP 0.047 0.001 TRP A 64 HIS 0.017 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00328 (35701) covalent geometry : angle 0.60711 (48580) SS BOND : bond 0.00439 ( 51) SS BOND : angle 1.84457 ( 102) hydrogen bonds : bond 0.03467 ( 899) hydrogen bonds : angle 4.73634 ( 2379) link_NAG-ASN : bond 0.00213 ( 18) link_NAG-ASN : angle 2.94932 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 588 time to evaluate : 0.818 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: 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 34 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7468 (mmt90) REVERT: A 64 TRP cc_start: 0.6194 (t60) cc_final: 0.5451 (t60) REVERT: A 117 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6996 (mt) REVERT: A 537 LYS cc_start: 0.7573 (tmtt) cc_final: 0.6683 (tmtt) REVERT: A 655 TYR cc_start: 0.7284 (t80) cc_final: 0.6986 (t80) REVERT: A 663 ASP cc_start: 0.7390 (t0) cc_final: 0.7106 (m-30) REVERT: A 675 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.6221 (tm-30) REVERT: A 720 ILE cc_start: 0.8901 (mp) cc_final: 0.8670 (mm) REVERT: A 776 LYS cc_start: 0.8345 (tmmt) cc_final: 0.8068 (tttm) REVERT: A 777 ASN cc_start: 0.8310 (m-40) cc_final: 0.7713 (m-40) REVERT: A 803 SER cc_start: 0.7968 (m) cc_final: 0.7697 (p) REVERT: A 868 GLU cc_start: 0.7033 (tp30) cc_final: 0.6538 (tp30) REVERT: A 921 LYS cc_start: 0.7754 (mmmt) cc_final: 0.7277 (mtmm) REVERT: A 922 LEU cc_start: 0.8266 (tp) cc_final: 0.7948 (tt) REVERT: A 925 ASN cc_start: 0.7973 (m-40) cc_final: 0.7593 (m-40) REVERT: A 933 LYS cc_start: 0.8052 (mtmm) cc_final: 0.7739 (mtmm) REVERT: A 945 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8106 (mp) REVERT: A 957 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7208 (tt0) REVERT: A 962 LEU cc_start: 0.8893 (tp) cc_final: 0.8569 (tp) REVERT: A 976 VAL cc_start: 0.8493 (t) cc_final: 0.8052 (p) REVERT: A 1072 GLU cc_start: 0.8024 (pm20) cc_final: 0.7600 (pm20) REVERT: A 1091 ARG cc_start: 0.7621 (ttm170) cc_final: 0.7322 (ttm-80) REVERT: A 1103 PHE cc_start: 0.8183 (m-80) cc_final: 0.7925 (m-10) REVERT: A 1107 ARG cc_start: 0.7530 (mtt90) cc_final: 0.6580 (mtt90) REVERT: B 46 SER cc_start: 0.8387 (m) cc_final: 0.7906 (p) REVERT: B 56 LEU cc_start: 0.8753 (tp) cc_final: 0.8536 (tt) REVERT: B 62 VAL cc_start: 0.8084 (m) cc_final: 0.7859 (p) REVERT: B 65 PHE cc_start: 0.7522 (m-80) cc_final: 0.6924 (m-10) REVERT: B 81 ASN cc_start: 0.7026 (p0) cc_final: 0.6757 (p0) REVERT: B 169 GLU cc_start: 0.6304 (pm20) cc_final: 0.5979 (pm20) REVERT: B 170 TYR cc_start: 0.7123 (t80) cc_final: 0.6762 (t80) REVERT: B 200 LYS cc_start: 0.8191 (mttt) cc_final: 0.7617 (mttm) REVERT: B 278 LYS cc_start: 0.8277 (ttmp) cc_final: 0.7989 (tttm) REVERT: B 297 SER cc_start: 0.8224 (m) cc_final: 0.7913 (p) REVERT: B 308 VAL cc_start: 0.8959 (t) cc_final: 0.8591 (m) REVERT: B 319 ARG cc_start: 0.6620 (ttm110) cc_final: 0.6295 (ttp-110) REVERT: B 465 GLU cc_start: 0.7050 (pt0) cc_final: 0.6618 (pt0) REVERT: B 542 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7350 (t0) REVERT: B 562 PHE cc_start: 0.8225 (p90) cc_final: 0.7946 (p90) REVERT: B 563 GLN cc_start: 0.7359 (mt0) cc_final: 0.6634 (mt0) REVERT: B 569 ILE cc_start: 0.7981 (pt) cc_final: 0.7738 (mp) REVERT: B 587 ILE cc_start: 0.8442 (mm) cc_final: 0.8227 (mm) REVERT: B 774 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7102 (mm-40) REVERT: B 790 LYS cc_start: 0.8220 (mppt) cc_final: 0.7849 (mtmm) REVERT: B 858 LEU cc_start: 0.8021 (mt) cc_final: 0.7625 (mt) REVERT: B 921 LYS cc_start: 0.7888 (mmmt) cc_final: 0.7494 (mmmm) REVERT: B 933 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7063 (mtpp) REVERT: B 957 GLN cc_start: 0.6550 (tm130) cc_final: 0.6127 (tm130) REVERT: B 964 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7837 (ttmm) REVERT: B 974 SER cc_start: 0.7500 (p) cc_final: 0.7144 (m) REVERT: B 1018 ILE cc_start: 0.8154 (mt) cc_final: 0.7951 (mm) REVERT: B 1081 ILE cc_start: 0.8440 (pt) cc_final: 0.8176 (pt) REVERT: B 1084 ASP cc_start: 0.7053 (p0) cc_final: 0.6709 (p0) REVERT: B 1121 PHE cc_start: 0.8088 (p90) cc_final: 0.7828 (p90) REVERT: C 32 PHE cc_start: 0.8286 (m-80) cc_final: 0.7959 (m-80) REVERT: C 129 LYS cc_start: 0.8261 (ttmt) cc_final: 0.7740 (tptt) REVERT: C 190 PHE cc_start: 0.6720 (m-80) cc_final: 0.6487 (m-80) REVERT: C 201 ILE cc_start: 0.8248 (mp) cc_final: 0.7963 (tt) REVERT: C 203 SER cc_start: 0.8231 (t) cc_final: 0.7989 (m) REVERT: C 224 GLU cc_start: 0.7423 (mp0) cc_final: 0.7177 (mp0) REVERT: C 281 GLU cc_start: 0.8369 (pm20) cc_final: 0.7825 (pm20) REVERT: C 321 GLN cc_start: 0.7941 (pm20) cc_final: 0.7680 (pm20) REVERT: C 324 GLU cc_start: 0.7279 (pm20) cc_final: 0.7065 (pm20) REVERT: C 326 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7620 (tt) REVERT: C 537 LYS cc_start: 0.8411 (tttt) cc_final: 0.7776 (tttt) REVERT: C 542 ASN cc_start: 0.7583 (t0) cc_final: 0.7304 (t0) REVERT: C 707 TYR cc_start: 0.7918 (t80) cc_final: 0.7568 (t80) REVERT: C 734 THR cc_start: 0.8340 (p) cc_final: 0.8086 (m) REVERT: C 740 MET cc_start: 0.7440 (mmm) cc_final: 0.7111 (mmm) REVERT: C 765 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.6945 (ttp-170) REVERT: C 780 GLU cc_start: 0.7270 (pt0) cc_final: 0.6945 (pt0) REVERT: C 790 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7479 (mtmm) REVERT: C 820 ASP cc_start: 0.7445 (t0) cc_final: 0.7221 (t0) REVERT: C 882 ILE cc_start: 0.8570 (pt) cc_final: 0.8126 (mt) REVERT: C 886 TRP cc_start: 0.8742 (p90) cc_final: 0.6715 (p90) REVERT: C 902 MET cc_start: 0.7917 (tpp) cc_final: 0.7696 (tpp) REVERT: C 904 TYR cc_start: 0.7767 (m-10) cc_final: 0.7513 (m-10) REVERT: C 925 ASN cc_start: 0.8327 (m-40) cc_final: 0.8080 (m-40) REVERT: C 973 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7494 (pp) REVERT: C 994 ASP cc_start: 0.7521 (m-30) cc_final: 0.7082 (p0) REVERT: C 998 THR cc_start: 0.8069 (m) cc_final: 0.7750 (p) REVERT: C 1019 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7502 (tpp-160) REVERT: C 1038 LYS cc_start: 0.7527 (mmtp) cc_final: 0.7260 (mmtt) REVERT: C 1077 THR cc_start: 0.8051 (t) cc_final: 0.7840 (t) REVERT: C 1083 HIS cc_start: 0.7394 (t70) cc_final: 0.7177 (t70) REVERT: C 1129 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.8005 (p) REVERT: D 176 VAL cc_start: 0.6025 (OUTLIER) cc_final: 0.5808 (t) REVERT: E 67 LYS cc_start: 0.0669 (OUTLIER) cc_final: 0.0435 (tmmm) REVERT: F 148 CYS cc_start: 0.4983 (OUTLIER) cc_final: 0.4715 (m) REVERT: F 153 PHE cc_start: -0.0979 (OUTLIER) cc_final: -0.2464 (m-80) REVERT: G 158 MET cc_start: 0.4956 (mmm) cc_final: 0.4604 (mmm) REVERT: G 207 MET cc_start: 0.3181 (mpp) cc_final: 0.1256 (ptp) REVERT: H 83 GLU cc_start: 0.2725 (OUTLIER) cc_final: 0.2468 (pp20) REVERT: H 129 GLN cc_start: 0.2757 (OUTLIER) cc_final: 0.2356 (pp30) REVERT: H 160 MET cc_start: 0.2635 (mmt) cc_final: -0.0488 (mtp) REVERT: H 208 MET cc_start: 0.4105 (mmm) cc_final: 0.1967 (tpt) REVERT: I 67 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7129 (tmmm) outliers start: 226 outliers final: 181 residues processed: 760 average time/residue: 0.2060 time to fit residues: 255.9168 Evaluate side-chains 761 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 563 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 329 PHE 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 552 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 221 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 361 optimal weight: 0.3980 chunk 394 optimal weight: 6.9990 chunk 174 optimal weight: 0.0010 chunk 190 optimal weight: 1.9990 chunk 407 optimal weight: 40.0000 chunk 24 optimal weight: 0.0070 chunk 160 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 overall best weight: 0.6806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 895 GLN B1002 GLN B1083 HIS ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.219071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.162593 restraints weight = 62278.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.161453 restraints weight = 41045.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163630 restraints weight = 23011.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.164008 restraints weight = 19384.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.164677 restraints weight = 15779.478| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35770 Z= 0.122 Angle : 0.604 17.375 48736 Z= 0.299 Chirality : 0.044 0.275 5467 Planarity : 0.004 0.054 6292 Dihedral : 7.063 82.439 5440 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 5.51 % Allowed : 18.20 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.12), residues: 4433 helix: 1.00 (0.21), residues: 667 sheet: -1.34 (0.17), residues: 901 loop : -2.67 (0.10), residues: 2865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 328 TYR 0.030 0.001 TYR B 674 PHE 0.041 0.001 PHE B 981 TRP 0.048 0.001 TRP A 64 HIS 0.016 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00274 (35701) covalent geometry : angle 0.59451 (48580) SS BOND : bond 0.00347 ( 51) SS BOND : angle 1.53351 ( 102) hydrogen bonds : bond 0.03265 ( 899) hydrogen bonds : angle 4.66441 ( 2379) link_NAG-ASN : bond 0.00306 ( 18) link_NAG-ASN : angle 2.63443 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 571 time to evaluate : 1.124 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: 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 34 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7447 (mtt90) REVERT: A 64 TRP cc_start: 0.6080 (t60) cc_final: 0.5801 (t60) REVERT: A 91 TYR cc_start: 0.7538 (t80) cc_final: 0.7081 (t80) REVERT: A 117 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6986 (mt) REVERT: A 274 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7493 (p) REVERT: A 537 LYS cc_start: 0.7604 (tmtt) cc_final: 0.6697 (tmtt) REVERT: A 586 ASP cc_start: 0.7422 (t0) cc_final: 0.7164 (t0) REVERT: A 663 ASP cc_start: 0.7377 (t0) cc_final: 0.7148 (m-30) REVERT: A 675 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.6174 (tm-30) REVERT: A 720 ILE cc_start: 0.8917 (mp) cc_final: 0.8693 (mm) REVERT: A 776 LYS cc_start: 0.8285 (tmmt) cc_final: 0.8041 (tttm) REVERT: A 777 ASN cc_start: 0.8252 (m-40) cc_final: 0.7645 (m-40) REVERT: A 803 SER cc_start: 0.7890 (m) cc_final: 0.7627 (p) REVERT: A 825 LYS cc_start: 0.7869 (mmtp) cc_final: 0.7500 (mttm) REVERT: A 868 GLU cc_start: 0.6993 (tp30) cc_final: 0.6489 (tp30) REVERT: A 921 LYS cc_start: 0.7776 (mmmt) cc_final: 0.7275 (mtmm) REVERT: A 922 LEU cc_start: 0.8290 (tp) cc_final: 0.7985 (tt) REVERT: A 925 ASN cc_start: 0.7995 (m-40) cc_final: 0.7608 (m-40) REVERT: A 933 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7733 (mtmm) REVERT: A 936 ASP cc_start: 0.7195 (m-30) cc_final: 0.6885 (m-30) REVERT: A 957 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: A 962 LEU cc_start: 0.8924 (tp) cc_final: 0.8708 (tp) REVERT: A 976 VAL cc_start: 0.8422 (t) cc_final: 0.7987 (p) REVERT: A 1072 GLU cc_start: 0.8036 (pm20) cc_final: 0.7630 (pm20) REVERT: A 1091 ARG cc_start: 0.7597 (ttm170) cc_final: 0.7285 (ttm-80) REVERT: A 1103 PHE cc_start: 0.8174 (m-80) cc_final: 0.7916 (m-10) REVERT: A 1107 ARG cc_start: 0.7493 (mtt90) cc_final: 0.6589 (mtt90) REVERT: B 44 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7726 (mtt-85) REVERT: B 46 SER cc_start: 0.8445 (m) cc_final: 0.8004 (p) REVERT: B 62 VAL cc_start: 0.8064 (m) cc_final: 0.7806 (p) REVERT: B 65 PHE cc_start: 0.7395 (m-80) cc_final: 0.6836 (m-10) REVERT: B 81 ASN cc_start: 0.7113 (p0) cc_final: 0.6863 (p0) REVERT: B 169 GLU cc_start: 0.6246 (pm20) cc_final: 0.5956 (pm20) REVERT: B 170 TYR cc_start: 0.7040 (t80) cc_final: 0.6671 (t80) REVERT: B 200 LYS cc_start: 0.8206 (mttt) cc_final: 0.7619 (mttm) REVERT: B 278 LYS cc_start: 0.8264 (ttmp) cc_final: 0.7996 (tttm) REVERT: B 297 SER cc_start: 0.8261 (m) cc_final: 0.7913 (p) REVERT: B 308 VAL cc_start: 0.8975 (t) cc_final: 0.8598 (m) REVERT: B 319 ARG cc_start: 0.6552 (ttm110) cc_final: 0.6240 (ttp-110) REVERT: B 562 PHE cc_start: 0.8207 (p90) cc_final: 0.7970 (p90) REVERT: B 563 GLN cc_start: 0.7337 (mt0) cc_final: 0.7085 (mt0) REVERT: B 774 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7055 (mm-40) REVERT: B 858 LEU cc_start: 0.7975 (mt) cc_final: 0.7563 (mt) REVERT: B 921 LYS cc_start: 0.7914 (mmmt) cc_final: 0.7465 (mmmm) REVERT: B 933 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7066 (mtpp) REVERT: B 957 GLN cc_start: 0.6501 (tm130) cc_final: 0.6025 (tm130) REVERT: B 964 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7836 (ttmm) REVERT: B 974 SER cc_start: 0.7402 (p) cc_final: 0.7043 (m) REVERT: B 1081 ILE cc_start: 0.8426 (pt) cc_final: 0.8143 (pt) REVERT: B 1084 ASP cc_start: 0.7072 (p0) cc_final: 0.6817 (p0) REVERT: B 1121 PHE cc_start: 0.8069 (p90) cc_final: 0.7831 (p90) REVERT: C 32 PHE cc_start: 0.8276 (m-80) cc_final: 0.8038 (m-80) REVERT: C 106 PHE cc_start: 0.6687 (m-80) cc_final: 0.6469 (m-80) REVERT: C 170 TYR cc_start: 0.6785 (t80) cc_final: 0.6459 (t80) REVERT: C 201 ILE cc_start: 0.8278 (mp) cc_final: 0.7924 (tt) REVERT: C 203 SER cc_start: 0.8339 (t) cc_final: 0.7975 (m) REVERT: C 224 GLU cc_start: 0.7343 (mp0) cc_final: 0.7076 (mp0) REVERT: C 281 GLU cc_start: 0.8507 (pm20) cc_final: 0.7980 (pm20) REVERT: C 321 GLN cc_start: 0.7933 (pm20) cc_final: 0.7708 (pm20) REVERT: C 326 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7600 (tt) REVERT: C 542 ASN cc_start: 0.7637 (t0) cc_final: 0.7379 (t0) REVERT: C 707 TYR cc_start: 0.7927 (t80) cc_final: 0.7610 (t80) REVERT: C 734 THR cc_start: 0.8338 (p) cc_final: 0.8081 (m) REVERT: C 740 MET cc_start: 0.7405 (mmm) cc_final: 0.7057 (mmm) REVERT: C 765 ARG cc_start: 0.7652 (ttp-110) cc_final: 0.6898 (ttp-170) REVERT: C 780 GLU cc_start: 0.7265 (pt0) cc_final: 0.6954 (pt0) REVERT: C 790 LYS cc_start: 0.7795 (mtmm) cc_final: 0.7512 (mtmm) REVERT: C 882 ILE cc_start: 0.8563 (pt) cc_final: 0.8177 (mt) REVERT: C 886 TRP cc_start: 0.8686 (p90) cc_final: 0.6760 (p90) REVERT: C 902 MET cc_start: 0.7879 (tpp) cc_final: 0.7675 (tpp) REVERT: C 904 TYR cc_start: 0.7805 (m-10) cc_final: 0.7479 (m-10) REVERT: C 925 ASN cc_start: 0.8334 (m-40) cc_final: 0.8060 (m-40) REVERT: C 973 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7565 (pp) REVERT: C 994 ASP cc_start: 0.7553 (m-30) cc_final: 0.7082 (p0) REVERT: C 998 THR cc_start: 0.8086 (m) cc_final: 0.7762 (p) REVERT: C 1077 THR cc_start: 0.8048 (t) cc_final: 0.7814 (t) REVERT: C 1083 HIS cc_start: 0.7383 (t70) cc_final: 0.7022 (t-90) REVERT: C 1129 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7976 (p) REVERT: D 176 VAL cc_start: 0.6040 (OUTLIER) cc_final: 0.5817 (t) REVERT: E 67 LYS cc_start: 0.0542 (OUTLIER) cc_final: 0.0325 (tmmm) REVERT: E 158 MET cc_start: 0.5971 (tpt) cc_final: 0.5555 (tpp) REVERT: F 111 LEU cc_start: 0.3196 (OUTLIER) cc_final: 0.2651 (tm) REVERT: F 148 CYS cc_start: 0.4966 (OUTLIER) cc_final: 0.4687 (m) REVERT: F 153 PHE cc_start: -0.0897 (OUTLIER) cc_final: -0.2493 (m-80) REVERT: G 158 MET cc_start: 0.4965 (mmm) cc_final: 0.4588 (mmm) REVERT: G 207 MET cc_start: 0.3053 (mpp) cc_final: 0.1188 (ptp) REVERT: H 49 MET cc_start: 0.5807 (mmm) cc_final: 0.5438 (mmm) REVERT: H 83 GLU cc_start: 0.2808 (OUTLIER) cc_final: 0.2543 (pp20) REVERT: H 129 GLN cc_start: 0.2730 (OUTLIER) cc_final: 0.2421 (pm20) REVERT: H 160 MET cc_start: 0.2769 (mmt) cc_final: -0.0349 (mtp) REVERT: H 234 MET cc_start: 0.3927 (tmm) cc_final: 0.3550 (tmm) REVERT: I 67 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7117 (tmmm) outliers start: 210 outliers final: 180 residues processed: 728 average time/residue: 0.2054 time to fit residues: 244.6457 Evaluate side-chains 754 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 558 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 329 PHE 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 533 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1048 HIS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 221 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 216 optimal weight: 0.9980 chunk 400 optimal weight: 0.8980 chunk 174 optimal weight: 0.0470 chunk 188 optimal weight: 4.9990 chunk 207 optimal weight: 0.0980 chunk 126 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 438 optimal weight: 20.0000 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1101 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.219299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162399 restraints weight = 61859.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.161699 restraints weight = 38047.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.162906 restraints weight = 22256.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.163767 restraints weight = 18845.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.164272 restraints weight = 16159.989| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35770 Z= 0.112 Angle : 0.599 15.802 48736 Z= 0.296 Chirality : 0.044 0.279 5467 Planarity : 0.004 0.054 6292 Dihedral : 6.960 82.486 5440 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 5.43 % Allowed : 18.36 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.12), residues: 4433 helix: 1.19 (0.21), residues: 658 sheet: -1.20 (0.17), residues: 897 loop : -2.61 (0.11), residues: 2878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C1019 TYR 0.026 0.001 TYR B 674 PHE 0.040 0.001 PHE B 981 TRP 0.041 0.001 TRP A 64 HIS 0.016 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00254 (35701) covalent geometry : angle 0.59062 (48580) SS BOND : bond 0.00324 ( 51) SS BOND : angle 1.39195 ( 102) hydrogen bonds : bond 0.03117 ( 899) hydrogen bonds : angle 4.60736 ( 2379) link_NAG-ASN : bond 0.00306 ( 18) link_NAG-ASN : angle 2.45222 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 567 time to evaluate : 1.258 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: 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 34 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7494 (mmt90) REVERT: A 64 TRP cc_start: 0.6113 (t60) cc_final: 0.5778 (t60) REVERT: A 91 TYR cc_start: 0.7569 (t80) cc_final: 0.7087 (t80) REVERT: A 117 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6931 (mt) REVERT: A 177 MET cc_start: 0.6843 (tmm) cc_final: 0.6370 (tmm) REVERT: A 274 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7467 (p) REVERT: A 537 LYS cc_start: 0.7551 (tmtt) cc_final: 0.6642 (tmtt) REVERT: A 586 ASP cc_start: 0.7415 (t0) cc_final: 0.7141 (t0) REVERT: A 663 ASP cc_start: 0.7384 (t0) cc_final: 0.7179 (m-30) REVERT: A 675 GLN cc_start: 0.6552 (OUTLIER) cc_final: 0.6186 (tm-30) REVERT: A 776 LYS cc_start: 0.8295 (tmmt) cc_final: 0.8056 (tttm) REVERT: A 777 ASN cc_start: 0.8192 (m-40) cc_final: 0.7599 (m-40) REVERT: A 811 LYS cc_start: 0.8663 (tmmt) cc_final: 0.8181 (tmmt) REVERT: A 868 GLU cc_start: 0.6945 (tp30) cc_final: 0.6436 (tp30) REVERT: A 921 LYS cc_start: 0.7778 (mmmt) cc_final: 0.7272 (mtmm) REVERT: A 922 LEU cc_start: 0.8272 (tp) cc_final: 0.7963 (tt) REVERT: A 925 ASN cc_start: 0.7993 (m-40) cc_final: 0.7618 (m-40) REVERT: A 933 LYS cc_start: 0.8043 (mtmm) cc_final: 0.7741 (mtmm) REVERT: A 936 ASP cc_start: 0.7225 (m-30) cc_final: 0.6999 (m-30) REVERT: A 957 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.7123 (tt0) REVERT: A 962 LEU cc_start: 0.8938 (tp) cc_final: 0.8635 (tp) REVERT: A 976 VAL cc_start: 0.8384 (t) cc_final: 0.7932 (p) REVERT: A 1072 GLU cc_start: 0.8050 (pm20) cc_final: 0.7657 (pm20) REVERT: A 1091 ARG cc_start: 0.7558 (ttm170) cc_final: 0.7245 (ttm-80) REVERT: A 1103 PHE cc_start: 0.8164 (m-80) cc_final: 0.7894 (m-10) REVERT: A 1107 ARG cc_start: 0.7520 (mtt90) cc_final: 0.6628 (mtt90) REVERT: B 46 SER cc_start: 0.8391 (m) cc_final: 0.7937 (p) REVERT: B 62 VAL cc_start: 0.8028 (m) cc_final: 0.7755 (p) REVERT: B 65 PHE cc_start: 0.7410 (m-80) cc_final: 0.6872 (m-10) REVERT: B 81 ASN cc_start: 0.7122 (p0) cc_final: 0.6895 (p0) REVERT: B 169 GLU cc_start: 0.6245 (pm20) cc_final: 0.5942 (pm20) REVERT: B 170 TYR cc_start: 0.7020 (t80) cc_final: 0.6630 (t80) REVERT: B 200 LYS cc_start: 0.8210 (mttt) cc_final: 0.7609 (mttm) REVERT: B 278 LYS cc_start: 0.8283 (ttmp) cc_final: 0.8027 (tttm) REVERT: B 297 SER cc_start: 0.8254 (m) cc_final: 0.7912 (p) REVERT: B 308 VAL cc_start: 0.8931 (t) cc_final: 0.8565 (m) REVERT: B 319 ARG cc_start: 0.6573 (ttm110) cc_final: 0.6232 (ttp-110) REVERT: B 335 LEU cc_start: 0.4496 (OUTLIER) cc_final: 0.4214 (mm) REVERT: B 562 PHE cc_start: 0.8224 (p90) cc_final: 0.7916 (p90) REVERT: B 563 GLN cc_start: 0.7391 (mt0) cc_final: 0.6829 (mt0) REVERT: B 725 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7286 (tp30) REVERT: B 737 ASP cc_start: 0.6739 (t0) cc_final: 0.6431 (t0) REVERT: B 774 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7002 (mm-40) REVERT: B 819 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6980 (mt-10) REVERT: B 858 LEU cc_start: 0.8093 (mt) cc_final: 0.7675 (mt) REVERT: B 921 LYS cc_start: 0.7896 (mmmt) cc_final: 0.7426 (mmmm) REVERT: B 957 GLN cc_start: 0.6609 (tm130) cc_final: 0.6115 (tm130) REVERT: B 964 LYS cc_start: 0.8196 (ttpp) cc_final: 0.7855 (ttmm) REVERT: B 974 SER cc_start: 0.7326 (p) cc_final: 0.7008 (m) REVERT: B 990 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: B 1081 ILE cc_start: 0.8331 (pt) cc_final: 0.8047 (pt) REVERT: B 1121 PHE cc_start: 0.8096 (p90) cc_final: 0.7841 (p90) REVERT: C 106 PHE cc_start: 0.6770 (m-80) cc_final: 0.6504 (m-80) REVERT: C 129 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7867 (ttmt) REVERT: C 168 PHE cc_start: 0.5114 (t80) cc_final: 0.4545 (t80) REVERT: C 201 ILE cc_start: 0.8255 (mp) cc_final: 0.7950 (tt) REVERT: C 203 SER cc_start: 0.8216 (t) cc_final: 0.7891 (m) REVERT: C 224 GLU cc_start: 0.7310 (mp0) cc_final: 0.7101 (mp0) REVERT: C 321 GLN cc_start: 0.7963 (pm20) cc_final: 0.7741 (pm20) REVERT: C 326 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7592 (tt) REVERT: C 542 ASN cc_start: 0.7698 (t0) cc_final: 0.7430 (t0) REVERT: C 563 GLN cc_start: 0.8375 (mt0) cc_final: 0.7986 (mt0) REVERT: C 707 TYR cc_start: 0.7932 (t80) cc_final: 0.7596 (t80) REVERT: C 720 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8546 (pt) REVERT: C 734 THR cc_start: 0.8245 (p) cc_final: 0.8043 (m) REVERT: C 762 GLN cc_start: 0.7333 (tm-30) cc_final: 0.6832 (tp40) REVERT: C 765 ARG cc_start: 0.7638 (ttp-110) cc_final: 0.6987 (ttp-170) REVERT: C 790 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7540 (mtmm) REVERT: C 882 ILE cc_start: 0.8574 (pt) cc_final: 0.8155 (mt) REVERT: C 886 TRP cc_start: 0.8652 (p90) cc_final: 0.6728 (p90) REVERT: C 904 TYR cc_start: 0.7777 (m-10) cc_final: 0.7486 (m-10) REVERT: C 925 ASN cc_start: 0.8288 (m-40) cc_final: 0.8043 (m-40) REVERT: C 973 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7569 (pp) REVERT: C 994 ASP cc_start: 0.7605 (m-30) cc_final: 0.7126 (p0) REVERT: C 998 THR cc_start: 0.8014 (m) cc_final: 0.7706 (p) REVERT: C 1019 ARG cc_start: 0.7928 (tpp-160) cc_final: 0.7709 (tpp-160) REVERT: C 1038 LYS cc_start: 0.7521 (mmtp) cc_final: 0.7275 (mmtt) REVERT: C 1077 THR cc_start: 0.8068 (t) cc_final: 0.7843 (t) REVERT: C 1083 HIS cc_start: 0.7345 (t70) cc_final: 0.7002 (t-90) REVERT: C 1129 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7947 (p) REVERT: D 176 VAL cc_start: 0.6030 (OUTLIER) cc_final: 0.5801 (t) REVERT: E 158 MET cc_start: 0.6000 (tpt) cc_final: 0.5585 (tpp) REVERT: F 111 LEU cc_start: 0.3228 (OUTLIER) cc_final: 0.2678 (tm) REVERT: F 148 CYS cc_start: 0.4929 (OUTLIER) cc_final: 0.4662 (m) REVERT: F 153 PHE cc_start: -0.0881 (OUTLIER) cc_final: -0.2445 (m-80) REVERT: G 158 MET cc_start: 0.4918 (mmm) cc_final: 0.4547 (mmm) REVERT: G 207 MET cc_start: 0.2993 (mpp) cc_final: 0.1132 (ptp) REVERT: G 234 TYR cc_start: 0.6025 (t80) cc_final: 0.5681 (t80) REVERT: H 49 MET cc_start: 0.5909 (mmm) cc_final: 0.5533 (mmm) REVERT: H 83 GLU cc_start: 0.2790 (OUTLIER) cc_final: 0.2388 (pp20) REVERT: H 129 GLN cc_start: 0.2661 (OUTLIER) cc_final: 0.2274 (pp30) REVERT: H 160 MET cc_start: 0.2828 (mmt) cc_final: -0.0295 (mtp) REVERT: H 208 MET cc_start: 0.3799 (mmm) cc_final: 0.1481 (tpp) REVERT: H 234 MET cc_start: 0.3882 (tmm) cc_final: 0.3464 (tmm) REVERT: I 67 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7107 (tmmm) outliers start: 207 outliers final: 168 residues processed: 723 average time/residue: 0.2086 time to fit residues: 246.3720 Evaluate side-chains 747 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 560 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 329 PHE 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 558 LYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 221 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 411 optimal weight: 0.6980 chunk 138 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 442 optimal weight: 9.9990 chunk 310 optimal weight: 0.7980 chunk 78 optimal weight: 0.0770 chunk 222 optimal weight: 0.4980 chunk 439 optimal weight: 40.0000 chunk 385 optimal weight: 10.0000 chunk 320 optimal weight: 5.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 919 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.217065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.160212 restraints weight = 61924.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.159628 restraints weight = 39278.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.161510 restraints weight = 22494.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.162102 restraints weight = 19546.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.162631 restraints weight = 15449.684| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35770 Z= 0.133 Angle : 0.618 15.664 48736 Z= 0.307 Chirality : 0.045 0.283 5467 Planarity : 0.004 0.053 6292 Dihedral : 6.851 82.131 5432 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 5.17 % Allowed : 18.86 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.12), residues: 4433 helix: 1.05 (0.21), residues: 664 sheet: -1.19 (0.17), residues: 920 loop : -2.58 (0.11), residues: 2849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 328 TYR 0.025 0.001 TYR B 674 PHE 0.045 0.001 PHE B 981 TRP 0.040 0.002 TRP A 64 HIS 0.021 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00301 (35701) covalent geometry : angle 0.61061 (48580) SS BOND : bond 0.00317 ( 51) SS BOND : angle 1.42426 ( 102) hydrogen bonds : bond 0.03301 ( 899) hydrogen bonds : angle 4.66020 ( 2379) link_NAG-ASN : bond 0.00304 ( 18) link_NAG-ASN : angle 2.39202 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 567 time to evaluate : 1.231 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: 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 34 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7342 (mmt90) REVERT: A 64 TRP cc_start: 0.6112 (t60) cc_final: 0.5793 (t60) REVERT: A 91 TYR cc_start: 0.7556 (t80) cc_final: 0.7064 (t80) REVERT: A 117 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7015 (mt) REVERT: A 177 MET cc_start: 0.6903 (tmm) cc_final: 0.6375 (tmm) REVERT: A 274 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7354 (p) REVERT: A 537 LYS cc_start: 0.7572 (tmtt) cc_final: 0.6637 (tmtt) REVERT: A 586 ASP cc_start: 0.7492 (t0) cc_final: 0.7235 (t0) REVERT: A 675 GLN cc_start: 0.6556 (OUTLIER) cc_final: 0.6187 (tm-30) REVERT: A 776 LYS cc_start: 0.8305 (tmmt) cc_final: 0.8044 (tttm) REVERT: A 777 ASN cc_start: 0.8243 (m-40) cc_final: 0.7621 (m-40) REVERT: A 803 SER cc_start: 0.7891 (m) cc_final: 0.7625 (p) REVERT: A 811 LYS cc_start: 0.8675 (tmmt) cc_final: 0.8248 (tmmt) REVERT: A 868 GLU cc_start: 0.6943 (tp30) cc_final: 0.6472 (tp30) REVERT: A 921 LYS cc_start: 0.7791 (mmmt) cc_final: 0.7270 (mtmm) REVERT: A 922 LEU cc_start: 0.8268 (tp) cc_final: 0.7957 (tt) REVERT: A 925 ASN cc_start: 0.8020 (m-40) cc_final: 0.7651 (m-40) REVERT: A 933 LYS cc_start: 0.8068 (mtmm) cc_final: 0.7795 (mtmm) REVERT: A 936 ASP cc_start: 0.7211 (m-30) cc_final: 0.6942 (m-30) REVERT: A 947 LYS cc_start: 0.8429 (mttp) cc_final: 0.8174 (mttp) REVERT: A 957 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.7120 (tt0) REVERT: A 962 LEU cc_start: 0.8933 (tp) cc_final: 0.8636 (tp) REVERT: A 976 VAL cc_start: 0.8382 (t) cc_final: 0.7969 (p) REVERT: A 1072 GLU cc_start: 0.8043 (pm20) cc_final: 0.7653 (pm20) REVERT: A 1091 ARG cc_start: 0.7568 (ttm170) cc_final: 0.7279 (ttm-80) REVERT: B 46 SER cc_start: 0.8401 (m) cc_final: 0.7928 (p) REVERT: B 62 VAL cc_start: 0.8015 (m) cc_final: 0.7758 (p) REVERT: B 65 PHE cc_start: 0.7458 (m-80) cc_final: 0.6910 (m-10) REVERT: B 169 GLU cc_start: 0.6281 (pm20) cc_final: 0.6016 (pm20) REVERT: B 170 TYR cc_start: 0.7033 (t80) cc_final: 0.6635 (t80) REVERT: B 200 LYS cc_start: 0.8206 (mttt) cc_final: 0.7610 (mttm) REVERT: B 218 GLN cc_start: 0.7699 (mm110) cc_final: 0.7468 (mm110) REVERT: B 278 LYS cc_start: 0.8318 (ttmp) cc_final: 0.8009 (tttm) REVERT: B 297 SER cc_start: 0.8104 (m) cc_final: 0.7785 (p) REVERT: B 298 GLU cc_start: 0.7265 (tt0) cc_final: 0.7043 (tm-30) REVERT: B 308 VAL cc_start: 0.8977 (t) cc_final: 0.8615 (m) REVERT: B 319 ARG cc_start: 0.6597 (ttm110) cc_final: 0.6250 (ttp-110) REVERT: B 562 PHE cc_start: 0.8224 (p90) cc_final: 0.7960 (p90) REVERT: B 563 GLN cc_start: 0.7338 (mt0) cc_final: 0.7122 (mt0) REVERT: B 569 ILE cc_start: 0.7953 (pt) cc_final: 0.7722 (mp) REVERT: B 725 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: B 774 GLN cc_start: 0.7562 (mm-40) cc_final: 0.6933 (mm-40) REVERT: B 819 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6971 (mt-10) REVERT: B 858 LEU cc_start: 0.8156 (mt) cc_final: 0.7746 (mt) REVERT: B 921 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7402 (mmmm) REVERT: B 964 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7821 (ttmm) REVERT: B 974 SER cc_start: 0.7345 (p) cc_final: 0.7047 (m) REVERT: B 990 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: B 1081 ILE cc_start: 0.8335 (pt) cc_final: 0.8040 (pt) REVERT: B 1121 PHE cc_start: 0.8091 (p90) cc_final: 0.7833 (p90) REVERT: C 129 LYS cc_start: 0.8249 (ttmt) cc_final: 0.7677 (tptt) REVERT: C 189 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7221 (mt-10) REVERT: C 190 PHE cc_start: 0.6801 (m-80) cc_final: 0.6543 (m-80) REVERT: C 203 SER cc_start: 0.8399 (t) cc_final: 0.7992 (m) REVERT: C 321 GLN cc_start: 0.8022 (pm20) cc_final: 0.7748 (pm20) REVERT: C 326 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7635 (tt) REVERT: C 537 LYS cc_start: 0.8494 (tttt) cc_final: 0.7820 (tttt) REVERT: C 542 ASN cc_start: 0.7748 (t0) cc_final: 0.7458 (t0) REVERT: C 557 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8114 (mtpp) REVERT: C 707 TYR cc_start: 0.7953 (t80) cc_final: 0.7617 (t80) REVERT: C 762 GLN cc_start: 0.7447 (tm-30) cc_final: 0.6944 (tp40) REVERT: C 765 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.6792 (ttp-170) REVERT: C 790 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7553 (mtmm) REVERT: C 882 ILE cc_start: 0.8554 (pt) cc_final: 0.8161 (mt) REVERT: C 886 TRP cc_start: 0.8666 (p90) cc_final: 0.6741 (p90) REVERT: C 925 ASN cc_start: 0.8296 (m-40) cc_final: 0.8065 (m-40) REVERT: C 973 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7703 (pp) REVERT: C 994 ASP cc_start: 0.7599 (m-30) cc_final: 0.7112 (p0) REVERT: C 998 THR cc_start: 0.8055 (m) cc_final: 0.7740 (p) REVERT: C 1019 ARG cc_start: 0.7959 (tpp-160) cc_final: 0.7009 (tpt170) REVERT: C 1072 GLU cc_start: 0.7745 (pm20) cc_final: 0.7245 (pm20) REVERT: C 1077 THR cc_start: 0.8064 (t) cc_final: 0.7848 (t) REVERT: C 1083 HIS cc_start: 0.7366 (t70) cc_final: 0.7021 (t-90) REVERT: C 1129 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7965 (p) REVERT: D 176 VAL cc_start: 0.6092 (OUTLIER) cc_final: 0.5856 (t) REVERT: E 158 MET cc_start: 0.5688 (tpt) cc_final: 0.5280 (tpp) REVERT: F 111 LEU cc_start: 0.3134 (OUTLIER) cc_final: 0.2586 (tm) REVERT: F 148 CYS cc_start: 0.5126 (OUTLIER) cc_final: 0.4889 (m) REVERT: F 153 PHE cc_start: -0.0813 (OUTLIER) cc_final: -0.2372 (m-80) REVERT: G 158 MET cc_start: 0.4848 (mmm) cc_final: 0.4498 (mmm) REVERT: G 207 MET cc_start: 0.3025 (mpp) cc_final: 0.1118 (ptp) REVERT: G 234 TYR cc_start: 0.5983 (t80) cc_final: 0.5656 (t80) REVERT: H 49 MET cc_start: 0.5986 (mmm) cc_final: 0.5581 (mmm) REVERT: H 83 GLU cc_start: 0.2695 (OUTLIER) cc_final: 0.2294 (pp20) REVERT: H 129 GLN cc_start: 0.2683 (OUTLIER) cc_final: 0.2260 (pp30) REVERT: H 160 MET cc_start: 0.2883 (mmt) cc_final: -0.0297 (mtp) REVERT: H 208 MET cc_start: 0.3817 (mmm) cc_final: 0.1698 (tpt) REVERT: I 67 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7106 (tmmm) outliers start: 197 outliers final: 169 residues processed: 713 average time/residue: 0.2101 time to fit residues: 244.6566 Evaluate side-chains 744 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 558 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 362 VAL 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 533 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 221 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 317 optimal weight: 50.0000 chunk 284 optimal weight: 1.9990 chunk 331 optimal weight: 40.0000 chunk 138 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 409 optimal weight: 4.9990 chunk 283 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 641 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 GLN H 209 ASN I 35 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.213402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.162738 restraints weight = 61738.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.158015 restraints weight = 41220.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.159591 restraints weight = 35458.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160391 restraints weight = 24197.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160534 restraints weight = 22009.941| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 35770 Z= 0.275 Angle : 0.720 15.171 48736 Z= 0.366 Chirality : 0.049 0.308 5467 Planarity : 0.005 0.066 6292 Dihedral : 7.264 82.047 5432 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 5.22 % Allowed : 18.86 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.12), residues: 4433 helix: 0.50 (0.20), residues: 683 sheet: -1.13 (0.17), residues: 949 loop : -2.69 (0.11), residues: 2801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 273 TYR 0.034 0.002 TYR A 655 PHE 0.050 0.002 PHE B 981 TRP 0.052 0.002 TRP C 104 HIS 0.013 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00600 (35701) covalent geometry : angle 0.70992 (48580) SS BOND : bond 0.00395 ( 51) SS BOND : angle 1.91017 ( 102) hydrogen bonds : bond 0.04427 ( 899) hydrogen bonds : angle 5.06946 ( 2379) link_NAG-ASN : bond 0.00504 ( 18) link_NAG-ASN : angle 2.83590 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6769.17 seconds wall clock time: 117 minutes 18.90 seconds (7038.90 seconds total)