Starting phenix.real_space_refine on Fri Mar 6 07:15:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whk_32503/03_2026/7whk_32503.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whk_32503/03_2026/7whk_32503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7whk_32503/03_2026/7whk_32503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whk_32503/03_2026/7whk_32503.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7whk_32503/03_2026/7whk_32503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whk_32503/03_2026/7whk_32503.map" } resolution = 3.01 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= 0.001 sd= 0.022 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 142 5.16 5 C 18606 2.51 5 N 4806 2.21 5 O 5596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s 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: 29150 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8101 Classifications: {'peptide': 1040} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 981} 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: 7999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 7999 Classifications: {'peptide': 1027} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 970} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 8129 Classifications: {'peptide': 1043} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 984} 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: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 899 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 893 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "G" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 893 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.51, per 1000 atoms: 0.22 Number of scatterers: 29150 At special positions: 0 Unit cell: (147.896, 171.304, 198.968, 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 142 16.00 O 5596 8.00 N 4806 7.00 C 18606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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 15 " - pdb=" SG CYS C 136 " 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=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A 122 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C 709 " Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.4 seconds 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6900 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 64 sheets defined 19.7% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.639A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 746 through 753 removed outlier: 3.642A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 756 No H-bonds generated for 'chain 'A' and resid 754 through 756' Processing helix chain 'A' and resid 758 through 780 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 853 through 857 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.847A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.634A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.074A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.573A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.723A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.154A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.516A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.564A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.526A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.551A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 751 Processing helix chain 'B' and resid 752 through 757 removed outlier: 3.676A pdb=" N GLN B 755 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 756 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 752 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.786A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 848 through 853 removed outlier: 3.625A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 857 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.908A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.184A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.527A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.944A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.588A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.085A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.855A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.859A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.860A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.613A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.677A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 854 Processing helix chain 'C' and resid 855 through 857 No H-bonds generated for 'chain 'C' and resid 855 through 857' Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.216A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.682A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.667A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.460A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.525A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 86 through 90' Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.692A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 removed outlier: 3.943A pdb=" N THR G 90 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.045A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG A 188 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N SER A 203 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.575A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 128 removed outlier: 3.844A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.943A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 326 removed outlier: 7.598A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 7.779A pdb=" N VAL A 433 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N PHE A 377 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA8, first strand: chain 'A' and resid 575 through 576 removed outlier: 3.643A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.905A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.211A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.777A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.703A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AB8, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.281A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ALA B 222 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N HIS B 205 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP B 228 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE B 199 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 186 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.281A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ALA B 222 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N HIS B 205 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP B 228 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE B 199 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.578A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.638A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.995A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.854A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.691A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.699A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 538 through 542 Processing sheet with id=AD2, first strand: chain 'B' and resid 565 through 566 removed outlier: 3.648A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.945A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.814A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.322A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.954A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.465A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.628A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.760A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 186 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.760A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 186 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.744A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.898A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AF2, first strand: chain 'C' and resid 539 through 542 removed outlier: 3.609A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.004A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.109A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.567A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.830A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF8, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.912A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET D 83 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 20 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.922A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 51 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TRP D 36 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.573A pdb=" N SER D 35 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AG3, first strand: chain 'E' and resid 46 through 50 removed outlier: 6.476A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AG5, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.663A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AG7, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.953A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 18 through 23 removed outlier: 3.817A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET H 83 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 45 through 47 Processing sheet with id=AH1, first strand: chain 'H' and resid 49 through 51 925 hydrogen bonds defined for protein. 2478 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: 6.74 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6270 1.33 - 1.45: 7201 1.45 - 1.57: 16174 1.57 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 29833 Sorted by residual: bond pdb=" CA LYS A 300 " pdb=" C LYS A 300 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.29e-02 6.01e+03 2.36e+01 bond pdb=" CA ASN C 331 " pdb=" C ASN C 331 " ideal model delta sigma weight residual 1.524 1.467 0.056 1.31e-02 5.83e+03 1.83e+01 bond pdb=" CA SER A 297 " pdb=" C SER A 297 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.39e-02 5.18e+03 1.69e+01 bond pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.33e-02 5.65e+03 1.68e+01 bond pdb=" CA CYS A 301 " pdb=" C CYS A 301 " ideal model delta sigma weight residual 1.522 1.464 0.057 1.40e-02 5.10e+03 1.66e+01 ... (remaining 29828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 39679 2.16 - 4.32: 828 4.32 - 6.47: 85 6.47 - 8.63: 16 8.63 - 10.79: 3 Bond angle restraints: 40611 Sorted by residual: angle pdb=" N ALA A 123 " pdb=" CA ALA A 123 " pdb=" C ALA A 123 " ideal model delta sigma weight residual 114.56 106.27 8.29 1.27e+00 6.20e-01 4.27e+01 angle pdb=" N ASP B 290 " pdb=" CA ASP B 290 " pdb=" C ASP B 290 " ideal model delta sigma weight residual 113.18 120.76 -7.58 1.21e+00 6.83e-01 3.92e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.31 114.80 5.51 9.80e-01 1.04e+00 3.16e+01 angle pdb=" N GLU A 298 " pdb=" CA GLU A 298 " pdb=" C GLU A 298 " ideal model delta sigma weight residual 111.36 105.75 5.61 1.09e+00 8.42e-01 2.65e+01 angle pdb=" C PRO A 330 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 120.87 128.05 -7.18 1.42e+00 4.96e-01 2.56e+01 ... (remaining 40606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 17066 17.89 - 35.78: 740 35.78 - 53.67: 219 53.67 - 71.56: 60 71.56 - 89.44: 17 Dihedral angle restraints: 18102 sinusoidal: 7352 harmonic: 10750 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 173.19 -80.19 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" C ASN A 343 " pdb=" N ASN A 343 " pdb=" CA ASN A 343 " pdb=" CB ASN A 343 " ideal model delta harmonic sigma weight residual -122.60 -110.16 -12.44 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -121.01 35.01 1 1.00e+01 1.00e-02 1.74e+01 ... (remaining 18099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.241: 4641 0.241 - 0.482: 12 0.482 - 0.722: 2 0.722 - 0.963: 0 0.963 - 1.204: 1 Chirality restraints: 4656 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.20 -1.20 2.00e-01 2.50e+01 3.62e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.90e+00 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.90e+00 ... (remaining 4653 not shown) Planarity restraints: 5241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " -0.340 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG A1306 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1310 " 0.320 2.00e-02 2.50e+03 2.69e-01 9.03e+02 pdb=" C7 NAG C1310 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C1310 " 0.194 2.00e-02 2.50e+03 pdb=" N2 NAG C1310 " -0.461 2.00e-02 2.50e+03 pdb=" O7 NAG C1310 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " -0.303 2.00e-02 2.50e+03 2.56e-01 8.16e+02 pdb=" C7 NAG C1304 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " 0.441 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " -0.032 2.00e-02 2.50e+03 ... (remaining 5238 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2786 2.75 - 3.28: 28075 3.28 - 3.82: 47948 3.82 - 4.36: 56113 4.36 - 4.90: 96411 Nonbonded interactions: 231333 Sorted by model distance: nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.208 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.231 3.040 nonbonded pdb=" OG SER C 735 " pdb=" OG1 THR C 859 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.235 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.266 3.040 ... (remaining 231328 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 177 or resid 182 through 244 or resid 262 throu \ gh 1308)) selection = (chain 'B' and (resid 26 through 827 or resid 848 through 1308)) selection = (chain 'C' and (resid 26 through 177 or resid 182 through 244 or resid 262 throu \ gh 827 or resid 848 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'E' and resid 1 through 116) selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.110 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 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 : 0.004 0.063 29907 Z= 0.265 Angle : 0.723 13.497 40787 Z= 0.429 Chirality : 0.054 1.204 4656 Planarity : 0.013 0.290 5213 Dihedral : 11.434 89.444 11064 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.58 % Favored : 94.15 % Rotamer: Outliers : 6.30 % Allowed : 6.42 % Favored : 87.28 % Cbeta Deviations : 0.03 % 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: -3.45 (0.12), residues: 3639 helix: -0.18 (0.20), residues: 609 sheet: -2.12 (0.16), residues: 883 loop : -3.16 (0.11), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 498 TYR 0.022 0.001 TYR A 265 PHE 0.018 0.001 PHE A 238 TRP 0.007 0.001 TRP A 886 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00397 (29833) covalent geometry : angle 0.69758 (40611) SS BOND : bond 0.00316 ( 46) SS BOND : angle 0.72077 ( 92) hydrogen bonds : bond 0.17121 ( 910) hydrogen bonds : angle 7.30805 ( 2478) link_NAG-ASN : bond 0.00846 ( 28) link_NAG-ASN : angle 4.21869 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 685 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7916 (mtt180) REVERT: A 83 VAL cc_start: 0.7382 (OUTLIER) cc_final: 0.6986 (t) REVERT: A 98 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.8065 (p) REVERT: A 99 ASN cc_start: 0.8104 (m-40) cc_final: 0.7196 (t0) REVERT: A 115 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6175 (tp40) REVERT: A 116 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7207 (p) REVERT: A 126 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7386 (m) REVERT: A 127 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.7942 (t) REVERT: A 129 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7016 (mtmm) REVERT: A 132 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6162 (mp0) REVERT: A 135 PHE cc_start: 0.5872 (OUTLIER) cc_final: 0.5380 (m-10) REVERT: A 138 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7301 (t0) REVERT: A 157 PHE cc_start: 0.5886 (OUTLIER) cc_final: 0.5491 (p90) REVERT: A 164 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7203 (m110) REVERT: A 171 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8500 (t) REVERT: A 175 PHE cc_start: 0.6022 (OUTLIER) cc_final: 0.5785 (p90) REVERT: A 186 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7237 (p0) REVERT: A 189 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7059 (mt-10) REVERT: A 193 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7802 (mtpt) REVERT: A 206 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8199 (p) REVERT: A 238 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7578 (p90) REVERT: A 287 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6990 (p0) REVERT: A 293 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6965 (tp) REVERT: A 362 VAL cc_start: 0.8765 (t) cc_final: 0.8279 (p) REVERT: A 364 ASP cc_start: 0.7232 (t0) cc_final: 0.6943 (t0) REVERT: A 386 LYS cc_start: 0.8078 (mtmm) cc_final: 0.7657 (ttmm) REVERT: A 513 LEU cc_start: 0.7557 (mp) cc_final: 0.7202 (mp) REVERT: A 643 PHE cc_start: 0.7760 (t80) cc_final: 0.7539 (t80) REVERT: A 756 TYR cc_start: 0.6960 (m-80) cc_final: 0.6586 (m-80) REVERT: A 790 LYS cc_start: 0.8309 (mmmm) cc_final: 0.8036 (mmmm) REVERT: A 796 TYR cc_start: 0.8055 (t80) cc_final: 0.7824 (t80) REVERT: A 933 LYS cc_start: 0.8509 (mtmm) cc_final: 0.8115 (mtmm) REVERT: A 976 VAL cc_start: 0.8709 (t) cc_final: 0.8499 (m) REVERT: A 994 ASP cc_start: 0.7045 (m-30) cc_final: 0.6538 (m-30) REVERT: A 1019 ARG cc_start: 0.7384 (ttm110) cc_final: 0.6531 (ttm110) REVERT: B 52 GLN cc_start: 0.7444 (tm-30) cc_final: 0.6935 (tm-30) REVERT: B 97 LYS cc_start: 0.7804 (tppt) cc_final: 0.7508 (tppt) REVERT: B 168 PHE cc_start: 0.7809 (t80) cc_final: 0.6224 (t80) REVERT: B 172 SER cc_start: 0.7067 (OUTLIER) cc_final: 0.6594 (m) REVERT: B 208 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8261 (pt) REVERT: B 378 LYS cc_start: 0.6602 (OUTLIER) cc_final: 0.6236 (ttpp) REVERT: B 461 LEU cc_start: 0.8686 (tp) cc_final: 0.8202 (tp) REVERT: B 581 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7787 (p) REVERT: B 658 ASN cc_start: 0.8306 (p0) cc_final: 0.7625 (p0) REVERT: B 675 GLN cc_start: 0.7359 (mm-40) cc_final: 0.7158 (mm110) REVERT: B 773 GLU cc_start: 0.6840 (tt0) cc_final: 0.6395 (tt0) REVERT: B 776 LYS cc_start: 0.8360 (ttpt) cc_final: 0.7985 (ttmm) REVERT: B 816 SER cc_start: 0.8349 (p) cc_final: 0.8129 (t) REVERT: B 935 GLN cc_start: 0.8308 (tt0) cc_final: 0.7831 (tt0) REVERT: B 949 GLN cc_start: 0.7794 (tp40) cc_final: 0.7465 (mm-40) REVERT: B 950 ASP cc_start: 0.6677 (t0) cc_final: 0.4707 (t0) REVERT: B 954 HIS cc_start: 0.6613 (m170) cc_final: 0.6287 (m170) REVERT: B 981 PHE cc_start: 0.7741 (m-80) cc_final: 0.7522 (m-80) REVERT: C 32 PHE cc_start: 0.7051 (m-80) cc_final: 0.6668 (m-80) REVERT: C 52 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7298 (tm-30) REVERT: C 96 GLU cc_start: 0.6118 (pp20) cc_final: 0.5838 (pp20) REVERT: C 239 GLN cc_start: 0.7184 (tt0) cc_final: 0.6828 (tp40) REVERT: C 323 THR cc_start: 0.8564 (m) cc_final: 0.8115 (m) REVERT: C 406 GLU cc_start: -0.1067 (OUTLIER) cc_final: -0.1464 (tp30) REVERT: C 518 LEU cc_start: 0.7795 (mp) cc_final: 0.7454 (mp) REVERT: C 541 PHE cc_start: 0.7788 (p90) cc_final: 0.7583 (p90) REVERT: C 587 ILE cc_start: 0.8615 (mt) cc_final: 0.8263 (mm) REVERT: C 619 GLU cc_start: 0.5128 (OUTLIER) cc_final: 0.4439 (pm20) REVERT: C 732 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8566 (p) REVERT: C 773 GLU cc_start: 0.7238 (tt0) cc_final: 0.6939 (tt0) REVERT: C 776 LYS cc_start: 0.8340 (ttpt) cc_final: 0.8111 (ttpp) REVERT: C 781 VAL cc_start: 0.8703 (t) cc_final: 0.8497 (p) REVERT: C 790 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7793 (mtmt) REVERT: C 931 ILE cc_start: 0.8397 (mm) cc_final: 0.8008 (tp) REVERT: C 964 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7642 (mtpp) REVERT: C 1002 GLN cc_start: 0.7250 (tm-30) cc_final: 0.6783 (tm-30) REVERT: D 34 MET cc_start: 0.5684 (ptp) cc_final: 0.5263 (ptp) REVERT: D 83 MET cc_start: 0.7560 (ptm) cc_final: 0.7140 (pmm) REVERT: E 82 MET cc_start: 0.5929 (ptm) cc_final: 0.5669 (ptm) REVERT: E 92 MET cc_start: 0.6844 (mtm) cc_final: 0.6192 (mtm) REVERT: E 94 TYR cc_start: 0.6954 (m-80) cc_final: 0.6581 (m-80) REVERT: F 69 ILE cc_start: -0.0114 (OUTLIER) cc_final: -0.0345 (tt) REVERT: G 51 MET cc_start: 0.5276 (OUTLIER) cc_final: 0.4757 (tpt) REVERT: G 69 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6137 (tt) REVERT: H 59 TYR cc_start: 0.6956 (m-10) cc_final: 0.6656 (m-80) REVERT: H 118 VAL cc_start: 0.7106 (OUTLIER) cc_final: 0.6889 (m) outliers start: 200 outliers final: 48 residues processed: 830 average time/residue: 0.1905 time to fit residues: 248.3826 Evaluate side-chains 612 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 532 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 99 TRP Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 118 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 314 GLN A 388 ASN A 409 GLN A 414 GLN A 556 ASN A 755 GLN A 762 GLN A 784 GLN A 907 ASN A1002 GLN A1048 HIS A1119 ASN B 205 HIS B 218 GLN B 239 GLN B 271 GLN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 784 GLN B 901 GLN B 907 ASN B1002 GLN B1048 HIS B1101 HIS B1106 GLN C 23 GLN C 66 HIS C 115 GLN C 173 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN C 394 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN C 422 ASN C 580 GLN C 641 ASN C 784 GLN C 901 GLN C 925 ASN C 935 GLN C 955 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1048 HIS C1106 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN E 81 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN G 13 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.166467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125248 restraints weight = 49459.516| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.66 r_work: 0.3443 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29907 Z= 0.193 Angle : 0.636 10.011 40787 Z= 0.319 Chirality : 0.046 0.369 4656 Planarity : 0.005 0.058 5213 Dihedral : 7.250 90.267 4721 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.50 % Allowed : 11.80 % Favored : 83.70 % 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: -2.63 (0.13), residues: 3639 helix: 0.85 (0.21), residues: 625 sheet: -1.65 (0.16), residues: 901 loop : -2.73 (0.11), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 273 TYR 0.024 0.001 TYR A 265 PHE 0.026 0.002 PHE C 199 TRP 0.010 0.001 TRP E 99 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00449 (29833) covalent geometry : angle 0.61886 (40611) SS BOND : bond 0.00709 ( 46) SS BOND : angle 1.85369 ( 92) hydrogen bonds : bond 0.03958 ( 910) hydrogen bonds : angle 5.42341 ( 2478) link_NAG-ASN : bond 0.00533 ( 28) link_NAG-ASN : angle 2.68002 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 544 time to evaluate : 1.102 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: A 99 ASN cc_start: 0.8266 (m-40) cc_final: 0.7497 (t0) REVERT: A 116 SER cc_start: 0.8429 (m) cc_final: 0.8042 (p) REVERT: A 126 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7615 (m) REVERT: A 132 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: A 138 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.7006 (t70) REVERT: A 157 PHE cc_start: 0.5394 (OUTLIER) cc_final: 0.4624 (p90) REVERT: A 164 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7677 (m-40) REVERT: A 171 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8436 (t) REVERT: A 175 PHE cc_start: 0.6287 (OUTLIER) cc_final: 0.5843 (p90) REVERT: A 206 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8149 (p) REVERT: A 220 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: A 228 ASP cc_start: 0.7505 (t0) cc_final: 0.7248 (t70) REVERT: A 238 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8554 (p90) REVERT: A 281 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6959 (pm20) REVERT: A 314 GLN cc_start: 0.8452 (tt0) cc_final: 0.8221 (tp40) REVERT: A 362 VAL cc_start: 0.8803 (t) cc_final: 0.8294 (p) REVERT: A 364 ASP cc_start: 0.7895 (t0) cc_final: 0.7570 (t0) REVERT: A 386 LYS cc_start: 0.8232 (mtmm) cc_final: 0.8010 (mtmm) REVERT: A 537 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8101 (ttpp) REVERT: A 546 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7836 (pp) REVERT: A 643 PHE cc_start: 0.8194 (t80) cc_final: 0.7935 (t80) REVERT: A 750 SER cc_start: 0.8606 (m) cc_final: 0.8323 (m) REVERT: A 773 GLU cc_start: 0.7554 (tt0) cc_final: 0.7340 (tt0) REVERT: A 776 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7984 (ttpp) REVERT: A 780 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7764 (mm-30) REVERT: A 790 LYS cc_start: 0.8683 (mmmm) cc_final: 0.8253 (mmmt) REVERT: A 907 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8592 (m-40) REVERT: A 933 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8111 (mtmm) REVERT: A 935 GLN cc_start: 0.8074 (tt0) cc_final: 0.7763 (tt0) REVERT: A 988 GLU cc_start: 0.8030 (tp30) cc_final: 0.7542 (tp30) REVERT: A 1019 ARG cc_start: 0.7904 (ttm110) cc_final: 0.7207 (ttm170) REVERT: B 52 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7491 (tm-30) REVERT: B 64 TRP cc_start: 0.7988 (t60) cc_final: 0.7788 (t60) REVERT: B 97 LYS cc_start: 0.8221 (tppt) cc_final: 0.7838 (tppt) REVERT: B 129 LYS cc_start: 0.8392 (ptpt) cc_final: 0.8148 (ptpt) REVERT: B 173 GLN cc_start: 0.6396 (OUTLIER) cc_final: 0.5986 (tm130) REVERT: B 208 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8271 (pt) REVERT: B 278 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8592 (ttpt) REVERT: B 764 LYS cc_start: 0.7951 (mmmt) cc_final: 0.7483 (mmmm) REVERT: B 773 GLU cc_start: 0.7720 (tt0) cc_final: 0.7434 (tt0) REVERT: B 776 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8025 (ttmm) REVERT: B 804 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8472 (mm-40) REVERT: B 816 SER cc_start: 0.8028 (p) cc_final: 0.7731 (t) REVERT: B 825 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8382 (mtmm) REVERT: B 949 GLN cc_start: 0.8358 (tp40) cc_final: 0.7957 (mm-40) REVERT: B 950 ASP cc_start: 0.8006 (t0) cc_final: 0.7680 (t0) REVERT: B 973 ILE cc_start: 0.8803 (pt) cc_final: 0.8487 (mt) REVERT: B 979 ASP cc_start: 0.7608 (t70) cc_final: 0.7326 (t0) REVERT: B 983 ARG cc_start: 0.8158 (mtm110) cc_final: 0.7750 (ttp-110) REVERT: B 1073 LYS cc_start: 0.8564 (ptmm) cc_final: 0.8146 (ptmm) REVERT: B 1123 SER cc_start: 0.8824 (m) cc_final: 0.8531 (p) REVERT: C 33 THR cc_start: 0.8067 (m) cc_final: 0.7634 (p) REVERT: C 64 TRP cc_start: 0.8078 (t60) cc_final: 0.7865 (t60) REVERT: C 96 GLU cc_start: 0.7304 (pp20) cc_final: 0.7008 (pp20) REVERT: C 102 ARG cc_start: 0.6564 (mmm-85) cc_final: 0.6264 (mmm-85) REVERT: C 188 ARG cc_start: 0.8271 (ptp90) cc_final: 0.8051 (ptp-170) REVERT: C 198 TYR cc_start: 0.7923 (m-80) cc_final: 0.7699 (m-80) REVERT: C 231 ILE cc_start: 0.6530 (tp) cc_final: 0.6139 (tt) REVERT: C 239 GLN cc_start: 0.8166 (tt0) cc_final: 0.7875 (tt0) REVERT: C 305 SER cc_start: 0.8989 (t) cc_final: 0.8687 (p) REVERT: C 324 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7471 (mm-30) REVERT: C 406 GLU cc_start: -0.1515 (OUTLIER) cc_final: -0.1826 (tp30) REVERT: C 518 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7384 (mp) REVERT: C 537 LYS cc_start: 0.8136 (ttpp) cc_final: 0.7727 (tttp) REVERT: C 541 PHE cc_start: 0.8008 (p90) cc_final: 0.7508 (p90) REVERT: C 555 SER cc_start: 0.8279 (m) cc_final: 0.7213 (p) REVERT: C 619 GLU cc_start: 0.5775 (OUTLIER) cc_final: 0.4403 (pm20) REVERT: C 690 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7722 (mm110) REVERT: C 762 GLN cc_start: 0.7674 (mt0) cc_final: 0.7417 (mt0) REVERT: C 776 LYS cc_start: 0.8720 (ttpt) cc_final: 0.8501 (ttpp) REVERT: C 790 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8118 (mtmt) REVERT: C 868 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7183 (tm-30) REVERT: C 945 LEU cc_start: 0.8675 (mm) cc_final: 0.8444 (mt) REVERT: C 950 ASP cc_start: 0.7844 (t0) cc_final: 0.7507 (t0) REVERT: C 964 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8163 (mtpp) REVERT: C 976 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8268 (m) REVERT: C 1002 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7409 (tm-30) REVERT: C 1111 GLU cc_start: 0.8402 (tt0) cc_final: 0.8170 (tt0) REVERT: D 34 MET cc_start: 0.5894 (ptp) cc_final: 0.5340 (ptp) REVERT: D 83 MET cc_start: 0.7666 (ptm) cc_final: 0.7186 (pmm) REVERT: E 35 SER cc_start: 0.7672 (t) cc_final: 0.7346 (m) REVERT: E 82 MET cc_start: 0.6546 (ptm) cc_final: 0.6219 (ptm) REVERT: E 92 MET cc_start: 0.7381 (mtm) cc_final: 0.6693 (mtm) REVERT: E 94 TYR cc_start: 0.7430 (m-80) cc_final: 0.6960 (m-80) REVERT: G 51 MET cc_start: 0.5229 (OUTLIER) cc_final: 0.4627 (tpt) REVERT: G 77 MET cc_start: 0.7777 (tpp) cc_final: 0.7496 (tpt) REVERT: H 77 ASN cc_start: 0.6386 (t0) cc_final: 0.5613 (t0) outliers start: 143 outliers final: 64 residues processed: 645 average time/residue: 0.1883 time to fit residues: 191.0135 Evaluate side-chains 590 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 506 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 99 TRP Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain H residue 50 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 240 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 276 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 228 optimal weight: 0.6980 chunk 224 optimal weight: 0.8980 chunk 335 optimal weight: 20.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 164 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 762 GLN A 955 ASN A1106 GLN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN C 194 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 957 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.164302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122798 restraints weight = 49099.048| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.62 r_work: 0.3364 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 29907 Z= 0.191 Angle : 0.632 11.864 40787 Z= 0.316 Chirality : 0.046 0.322 4656 Planarity : 0.005 0.060 5213 Dihedral : 6.089 89.657 4660 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.93 % Allowed : 13.44 % Favored : 82.63 % 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: -2.18 (0.13), residues: 3639 helix: 1.04 (0.21), residues: 638 sheet: -1.33 (0.16), residues: 909 loop : -2.41 (0.12), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 273 TYR 0.025 0.001 TYR A 265 PHE 0.017 0.002 PHE A 515 TRP 0.028 0.001 TRP A 353 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00449 (29833) covalent geometry : angle 0.61628 (40611) SS BOND : bond 0.00452 ( 46) SS BOND : angle 1.83316 ( 92) hydrogen bonds : bond 0.03936 ( 910) hydrogen bonds : angle 5.23832 ( 2478) link_NAG-ASN : bond 0.00750 ( 28) link_NAG-ASN : angle 2.54240 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 532 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8279 (m-40) cc_final: 0.7638 (t0) REVERT: A 102 ARG cc_start: 0.8314 (ttm170) cc_final: 0.7443 (ttm110) REVERT: A 116 SER cc_start: 0.8396 (m) cc_final: 0.7955 (p) REVERT: A 132 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: A 164 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7612 (m-40) REVERT: A 169 GLU cc_start: 0.8372 (mp0) cc_final: 0.8167 (mp0) REVERT: A 175 PHE cc_start: 0.6472 (OUTLIER) cc_final: 0.6000 (p90) REVERT: A 206 THR cc_start: 0.8582 (p) cc_final: 0.8382 (p) REVERT: A 220 PHE cc_start: 0.8398 (t80) cc_final: 0.7973 (m-80) REVERT: A 238 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8734 (p90) REVERT: A 328 ARG cc_start: 0.8390 (tpp80) cc_final: 0.8104 (tpt-90) REVERT: A 364 ASP cc_start: 0.8056 (t0) cc_final: 0.7759 (t0) REVERT: A 386 LYS cc_start: 0.8317 (mtmm) cc_final: 0.8081 (mtmm) REVERT: A 537 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8417 (ttpp) REVERT: A 546 LEU cc_start: 0.8476 (pp) cc_final: 0.8181 (pp) REVERT: A 571 ASP cc_start: 0.7151 (t0) cc_final: 0.6941 (t70) REVERT: A 578 ASP cc_start: 0.8104 (t0) cc_final: 0.7807 (t0) REVERT: A 643 PHE cc_start: 0.8456 (t80) cc_final: 0.8225 (t80) REVERT: A 750 SER cc_start: 0.8717 (m) cc_final: 0.8448 (m) REVERT: A 751 ASN cc_start: 0.8526 (m-40) cc_final: 0.8304 (m-40) REVERT: A 776 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8198 (ttpp) REVERT: A 790 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8381 (mmmt) REVERT: A 851 CYS cc_start: 0.8965 (t) cc_final: 0.8764 (m) REVERT: A 988 GLU cc_start: 0.8571 (tp30) cc_final: 0.8260 (tp30) REVERT: B 64 TRP cc_start: 0.8342 (t60) cc_final: 0.8099 (t60) REVERT: B 97 LYS cc_start: 0.8394 (tppt) cc_final: 0.8023 (tppt) REVERT: B 173 GLN cc_start: 0.6555 (OUTLIER) cc_final: 0.6065 (tm130) REVERT: B 278 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8665 (ttpt) REVERT: B 304 LYS cc_start: 0.9007 (mptt) cc_final: 0.8773 (mmtm) REVERT: B 340 GLU cc_start: 0.8097 (pm20) cc_final: 0.7796 (pm20) REVERT: B 378 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7858 (mtpp) REVERT: B 380 TYR cc_start: 0.8888 (m-80) cc_final: 0.8177 (m-80) REVERT: B 473 TYR cc_start: 0.8391 (t80) cc_final: 0.8168 (t80) REVERT: B 498 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7496 (mmm-85) REVERT: B 619 GLU cc_start: 0.8006 (pm20) cc_final: 0.7685 (pm20) REVERT: B 654 GLU cc_start: 0.7897 (pm20) cc_final: 0.7679 (pt0) REVERT: B 776 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8176 (ttmm) REVERT: B 780 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: B 804 GLN cc_start: 0.9096 (mt0) cc_final: 0.8775 (mm-40) REVERT: B 816 SER cc_start: 0.8121 (p) cc_final: 0.7890 (t) REVERT: B 949 GLN cc_start: 0.8536 (tp40) cc_final: 0.8143 (mm-40) REVERT: B 950 ASP cc_start: 0.8351 (t0) cc_final: 0.7995 (t0) REVERT: B 979 ASP cc_start: 0.7816 (t70) cc_final: 0.7582 (t0) REVERT: B 983 ARG cc_start: 0.8359 (mtm110) cc_final: 0.7999 (ttp-110) REVERT: B 1123 SER cc_start: 0.8957 (m) cc_final: 0.8640 (p) REVERT: C 102 ARG cc_start: 0.6843 (mmm-85) cc_final: 0.6527 (mmm-85) REVERT: C 189 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7842 (mt-10) REVERT: C 239 GLN cc_start: 0.8489 (tt0) cc_final: 0.8229 (tt0) REVERT: C 281 GLU cc_start: 0.7961 (pp20) cc_final: 0.7588 (pp20) REVERT: C 305 SER cc_start: 0.9135 (t) cc_final: 0.8811 (p) REVERT: C 324 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7667 (mm-30) REVERT: C 518 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7450 (mp) REVERT: C 537 LYS cc_start: 0.8367 (ttpp) cc_final: 0.7968 (tttp) REVERT: C 558 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8573 (ptpt) REVERT: C 586 ASP cc_start: 0.8114 (m-30) cc_final: 0.7630 (m-30) REVERT: C 599 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8993 (p) REVERT: C 619 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5321 (pm20) REVERT: C 690 GLN cc_start: 0.8364 (mm-40) cc_final: 0.7890 (mm110) REVERT: C 762 GLN cc_start: 0.8029 (mt0) cc_final: 0.7819 (mt0) REVERT: C 776 LYS cc_start: 0.8849 (ttpt) cc_final: 0.8631 (ttpp) REVERT: C 790 LYS cc_start: 0.8727 (mtmt) cc_final: 0.8228 (mtmm) REVERT: C 804 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8291 (mm-40) REVERT: C 868 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7166 (tm-30) REVERT: C 872 GLN cc_start: 0.8572 (mt0) cc_final: 0.8246 (mt0) REVERT: C 945 LEU cc_start: 0.8803 (mm) cc_final: 0.8575 (mt) REVERT: C 964 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8414 (mtpp) REVERT: C 976 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.8224 (m) REVERT: C 1002 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7870 (tm-30) REVERT: C 1091 ARG cc_start: 0.8645 (ttm-80) cc_final: 0.8369 (ttm170) REVERT: C 1111 GLU cc_start: 0.8746 (tt0) cc_final: 0.8504 (tt0) REVERT: D 34 MET cc_start: 0.5914 (ptp) cc_final: 0.5356 (ptp) REVERT: D 83 MET cc_start: 0.7679 (ptm) cc_final: 0.7199 (pmm) REVERT: E 82 MET cc_start: 0.6925 (ptm) cc_final: 0.6612 (ptm) REVERT: E 92 MET cc_start: 0.7534 (mtm) cc_final: 0.6796 (mtm) REVERT: E 94 TYR cc_start: 0.7635 (m-80) cc_final: 0.7068 (m-80) REVERT: G 51 MET cc_start: 0.5361 (OUTLIER) cc_final: 0.4178 (tpt) REVERT: G 69 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6407 (tt) REVERT: G 77 MET cc_start: 0.7765 (tpp) cc_final: 0.7420 (tpt) REVERT: H 77 ASN cc_start: 0.6581 (t0) cc_final: 0.5925 (t0) REVERT: H 83 MET cc_start: 0.7820 (ptm) cc_final: 0.7605 (ptm) outliers start: 125 outliers final: 73 residues processed: 620 average time/residue: 0.1920 time to fit residues: 186.5564 Evaluate side-chains 585 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 500 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 99 TRP Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 361 optimal weight: 0.7980 chunk 233 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 354 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 300 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 186 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 556 ASN A 762 GLN A 901 GLN B 895 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C 992 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.164197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.122708 restraints weight = 48717.831| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.63 r_work: 0.3374 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29907 Z= 0.150 Angle : 0.602 13.592 40787 Z= 0.299 Chirality : 0.045 0.332 4656 Planarity : 0.004 0.059 5213 Dihedral : 5.588 90.338 4639 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.65 % Allowed : 14.32 % Favored : 82.03 % 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: -1.90 (0.13), residues: 3639 helix: 1.22 (0.21), residues: 646 sheet: -1.19 (0.16), residues: 911 loop : -2.20 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 995 TYR 0.026 0.001 TYR A 265 PHE 0.028 0.001 PHE B 374 TRP 0.019 0.001 TRP C 64 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00355 (29833) covalent geometry : angle 0.58728 (40611) SS BOND : bond 0.00471 ( 46) SS BOND : angle 1.75110 ( 92) hydrogen bonds : bond 0.03582 ( 910) hydrogen bonds : angle 5.07945 ( 2478) link_NAG-ASN : bond 0.00278 ( 28) link_NAG-ASN : angle 2.37253 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 507 time to evaluate : 0.658 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: A 99 ASN cc_start: 0.8415 (m-40) cc_final: 0.7261 (t0) REVERT: A 102 ARG cc_start: 0.8255 (ttm170) cc_final: 0.7264 (ptp-110) REVERT: A 116 SER cc_start: 0.8140 (m) cc_final: 0.7720 (p) REVERT: A 132 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6488 (mp0) REVERT: A 164 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7607 (m-40) REVERT: A 175 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.6170 (p90) REVERT: A 186 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.7912 (p0) REVERT: A 188 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.8346 (mtt90) REVERT: A 206 THR cc_start: 0.8529 (p) cc_final: 0.8316 (p) REVERT: A 220 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: A 269 TYR cc_start: 0.8716 (m-10) cc_final: 0.8488 (m-80) REVERT: A 364 ASP cc_start: 0.8026 (t0) cc_final: 0.7734 (t0) REVERT: A 386 LYS cc_start: 0.8294 (mtmm) cc_final: 0.8086 (mtmm) REVERT: A 546 LEU cc_start: 0.8509 (pp) cc_final: 0.8217 (pp) REVERT: A 571 ASP cc_start: 0.7207 (t0) cc_final: 0.6914 (t70) REVERT: A 578 ASP cc_start: 0.8142 (t0) cc_final: 0.7838 (t0) REVERT: A 643 PHE cc_start: 0.8517 (t80) cc_final: 0.8301 (t80) REVERT: A 751 ASN cc_start: 0.8472 (m-40) cc_final: 0.8259 (m-40) REVERT: A 776 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8141 (ttpp) REVERT: A 790 LYS cc_start: 0.8781 (mmmm) cc_final: 0.8450 (mmmm) REVERT: A 808 ASP cc_start: 0.8198 (t0) cc_final: 0.7556 (t0) REVERT: A 851 CYS cc_start: 0.8964 (t) cc_final: 0.8764 (m) REVERT: A 988 GLU cc_start: 0.8679 (tp30) cc_final: 0.8338 (tp30) REVERT: A 1041 ASP cc_start: 0.8397 (t0) cc_final: 0.8023 (t0) REVERT: B 64 TRP cc_start: 0.8321 (t60) cc_final: 0.8080 (t60) REVERT: B 97 LYS cc_start: 0.8400 (tppt) cc_final: 0.8059 (tppt) REVERT: B 173 GLN cc_start: 0.6426 (OUTLIER) cc_final: 0.5917 (tm130) REVERT: B 221 SER cc_start: 0.8946 (m) cc_final: 0.8491 (p) REVERT: B 237 ARG cc_start: 0.8552 (mtm180) cc_final: 0.8349 (mtm180) REVERT: B 278 LYS cc_start: 0.9045 (ttpt) cc_final: 0.8653 (ttpt) REVERT: B 304 LYS cc_start: 0.9005 (mptt) cc_final: 0.8799 (mmtm) REVERT: B 338 PHE cc_start: 0.9081 (m-80) cc_final: 0.8754 (m-80) REVERT: B 340 GLU cc_start: 0.8259 (pm20) cc_final: 0.7936 (pm20) REVERT: B 361 CYS cc_start: 0.7276 (m) cc_final: 0.6975 (m) REVERT: B 380 TYR cc_start: 0.8912 (m-80) cc_final: 0.8591 (m-80) REVERT: B 619 GLU cc_start: 0.8047 (pm20) cc_final: 0.7843 (pm20) REVERT: B 765 ARG cc_start: 0.8235 (ttm-80) cc_final: 0.8030 (ttm110) REVERT: B 776 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8189 (ttpp) REVERT: B 780 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7798 (mt-10) REVERT: B 804 GLN cc_start: 0.9081 (mt0) cc_final: 0.8854 (mm-40) REVERT: B 816 SER cc_start: 0.8138 (p) cc_final: 0.7882 (t) REVERT: B 949 GLN cc_start: 0.8517 (tp40) cc_final: 0.8152 (mm-40) REVERT: B 950 ASP cc_start: 0.8258 (t0) cc_final: 0.7948 (t0) REVERT: B 979 ASP cc_start: 0.7817 (t70) cc_final: 0.7563 (t0) REVERT: B 983 ARG cc_start: 0.8405 (mtm110) cc_final: 0.8102 (ttp-110) REVERT: B 995 ARG cc_start: 0.8443 (mtp85) cc_final: 0.7879 (ptm160) REVERT: B 1123 SER cc_start: 0.8963 (m) cc_final: 0.8632 (p) REVERT: B 1130 ILE cc_start: 0.8977 (mm) cc_final: 0.8746 (mt) REVERT: C 65 PHE cc_start: 0.8218 (m-80) cc_final: 0.7954 (m-80) REVERT: C 102 ARG cc_start: 0.6827 (mmm-85) cc_final: 0.6409 (mmm-85) REVERT: C 189 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7816 (mt-10) REVERT: C 239 GLN cc_start: 0.8476 (tt0) cc_final: 0.8179 (tt0) REVERT: C 281 GLU cc_start: 0.8010 (pp20) cc_final: 0.7715 (pm20) REVERT: C 324 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7798 (mm-30) REVERT: C 518 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7358 (mp) REVERT: C 537 LYS cc_start: 0.8375 (ttpp) cc_final: 0.8116 (ptmm) REVERT: C 558 LYS cc_start: 0.8881 (mtmt) cc_final: 0.8627 (ptpp) REVERT: C 619 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5283 (pm20) REVERT: C 690 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7948 (mm110) REVERT: C 776 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8617 (ttpp) REVERT: C 790 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8308 (mtmt) REVERT: C 804 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8290 (mm-40) REVERT: C 868 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7171 (tm-30) REVERT: C 869 MET cc_start: 0.8844 (mtt) cc_final: 0.8522 (mtm) REVERT: C 872 GLN cc_start: 0.8550 (mt0) cc_final: 0.8237 (mt0) REVERT: C 945 LEU cc_start: 0.8784 (mm) cc_final: 0.8570 (mt) REVERT: C 964 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8425 (mtpp) REVERT: C 976 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8199 (m) REVERT: C 1002 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7850 (tm-30) REVERT: C 1091 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8417 (ttm170) REVERT: C 1111 GLU cc_start: 0.8736 (tt0) cc_final: 0.8482 (tt0) REVERT: D 34 MET cc_start: 0.5936 (ptp) cc_final: 0.5380 (ptp) REVERT: D 83 MET cc_start: 0.7646 (ptm) cc_final: 0.7177 (pmm) REVERT: E 34 MET cc_start: 0.8116 (mmm) cc_final: 0.7798 (mmt) REVERT: E 77 MET cc_start: 0.6998 (mmm) cc_final: 0.6734 (mmm) REVERT: E 82 MET cc_start: 0.6960 (ptm) cc_final: 0.6622 (ptm) REVERT: E 92 MET cc_start: 0.7474 (mtm) cc_final: 0.6735 (mtm) REVERT: E 94 TYR cc_start: 0.7604 (m-80) cc_final: 0.6990 (m-80) REVERT: F 112 THR cc_start: 0.4997 (OUTLIER) cc_final: 0.4766 (p) REVERT: G 69 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.6433 (tt) REVERT: G 77 MET cc_start: 0.7735 (tpp) cc_final: 0.7427 (tpt) REVERT: H 77 ASN cc_start: 0.6574 (t0) cc_final: 0.5931 (t0) outliers start: 116 outliers final: 83 residues processed: 600 average time/residue: 0.1897 time to fit residues: 179.1512 Evaluate side-chains 592 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 498 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 99 TRP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 172 optimal weight: 0.0070 chunk 57 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 347 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 164 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 overall best weight: 0.6600 ------------------------------------------------------------------------------- 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 556 ASN A 965 GLN A1010 GLN B 30 ASN B 271 GLN B 580 GLN B 955 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1010 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.164879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.123450 restraints weight = 48781.964| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.63 r_work: 0.3388 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29907 Z= 0.130 Angle : 0.583 12.275 40787 Z= 0.291 Chirality : 0.044 0.272 4656 Planarity : 0.004 0.057 5213 Dihedral : 5.385 91.185 4633 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.75 % Allowed : 15.14 % Favored : 81.11 % 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: -1.67 (0.13), residues: 3639 helix: 1.48 (0.21), residues: 645 sheet: -1.06 (0.16), residues: 907 loop : -2.06 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 38 TYR 0.023 0.001 TYR A 265 PHE 0.029 0.001 PHE B 374 TRP 0.014 0.001 TRP C 64 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00308 (29833) covalent geometry : angle 0.57061 (40611) SS BOND : bond 0.00443 ( 46) SS BOND : angle 1.65707 ( 92) hydrogen bonds : bond 0.03361 ( 910) hydrogen bonds : angle 4.98985 ( 2478) link_NAG-ASN : bond 0.00264 ( 28) link_NAG-ASN : angle 2.15088 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 518 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8350 (m-40) cc_final: 0.7352 (t0) REVERT: A 102 ARG cc_start: 0.8282 (ttm170) cc_final: 0.7505 (ptp-110) REVERT: A 116 SER cc_start: 0.8059 (m) cc_final: 0.7677 (p) REVERT: A 129 LYS cc_start: 0.8182 (mttm) cc_final: 0.7863 (mptt) REVERT: A 164 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7614 (m-40) REVERT: A 175 PHE cc_start: 0.6531 (OUTLIER) cc_final: 0.6050 (p90) REVERT: A 206 THR cc_start: 0.8516 (p) cc_final: 0.8294 (p) REVERT: A 220 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: A 319 ARG cc_start: 0.8298 (ptp-110) cc_final: 0.8087 (ptp90) REVERT: A 328 ARG cc_start: 0.8270 (tpp80) cc_final: 0.7968 (tpt-90) REVERT: A 364 ASP cc_start: 0.7991 (t0) cc_final: 0.7753 (t0) REVERT: A 386 LYS cc_start: 0.8268 (mtmm) cc_final: 0.8048 (mtmm) REVERT: A 546 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8246 (pp) REVERT: A 571 ASP cc_start: 0.7238 (t0) cc_final: 0.6943 (t70) REVERT: A 578 ASP cc_start: 0.8133 (t0) cc_final: 0.7903 (t0) REVERT: A 643 PHE cc_start: 0.8516 (t80) cc_final: 0.8271 (t80) REVERT: A 702 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7309 (mm-30) REVERT: A 773 GLU cc_start: 0.7963 (tt0) cc_final: 0.7710 (tt0) REVERT: A 776 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8064 (ttpp) REVERT: A 790 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8461 (mmmm) REVERT: A 808 ASP cc_start: 0.8221 (t0) cc_final: 0.7594 (t0) REVERT: A 851 CYS cc_start: 0.8971 (t) cc_final: 0.8745 (m) REVERT: A 988 GLU cc_start: 0.8698 (tp30) cc_final: 0.8348 (tp30) REVERT: A 1041 ASP cc_start: 0.8389 (t0) cc_final: 0.8053 (t0) REVERT: A 1111 GLU cc_start: 0.8128 (pm20) cc_final: 0.7916 (pm20) REVERT: B 29 THR cc_start: 0.8416 (m) cc_final: 0.8033 (m) REVERT: B 173 GLN cc_start: 0.6365 (OUTLIER) cc_final: 0.5881 (tm130) REVERT: B 278 LYS cc_start: 0.9056 (ttpt) cc_final: 0.8630 (ttpt) REVERT: B 304 LYS cc_start: 0.9006 (mptt) cc_final: 0.8806 (mmtm) REVERT: B 338 PHE cc_start: 0.9102 (m-80) cc_final: 0.8883 (m-80) REVERT: B 340 GLU cc_start: 0.8262 (pm20) cc_final: 0.7876 (pm20) REVERT: B 361 CYS cc_start: 0.7346 (m) cc_final: 0.7095 (m) REVERT: B 764 LYS cc_start: 0.8186 (mmmt) cc_final: 0.7950 (tmmt) REVERT: B 776 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8248 (ttpp) REVERT: B 816 SER cc_start: 0.8127 (p) cc_final: 0.7889 (t) REVERT: B 825 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8533 (mtmm) REVERT: B 949 GLN cc_start: 0.8541 (tp40) cc_final: 0.8169 (mm-40) REVERT: B 950 ASP cc_start: 0.8288 (t0) cc_final: 0.7973 (t0) REVERT: B 979 ASP cc_start: 0.7882 (t70) cc_final: 0.7589 (t0) REVERT: B 995 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8149 (ptm160) REVERT: B 1123 SER cc_start: 0.8923 (m) cc_final: 0.8573 (p) REVERT: B 1130 ILE cc_start: 0.8980 (mm) cc_final: 0.8755 (mt) REVERT: C 65 PHE cc_start: 0.8163 (m-80) cc_final: 0.7897 (m-80) REVERT: C 102 ARG cc_start: 0.6904 (mmm-85) cc_final: 0.6475 (mmm-85) REVERT: C 170 TYR cc_start: 0.7574 (t80) cc_final: 0.7310 (t80) REVERT: C 189 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7824 (mt-10) REVERT: C 239 GLN cc_start: 0.8486 (tt0) cc_final: 0.8183 (tt0) REVERT: C 281 GLU cc_start: 0.7992 (pp20) cc_final: 0.7651 (pm20) REVERT: C 305 SER cc_start: 0.9118 (t) cc_final: 0.8779 (p) REVERT: C 324 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7811 (mm-30) REVERT: C 537 LYS cc_start: 0.8429 (ttpp) cc_final: 0.8196 (ptmm) REVERT: C 558 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8594 (ptpp) REVERT: C 619 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5115 (pm20) REVERT: C 690 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7976 (mm110) REVERT: C 776 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8586 (ttpp) REVERT: C 790 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8110 (mtmt) REVERT: C 804 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8290 (mm-40) REVERT: C 868 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7247 (tm-30) REVERT: C 869 MET cc_start: 0.8849 (mtt) cc_final: 0.8497 (mtm) REVERT: C 872 GLN cc_start: 0.8534 (mt0) cc_final: 0.8253 (mt0) REVERT: C 945 LEU cc_start: 0.8805 (mm) cc_final: 0.8578 (mt) REVERT: C 976 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8179 (m) REVERT: C 1002 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7804 (tm-30) REVERT: C 1091 ARG cc_start: 0.8690 (ttm-80) cc_final: 0.8458 (ttm170) REVERT: C 1111 GLU cc_start: 0.8732 (tt0) cc_final: 0.8474 (tt0) REVERT: D 34 MET cc_start: 0.5919 (ptp) cc_final: 0.5352 (ptp) REVERT: D 83 MET cc_start: 0.7638 (ptm) cc_final: 0.7185 (pmm) REVERT: E 34 MET cc_start: 0.7935 (mmm) cc_final: 0.7471 (mmt) REVERT: E 35 SER cc_start: 0.7625 (OUTLIER) cc_final: 0.7285 (t) REVERT: E 58 TYR cc_start: 0.8640 (t80) cc_final: 0.8198 (t80) REVERT: E 82 MET cc_start: 0.6949 (ptm) cc_final: 0.6616 (ptm) REVERT: E 92 MET cc_start: 0.7385 (mtm) cc_final: 0.6720 (mtm) REVERT: E 94 TYR cc_start: 0.7613 (m-80) cc_final: 0.7028 (m-80) REVERT: F 112 THR cc_start: 0.4897 (OUTLIER) cc_final: 0.4664 (p) REVERT: G 51 MET cc_start: 0.5711 (ttm) cc_final: 0.5164 (tpp) REVERT: G 77 MET cc_start: 0.7765 (tpp) cc_final: 0.7230 (ppp) REVERT: H 34 MET cc_start: 0.8030 (ptp) cc_final: 0.7777 (ptp) REVERT: H 59 TYR cc_start: 0.7391 (m-80) cc_final: 0.6676 (m-80) REVERT: H 77 ASN cc_start: 0.6561 (t0) cc_final: 0.5950 (t0) REVERT: H 83 MET cc_start: 0.7937 (ptm) cc_final: 0.7650 (ptm) outliers start: 119 outliers final: 80 residues processed: 607 average time/residue: 0.1944 time to fit residues: 184.6651 Evaluate side-chains 590 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 501 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 99 TRP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 221 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 239 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 305 optimal weight: 0.8980 chunk 63 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN A 186 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN B 121 ASN B 271 GLN B 955 ASN B1119 ASN C 134 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.164663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.123261 restraints weight = 48715.613| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.62 r_work: 0.3373 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29907 Z= 0.130 Angle : 0.587 14.210 40787 Z= 0.293 Chirality : 0.044 0.293 4656 Planarity : 0.004 0.057 5213 Dihedral : 5.318 90.756 4629 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.90 % Allowed : 15.33 % Favored : 80.77 % 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: -1.49 (0.14), residues: 3639 helix: 1.62 (0.22), residues: 640 sheet: -0.97 (0.16), residues: 908 loop : -1.92 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.022 0.001 TYR A 265 PHE 0.030 0.001 PHE B 374 TRP 0.026 0.001 TRP B 64 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00308 (29833) covalent geometry : angle 0.57546 (40611) SS BOND : bond 0.00466 ( 46) SS BOND : angle 1.60320 ( 92) hydrogen bonds : bond 0.03323 ( 910) hydrogen bonds : angle 4.96258 ( 2478) link_NAG-ASN : bond 0.00235 ( 28) link_NAG-ASN : angle 2.04034 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 510 time to evaluate : 0.999 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: A 99 ASN cc_start: 0.8406 (m-40) cc_final: 0.7326 (t0) REVERT: A 102 ARG cc_start: 0.8360 (ttm170) cc_final: 0.7629 (ptp-110) REVERT: A 116 SER cc_start: 0.8200 (m) cc_final: 0.7838 (p) REVERT: A 164 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7466 (m-40) REVERT: A 175 PHE cc_start: 0.6475 (OUTLIER) cc_final: 0.5960 (p90) REVERT: A 188 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.8206 (mtm-85) REVERT: A 206 THR cc_start: 0.8480 (p) cc_final: 0.8262 (p) REVERT: A 220 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: A 319 ARG cc_start: 0.8302 (ptp-110) cc_final: 0.8087 (ptp90) REVERT: A 328 ARG cc_start: 0.8248 (tpp80) cc_final: 0.7962 (tpt-90) REVERT: A 364 ASP cc_start: 0.7958 (t0) cc_final: 0.7721 (t0) REVERT: A 386 LYS cc_start: 0.8254 (mtmm) cc_final: 0.8021 (mtmm) REVERT: A 546 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8307 (pp) REVERT: A 571 ASP cc_start: 0.7310 (t0) cc_final: 0.7016 (t70) REVERT: A 578 ASP cc_start: 0.8183 (t0) cc_final: 0.7919 (t0) REVERT: A 643 PHE cc_start: 0.8524 (t80) cc_final: 0.8306 (t80) REVERT: A 702 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7298 (mm-30) REVERT: A 773 GLU cc_start: 0.7970 (tt0) cc_final: 0.7744 (tt0) REVERT: A 776 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8081 (ttpp) REVERT: A 790 LYS cc_start: 0.8782 (mmmm) cc_final: 0.8470 (mmmm) REVERT: A 808 ASP cc_start: 0.8225 (t0) cc_final: 0.7598 (t0) REVERT: A 851 CYS cc_start: 0.8994 (t) cc_final: 0.8757 (m) REVERT: A 988 GLU cc_start: 0.8716 (tp30) cc_final: 0.8372 (tp30) REVERT: A 1041 ASP cc_start: 0.8387 (t0) cc_final: 0.8053 (t0) REVERT: B 29 THR cc_start: 0.8174 (m) cc_final: 0.7872 (m) REVERT: B 173 GLN cc_start: 0.6348 (OUTLIER) cc_final: 0.5847 (tm130) REVERT: B 237 ARG cc_start: 0.8561 (mtm180) cc_final: 0.8247 (mtm110) REVERT: B 278 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8633 (ttpt) REVERT: B 304 LYS cc_start: 0.9021 (mptt) cc_final: 0.8802 (mmmm) REVERT: B 338 PHE cc_start: 0.9099 (m-80) cc_final: 0.8889 (m-80) REVERT: B 340 GLU cc_start: 0.8257 (pm20) cc_final: 0.7870 (pm20) REVERT: B 361 CYS cc_start: 0.7238 (m) cc_final: 0.6977 (m) REVERT: B 421 TYR cc_start: 0.8744 (m-10) cc_final: 0.8537 (m-10) REVERT: B 776 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8134 (ttpp) REVERT: B 780 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7777 (mt-10) REVERT: B 816 SER cc_start: 0.8176 (p) cc_final: 0.7895 (t) REVERT: B 825 LYS cc_start: 0.9018 (mtpp) cc_final: 0.8581 (mtmm) REVERT: B 949 GLN cc_start: 0.8582 (tp40) cc_final: 0.8249 (mm-40) REVERT: B 950 ASP cc_start: 0.8271 (t0) cc_final: 0.7974 (t0) REVERT: B 979 ASP cc_start: 0.7839 (t70) cc_final: 0.7549 (t0) REVERT: B 983 ARG cc_start: 0.8442 (mtm110) cc_final: 0.8085 (ttp-110) REVERT: B 1123 SER cc_start: 0.8946 (m) cc_final: 0.8588 (p) REVERT: B 1130 ILE cc_start: 0.8996 (mm) cc_final: 0.8777 (mt) REVERT: C 65 PHE cc_start: 0.8159 (m-80) cc_final: 0.7894 (m-80) REVERT: C 97 LYS cc_start: 0.8388 (mmmm) cc_final: 0.8135 (mmmt) REVERT: C 102 ARG cc_start: 0.6954 (mmm-85) cc_final: 0.6531 (mmm-85) REVERT: C 189 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7847 (mt-10) REVERT: C 239 GLN cc_start: 0.8508 (tt0) cc_final: 0.8191 (tt0) REVERT: C 269 TYR cc_start: 0.8290 (m-80) cc_final: 0.8003 (m-80) REVERT: C 281 GLU cc_start: 0.8016 (pp20) cc_final: 0.7655 (pm20) REVERT: C 305 SER cc_start: 0.9114 (t) cc_final: 0.8775 (p) REVERT: C 324 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7863 (mm-30) REVERT: C 518 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7462 (mp) REVERT: C 537 LYS cc_start: 0.8449 (ttpp) cc_final: 0.8238 (ptmm) REVERT: C 558 LYS cc_start: 0.8934 (mtmt) cc_final: 0.8635 (ptpp) REVERT: C 584 ILE cc_start: 0.8737 (mm) cc_final: 0.8338 (mm) REVERT: C 619 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.4915 (pm20) REVERT: C 690 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7975 (mm110) REVERT: C 773 GLU cc_start: 0.8685 (tp30) cc_final: 0.8400 (tt0) REVERT: C 790 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8120 (mtmt) REVERT: C 868 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7318 (tm-30) REVERT: C 869 MET cc_start: 0.8866 (mtt) cc_final: 0.8490 (mtm) REVERT: C 872 GLN cc_start: 0.8511 (mt0) cc_final: 0.8231 (mt0) REVERT: C 945 LEU cc_start: 0.8824 (mm) cc_final: 0.8596 (mt) REVERT: C 957 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: C 976 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8240 (m) REVERT: C 995 ARG cc_start: 0.8219 (mtm110) cc_final: 0.7890 (ttm110) REVERT: C 1002 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7823 (tm-30) REVERT: C 1091 ARG cc_start: 0.8696 (ttm-80) cc_final: 0.8387 (ttm170) REVERT: C 1111 GLU cc_start: 0.8726 (tt0) cc_final: 0.8458 (tt0) REVERT: D 34 MET cc_start: 0.5913 (ptp) cc_final: 0.5353 (ptp) REVERT: D 83 MET cc_start: 0.7599 (ptm) cc_final: 0.7177 (pmm) REVERT: E 37 VAL cc_start: 0.8728 (m) cc_final: 0.8295 (p) REVERT: E 77 MET cc_start: 0.7071 (mmm) cc_final: 0.6850 (mmm) REVERT: E 82 MET cc_start: 0.6995 (ptm) cc_final: 0.6660 (ptm) REVERT: E 92 MET cc_start: 0.7403 (mtm) cc_final: 0.6766 (mtm) REVERT: E 94 TYR cc_start: 0.7584 (m-80) cc_final: 0.6993 (m-80) REVERT: F 112 THR cc_start: 0.4952 (OUTLIER) cc_final: 0.4714 (p) REVERT: G 51 MET cc_start: 0.5686 (ttm) cc_final: 0.4614 (tpp) REVERT: G 77 MET cc_start: 0.7662 (tpp) cc_final: 0.7137 (ppp) REVERT: H 34 MET cc_start: 0.8054 (ptp) cc_final: 0.7752 (ptp) REVERT: H 59 TYR cc_start: 0.7373 (m-80) cc_final: 0.6830 (m-80) REVERT: H 77 ASN cc_start: 0.6567 (t0) cc_final: 0.5990 (t0) REVERT: H 83 MET cc_start: 0.7830 (ptm) cc_final: 0.7575 (ptm) outliers start: 124 outliers final: 88 residues processed: 603 average time/residue: 0.1913 time to fit residues: 182.7699 Evaluate side-chains 594 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 496 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 99 TRP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 363 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 214 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 362 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 289 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 762 GLN B 218 GLN B 239 GLN B 955 ASN B 957 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.163831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122386 restraints weight = 48911.618| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.64 r_work: 0.3381 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29907 Z= 0.150 Angle : 0.605 13.084 40787 Z= 0.303 Chirality : 0.045 0.261 4656 Planarity : 0.004 0.057 5213 Dihedral : 5.366 90.104 4628 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.65 % Allowed : 16.05 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3639 helix: 1.64 (0.22), residues: 640 sheet: -0.97 (0.16), residues: 919 loop : -1.86 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.022 0.001 TYR A 265 PHE 0.033 0.001 PHE B 32 TRP 0.033 0.001 TRP B 64 HIS 0.005 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00356 (29833) covalent geometry : angle 0.59369 (40611) SS BOND : bond 0.00456 ( 46) SS BOND : angle 1.66961 ( 92) hydrogen bonds : bond 0.03461 ( 910) hydrogen bonds : angle 4.97457 ( 2478) link_NAG-ASN : bond 0.00238 ( 28) link_NAG-ASN : angle 2.01679 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 505 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8332 (m-40) cc_final: 0.7546 (t0) REVERT: A 102 ARG cc_start: 0.8388 (ttm170) cc_final: 0.7946 (ptp90) REVERT: A 116 SER cc_start: 0.8237 (m) cc_final: 0.7891 (p) REVERT: A 164 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7453 (m-40) REVERT: A 175 PHE cc_start: 0.6433 (OUTLIER) cc_final: 0.5906 (p90) REVERT: A 188 ARG cc_start: 0.8601 (mtt-85) cc_final: 0.8189 (mpt-90) REVERT: A 206 THR cc_start: 0.8466 (p) cc_final: 0.8240 (p) REVERT: A 220 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8087 (m-80) REVERT: A 319 ARG cc_start: 0.8319 (ptp-110) cc_final: 0.8104 (ptp90) REVERT: A 364 ASP cc_start: 0.7931 (t0) cc_final: 0.7713 (t0) REVERT: A 386 LYS cc_start: 0.8247 (mtmm) cc_final: 0.7985 (mtmm) REVERT: A 546 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8366 (pp) REVERT: A 571 ASP cc_start: 0.7430 (t0) cc_final: 0.7124 (t70) REVERT: A 578 ASP cc_start: 0.8270 (t0) cc_final: 0.7983 (t0) REVERT: A 643 PHE cc_start: 0.8564 (t80) cc_final: 0.8343 (t80) REVERT: A 702 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7274 (mm-30) REVERT: A 773 GLU cc_start: 0.8012 (tt0) cc_final: 0.7811 (tt0) REVERT: A 776 LYS cc_start: 0.8430 (ttpt) cc_final: 0.8045 (ttpp) REVERT: A 790 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8462 (mmmm) REVERT: A 808 ASP cc_start: 0.8196 (t0) cc_final: 0.7569 (t0) REVERT: A 851 CYS cc_start: 0.9008 (t) cc_final: 0.8756 (m) REVERT: A 988 GLU cc_start: 0.8769 (tp30) cc_final: 0.8415 (tp30) REVERT: A 1002 GLN cc_start: 0.8550 (tt0) cc_final: 0.8149 (tp-100) REVERT: A 1041 ASP cc_start: 0.8393 (t0) cc_final: 0.8154 (t0) REVERT: B 29 THR cc_start: 0.8138 (m) cc_final: 0.7862 (m) REVERT: B 173 GLN cc_start: 0.6330 (OUTLIER) cc_final: 0.5870 (tm130) REVERT: B 278 LYS cc_start: 0.9044 (ttpt) cc_final: 0.8577 (ttpt) REVERT: B 304 LYS cc_start: 0.9019 (mptt) cc_final: 0.8769 (mmtp) REVERT: B 338 PHE cc_start: 0.9108 (m-80) cc_final: 0.8906 (m-80) REVERT: B 340 GLU cc_start: 0.8260 (pm20) cc_final: 0.7867 (pm20) REVERT: B 361 CYS cc_start: 0.7237 (m) cc_final: 0.6963 (m) REVERT: B 377 PHE cc_start: 0.7089 (t80) cc_final: 0.6597 (t80) REVERT: B 380 TYR cc_start: 0.8796 (m-80) cc_final: 0.8537 (m-80) REVERT: B 574 ASP cc_start: 0.8226 (t0) cc_final: 0.7970 (t0) REVERT: B 764 LYS cc_start: 0.8174 (mmmt) cc_final: 0.7951 (tmmt) REVERT: B 776 LYS cc_start: 0.8540 (ttpt) cc_final: 0.8198 (ttpp) REVERT: B 780 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7894 (mt-10) REVERT: B 816 SER cc_start: 0.8180 (p) cc_final: 0.7932 (t) REVERT: B 825 LYS cc_start: 0.9017 (mtpp) cc_final: 0.8797 (mtpp) REVERT: B 949 GLN cc_start: 0.8582 (tp40) cc_final: 0.8253 (mm-40) REVERT: B 950 ASP cc_start: 0.8275 (t0) cc_final: 0.7993 (t0) REVERT: B 979 ASP cc_start: 0.7852 (t70) cc_final: 0.7472 (t0) REVERT: B 983 ARG cc_start: 0.8439 (mtm110) cc_final: 0.8041 (mtm-85) REVERT: B 1123 SER cc_start: 0.8931 (m) cc_final: 0.8570 (p) REVERT: B 1130 ILE cc_start: 0.9006 (mm) cc_final: 0.8798 (mt) REVERT: C 64 TRP cc_start: 0.8522 (t60) cc_final: 0.8171 (t60) REVERT: C 99 ASN cc_start: 0.7956 (t0) cc_final: 0.7517 (t0) REVERT: C 102 ARG cc_start: 0.6974 (mmm-85) cc_final: 0.6509 (mmm-85) REVERT: C 189 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7808 (mt-10) REVERT: C 239 GLN cc_start: 0.8439 (tt0) cc_final: 0.8104 (tt0) REVERT: C 269 TYR cc_start: 0.8302 (m-80) cc_final: 0.8055 (m-80) REVERT: C 305 SER cc_start: 0.9110 (t) cc_final: 0.8764 (p) REVERT: C 324 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7844 (mm-30) REVERT: C 518 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7461 (mp) REVERT: C 558 LYS cc_start: 0.8880 (mtmt) cc_final: 0.8610 (ptpp) REVERT: C 619 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.4903 (pm20) REVERT: C 690 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7928 (mm110) REVERT: C 773 GLU cc_start: 0.8633 (tp30) cc_final: 0.8319 (tt0) REVERT: C 790 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8095 (mtmm) REVERT: C 868 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7389 (tm-30) REVERT: C 869 MET cc_start: 0.8851 (mtt) cc_final: 0.8483 (mtm) REVERT: C 872 GLN cc_start: 0.8575 (mt0) cc_final: 0.8313 (mt0) REVERT: C 970 PHE cc_start: 0.8347 (m-80) cc_final: 0.8049 (m-80) REVERT: C 976 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8264 (m) REVERT: C 995 ARG cc_start: 0.8196 (mtm110) cc_final: 0.7944 (ttp-110) REVERT: C 1002 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7831 (tm-30) REVERT: C 1091 ARG cc_start: 0.8754 (ttm-80) cc_final: 0.8449 (ttm170) REVERT: C 1111 GLU cc_start: 0.8706 (tt0) cc_final: 0.8419 (tt0) REVERT: D 34 MET cc_start: 0.5980 (ptp) cc_final: 0.5408 (ptp) REVERT: D 83 MET cc_start: 0.7613 (ptm) cc_final: 0.7205 (pmm) REVERT: E 33 GLU cc_start: 0.7454 (tm-30) cc_final: 0.6981 (tm-30) REVERT: E 35 SER cc_start: 0.7746 (t) cc_final: 0.7247 (p) REVERT: E 37 VAL cc_start: 0.8792 (m) cc_final: 0.8288 (p) REVERT: E 77 MET cc_start: 0.6977 (mmm) cc_final: 0.6717 (mmm) REVERT: E 82 MET cc_start: 0.6997 (ptm) cc_final: 0.6655 (ptm) REVERT: E 92 MET cc_start: 0.7437 (mtm) cc_final: 0.6808 (mtm) REVERT: E 94 TYR cc_start: 0.7632 (m-80) cc_final: 0.7068 (m-80) REVERT: F 112 THR cc_start: 0.4911 (OUTLIER) cc_final: 0.4674 (p) REVERT: G 77 MET cc_start: 0.7679 (tpp) cc_final: 0.7190 (ppp) REVERT: H 34 MET cc_start: 0.8134 (ptp) cc_final: 0.7766 (ptp) REVERT: H 59 TYR cc_start: 0.7399 (m-80) cc_final: 0.6897 (m-80) REVERT: H 77 ASN cc_start: 0.6573 (t0) cc_final: 0.6033 (t0) REVERT: H 83 MET cc_start: 0.7834 (ptm) cc_final: 0.7604 (ptm) outliers start: 116 outliers final: 88 residues processed: 596 average time/residue: 0.1898 time to fit residues: 178.3986 Evaluate side-chains 592 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 495 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 99 TRP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 235 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 345 optimal weight: 6.9990 chunk 316 optimal weight: 20.0000 chunk 210 optimal weight: 0.7980 chunk 287 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 762 GLN B 30 ASN B 955 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.161499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119937 restraints weight = 48436.405| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.66 r_work: 0.3349 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 29907 Z= 0.217 Angle : 0.660 14.068 40787 Z= 0.332 Chirality : 0.046 0.287 4656 Planarity : 0.004 0.058 5213 Dihedral : 5.599 89.903 4627 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.62 % Allowed : 16.02 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.14), residues: 3639 helix: 1.33 (0.21), residues: 665 sheet: -0.97 (0.16), residues: 968 loop : -1.84 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.024 0.001 TYR A 265 PHE 0.031 0.002 PHE B 32 TRP 0.048 0.002 TRP B 64 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00512 (29833) covalent geometry : angle 0.64740 (40611) SS BOND : bond 0.00507 ( 46) SS BOND : angle 1.97541 ( 92) hydrogen bonds : bond 0.04000 ( 910) hydrogen bonds : angle 5.12732 ( 2478) link_NAG-ASN : bond 0.00306 ( 28) link_NAG-ASN : angle 2.17407 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 508 time to evaluate : 0.903 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: A 99 ASN cc_start: 0.8389 (m-40) cc_final: 0.7330 (t0) REVERT: A 116 SER cc_start: 0.8329 (m) cc_final: 0.7953 (p) REVERT: A 164 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7541 (m-40) REVERT: A 175 PHE cc_start: 0.6532 (OUTLIER) cc_final: 0.6025 (p90) REVERT: A 188 ARG cc_start: 0.8556 (mtt-85) cc_final: 0.8146 (mpt-90) REVERT: A 206 THR cc_start: 0.8500 (p) cc_final: 0.8267 (p) REVERT: A 220 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: A 319 ARG cc_start: 0.8307 (ptp-110) cc_final: 0.8095 (ptp90) REVERT: A 364 ASP cc_start: 0.8020 (t0) cc_final: 0.7804 (t0) REVERT: A 546 LEU cc_start: 0.8719 (pp) cc_final: 0.8488 (pp) REVERT: A 571 ASP cc_start: 0.7617 (t0) cc_final: 0.7312 (t70) REVERT: A 578 ASP cc_start: 0.8319 (t0) cc_final: 0.8099 (t0) REVERT: A 702 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7304 (mm-30) REVERT: A 745 ASP cc_start: 0.6715 (t0) cc_final: 0.6295 (t70) REVERT: A 776 LYS cc_start: 0.8502 (ttpt) cc_final: 0.8158 (ttpp) REVERT: A 790 LYS cc_start: 0.8738 (mmmm) cc_final: 0.8421 (mmmm) REVERT: A 808 ASP cc_start: 0.8211 (t0) cc_final: 0.7566 (t0) REVERT: A 851 CYS cc_start: 0.9022 (t) cc_final: 0.8771 (m) REVERT: A 988 GLU cc_start: 0.8771 (tp30) cc_final: 0.8418 (tp30) REVERT: A 990 GLU cc_start: 0.8233 (mm-30) cc_final: 0.8011 (mm-30) REVERT: A 1002 GLN cc_start: 0.8579 (tt0) cc_final: 0.8297 (tp40) REVERT: A 1041 ASP cc_start: 0.8382 (t0) cc_final: 0.8050 (t0) REVERT: B 29 THR cc_start: 0.8254 (m) cc_final: 0.8019 (m) REVERT: B 173 GLN cc_start: 0.6384 (OUTLIER) cc_final: 0.5972 (tm130) REVERT: B 221 SER cc_start: 0.9049 (m) cc_final: 0.8637 (p) REVERT: B 224 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 237 ARG cc_start: 0.8611 (mtm180) cc_final: 0.8274 (mtm180) REVERT: B 278 LYS cc_start: 0.9031 (ttpt) cc_final: 0.8606 (ttpt) REVERT: B 304 LYS cc_start: 0.9030 (mptt) cc_final: 0.8803 (mmtp) REVERT: B 326 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8165 (pt) REVERT: B 338 PHE cc_start: 0.9043 (m-80) cc_final: 0.8757 (m-80) REVERT: B 340 GLU cc_start: 0.8302 (pm20) cc_final: 0.7901 (pm20) REVERT: B 440 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8319 (ttpt) REVERT: B 498 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.7294 (mmm-85) REVERT: B 574 ASP cc_start: 0.8295 (t0) cc_final: 0.8009 (t0) REVERT: B 776 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8105 (ttpp) REVERT: B 780 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7821 (mt-10) REVERT: B 816 SER cc_start: 0.8247 (p) cc_final: 0.7981 (t) REVERT: B 825 LYS cc_start: 0.8982 (mtpp) cc_final: 0.8559 (mtmm) REVERT: B 921 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8386 (tppt) REVERT: B 949 GLN cc_start: 0.8585 (tp40) cc_final: 0.8247 (mm-40) REVERT: B 950 ASP cc_start: 0.8317 (t0) cc_final: 0.8032 (t0) REVERT: B 979 ASP cc_start: 0.7811 (t70) cc_final: 0.7534 (t0) REVERT: B 983 ARG cc_start: 0.8449 (mtm110) cc_final: 0.8138 (ttp-110) REVERT: B 995 ARG cc_start: 0.8591 (mtp85) cc_final: 0.8211 (ptm160) REVERT: B 1019 ARG cc_start: 0.8170 (ttp80) cc_final: 0.7853 (ttp80) REVERT: B 1123 SER cc_start: 0.8950 (m) cc_final: 0.8544 (p) REVERT: C 64 TRP cc_start: 0.8638 (t60) cc_final: 0.8400 (t60) REVERT: C 95 ILE cc_start: 0.8405 (mt) cc_final: 0.7993 (tp) REVERT: C 99 ASN cc_start: 0.8054 (t0) cc_final: 0.7623 (t0) REVERT: C 102 ARG cc_start: 0.7063 (mmm-85) cc_final: 0.6579 (mmm-85) REVERT: C 189 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7855 (mt-10) REVERT: C 239 GLN cc_start: 0.8441 (tt0) cc_final: 0.8098 (tt0) REVERT: C 269 TYR cc_start: 0.8445 (m-80) cc_final: 0.8226 (m-80) REVERT: C 281 GLU cc_start: 0.7951 (pm20) cc_final: 0.7434 (pm20) REVERT: C 305 SER cc_start: 0.9159 (t) cc_final: 0.8795 (p) REVERT: C 324 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7926 (mp0) REVERT: C 518 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7545 (mp) REVERT: C 537 LYS cc_start: 0.8526 (ptmm) cc_final: 0.8149 (ptmm) REVERT: C 549 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8242 (m) REVERT: C 558 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8710 (ptpp) REVERT: C 619 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.4971 (pm20) REVERT: C 690 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7927 (mm110) REVERT: C 726 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8963 (mm) REVERT: C 737 ASP cc_start: 0.8317 (t0) cc_final: 0.8099 (t0) REVERT: C 773 GLU cc_start: 0.8729 (tp30) cc_final: 0.8427 (tt0) REVERT: C 790 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8075 (mtmm) REVERT: C 804 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8170 (mm-40) REVERT: C 868 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7314 (tm-30) REVERT: C 872 GLN cc_start: 0.8516 (mt0) cc_final: 0.8223 (mt0) REVERT: C 976 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8151 (m) REVERT: C 995 ARG cc_start: 0.8309 (mtm110) cc_final: 0.8040 (ttp-110) REVERT: C 1002 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7852 (tm-30) REVERT: C 1091 ARG cc_start: 0.8797 (ttm-80) cc_final: 0.8472 (ttm170) REVERT: C 1101 HIS cc_start: 0.8571 (m90) cc_final: 0.8216 (m-70) REVERT: D 34 MET cc_start: 0.6033 (ptp) cc_final: 0.5465 (ptp) REVERT: D 83 MET cc_start: 0.7548 (ptm) cc_final: 0.7174 (pmm) REVERT: E 33 GLU cc_start: 0.7490 (tm-30) cc_final: 0.6904 (tm-30) REVERT: E 37 VAL cc_start: 0.8801 (m) cc_final: 0.8380 (p) REVERT: E 82 MET cc_start: 0.7077 (ptm) cc_final: 0.6758 (ptm) REVERT: E 92 MET cc_start: 0.7511 (mtm) cc_final: 0.6952 (mtm) REVERT: E 94 TYR cc_start: 0.7572 (m-80) cc_final: 0.7061 (m-80) REVERT: F 112 THR cc_start: 0.4707 (OUTLIER) cc_final: 0.4477 (p) REVERT: H 34 MET cc_start: 0.8219 (ptp) cc_final: 0.7767 (ptp) REVERT: H 59 TYR cc_start: 0.7570 (m-80) cc_final: 0.7171 (m-80) REVERT: H 60 TYR cc_start: 0.7935 (m-80) cc_final: 0.7162 (m-80) REVERT: H 77 ASN cc_start: 0.6643 (t0) cc_final: 0.6200 (t0) REVERT: H 83 MET cc_start: 0.7741 (ptm) cc_final: 0.7269 (ptm) outliers start: 115 outliers final: 85 residues processed: 593 average time/residue: 0.1927 time to fit residues: 178.8467 Evaluate side-chains 589 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 493 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 99 TRP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 251 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 283 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 160 optimal weight: 0.1980 chunk 20 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 762 GLN A 935 GLN B 239 GLN B 955 ASN B 957 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** 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 = 0.4099 r_free = 0.4099 target = 0.160288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118757 restraints weight = 48253.273| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.61 r_work: 0.3346 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 29907 Z= 0.253 Angle : 0.691 14.299 40787 Z= 0.347 Chirality : 0.048 0.334 4656 Planarity : 0.005 0.058 5213 Dihedral : 5.792 89.732 4627 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.49 % Allowed : 16.81 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.14), residues: 3639 helix: 1.23 (0.21), residues: 664 sheet: -0.90 (0.16), residues: 941 loop : -1.86 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.025 0.002 TYR A 265 PHE 0.028 0.002 PHE C 133 TRP 0.055 0.002 TRP B 64 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00598 (29833) covalent geometry : angle 0.67817 (40611) SS BOND : bond 0.00566 ( 46) SS BOND : angle 2.06470 ( 92) hydrogen bonds : bond 0.04157 ( 910) hydrogen bonds : angle 5.20633 ( 2478) link_NAG-ASN : bond 0.00351 ( 28) link_NAG-ASN : angle 2.23684 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 517 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8399 (m-40) cc_final: 0.7025 (t0) REVERT: A 102 ARG cc_start: 0.8525 (ttm170) cc_final: 0.7535 (ptp-110) REVERT: A 116 SER cc_start: 0.8431 (m) cc_final: 0.8004 (t) REVERT: A 129 LYS cc_start: 0.8368 (mttm) cc_final: 0.8047 (mtmm) REVERT: A 164 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7539 (m-40) REVERT: A 175 PHE cc_start: 0.6627 (OUTLIER) cc_final: 0.6094 (p90) REVERT: A 188 ARG cc_start: 0.8564 (mtt-85) cc_final: 0.8168 (mpt-90) REVERT: A 206 THR cc_start: 0.8550 (p) cc_final: 0.8319 (p) REVERT: A 546 LEU cc_start: 0.8881 (pp) cc_final: 0.8679 (pp) REVERT: A 571 ASP cc_start: 0.7714 (t0) cc_final: 0.7418 (t70) REVERT: A 578 ASP cc_start: 0.8307 (t0) cc_final: 0.8069 (t0) REVERT: A 702 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7360 (mm-30) REVERT: A 745 ASP cc_start: 0.6736 (t0) cc_final: 0.6332 (t70) REVERT: A 751 ASN cc_start: 0.8574 (m-40) cc_final: 0.8326 (m-40) REVERT: A 776 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8259 (ttpp) REVERT: A 790 LYS cc_start: 0.8746 (mmmm) cc_final: 0.8440 (mmmm) REVERT: A 808 ASP cc_start: 0.8228 (t0) cc_final: 0.7634 (t0) REVERT: A 954 HIS cc_start: 0.8152 (m-70) cc_final: 0.7771 (m-70) REVERT: A 964 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8618 (mmmm) REVERT: A 988 GLU cc_start: 0.8770 (tp30) cc_final: 0.8405 (tp30) REVERT: A 1002 GLN cc_start: 0.8596 (tt0) cc_final: 0.8339 (tp40) REVERT: A 1019 ARG cc_start: 0.8052 (ttm110) cc_final: 0.7722 (ttm110) REVERT: A 1041 ASP cc_start: 0.8354 (t0) cc_final: 0.8043 (t0) REVERT: B 221 SER cc_start: 0.9081 (m) cc_final: 0.8703 (p) REVERT: B 224 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7587 (mm-30) REVERT: B 237 ARG cc_start: 0.8563 (mtm180) cc_final: 0.8275 (mtm110) REVERT: B 278 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8592 (ttpt) REVERT: B 304 LYS cc_start: 0.9055 (mptt) cc_final: 0.8834 (mmtp) REVERT: B 326 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8208 (pt) REVERT: B 338 PHE cc_start: 0.9020 (m-80) cc_final: 0.8765 (m-80) REVERT: B 380 TYR cc_start: 0.8887 (m-80) cc_final: 0.8670 (m-80) REVERT: B 440 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8276 (ttpt) REVERT: B 574 ASP cc_start: 0.8335 (t0) cc_final: 0.8035 (t0) REVERT: B 764 LYS cc_start: 0.8275 (tmmt) cc_final: 0.8042 (tmmt) REVERT: B 776 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8157 (ttpp) REVERT: B 780 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7844 (mt-10) REVERT: B 816 SER cc_start: 0.8254 (p) cc_final: 0.8010 (t) REVERT: B 825 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8568 (mtmm) REVERT: B 921 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8418 (tppt) REVERT: B 949 GLN cc_start: 0.8631 (tp40) cc_final: 0.8296 (mm-40) REVERT: B 950 ASP cc_start: 0.8376 (t0) cc_final: 0.8094 (t0) REVERT: B 995 ARG cc_start: 0.8560 (mtp85) cc_final: 0.8205 (ptm160) REVERT: B 1123 SER cc_start: 0.8943 (m) cc_final: 0.8502 (p) REVERT: C 95 ILE cc_start: 0.8453 (mt) cc_final: 0.7916 (tt) REVERT: C 99 ASN cc_start: 0.8076 (t0) cc_final: 0.7627 (t0) REVERT: C 102 ARG cc_start: 0.7106 (mmm-85) cc_final: 0.6634 (mmm-85) REVERT: C 170 TYR cc_start: 0.7530 (t80) cc_final: 0.7288 (t80) REVERT: C 239 GLN cc_start: 0.8422 (tt0) cc_final: 0.8105 (tt0) REVERT: C 269 TYR cc_start: 0.8426 (m-80) cc_final: 0.8217 (m-80) REVERT: C 281 GLU cc_start: 0.7912 (pm20) cc_final: 0.7384 (pm20) REVERT: C 324 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7906 (mp0) REVERT: C 518 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7663 (mp) REVERT: C 537 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8232 (ptmm) REVERT: C 549 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8298 (m) REVERT: C 558 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8650 (ptpp) REVERT: C 564 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8271 (mm110) REVERT: C 619 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.4783 (pm20) REVERT: C 690 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7859 (mm-40) REVERT: C 726 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8973 (mp) REVERT: C 773 GLU cc_start: 0.8742 (tp30) cc_final: 0.8410 (tt0) REVERT: C 790 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8127 (mtmm) REVERT: C 868 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7414 (tm-30) REVERT: C 872 GLN cc_start: 0.8541 (mt0) cc_final: 0.8278 (mt0) REVERT: C 976 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8282 (m) REVERT: C 995 ARG cc_start: 0.8303 (mtm110) cc_final: 0.7997 (mtp-110) REVERT: C 1002 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7869 (tm-30) REVERT: C 1091 ARG cc_start: 0.8811 (ttm-80) cc_final: 0.8489 (ttm170) REVERT: C 1101 HIS cc_start: 0.8592 (m90) cc_final: 0.8218 (m-70) REVERT: D 34 MET cc_start: 0.6040 (ptp) cc_final: 0.5484 (ptp) REVERT: D 83 MET cc_start: 0.7546 (ptm) cc_final: 0.7187 (pmm) REVERT: E 34 MET cc_start: 0.7945 (mmm) cc_final: 0.7299 (mpp) REVERT: E 35 SER cc_start: 0.8166 (t) cc_final: 0.7498 (m) REVERT: E 37 VAL cc_start: 0.8819 (m) cc_final: 0.8355 (p) REVERT: E 82 MET cc_start: 0.7085 (ptm) cc_final: 0.6808 (ptm) REVERT: E 92 MET cc_start: 0.7461 (mtm) cc_final: 0.6890 (mtm) REVERT: E 94 TYR cc_start: 0.7644 (m-80) cc_final: 0.7101 (m-80) REVERT: F 112 THR cc_start: 0.4615 (OUTLIER) cc_final: 0.4388 (p) REVERT: G 77 MET cc_start: 0.7510 (tpp) cc_final: 0.6730 (tmm) REVERT: H 34 MET cc_start: 0.8253 (ptp) cc_final: 0.7801 (ptp) REVERT: H 59 TYR cc_start: 0.7627 (m-80) cc_final: 0.7152 (m-80) REVERT: H 77 ASN cc_start: 0.6711 (t0) cc_final: 0.6333 (t0) REVERT: H 83 MET cc_start: 0.7708 (ptm) cc_final: 0.7238 (ptm) outliers start: 111 outliers final: 91 residues processed: 594 average time/residue: 0.1948 time to fit residues: 180.7608 Evaluate side-chains 612 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 511 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 269 optimal weight: 0.4980 chunk 219 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 198 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 202 optimal weight: 0.6980 chunk 236 optimal weight: 5.9990 chunk 342 optimal weight: 50.0000 chunk 290 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 227 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN B 30 ASN B 955 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** 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 = 0.4130 r_free = 0.4130 target = 0.162827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121649 restraints weight = 48098.873| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.62 r_work: 0.3383 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29907 Z= 0.138 Angle : 0.637 13.682 40787 Z= 0.318 Chirality : 0.045 0.247 4656 Planarity : 0.004 0.058 5213 Dihedral : 5.512 91.093 4622 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.05 % Allowed : 17.47 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3639 helix: 1.42 (0.21), residues: 670 sheet: -0.91 (0.16), residues: 945 loop : -1.71 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.020 0.001 TYR A 265 PHE 0.030 0.001 PHE C 133 TRP 0.043 0.002 TRP A 353 HIS 0.005 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00327 (29833) covalent geometry : angle 0.62624 (40611) SS BOND : bond 0.00456 ( 46) SS BOND : angle 1.76258 ( 92) hydrogen bonds : bond 0.03465 ( 910) hydrogen bonds : angle 5.05495 ( 2478) link_NAG-ASN : bond 0.00229 ( 28) link_NAG-ASN : angle 1.97620 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 502 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7965 (OUTLIER) cc_final: 0.7697 (p) REVERT: A 99 ASN cc_start: 0.8380 (m-40) cc_final: 0.7266 (t0) REVERT: A 116 SER cc_start: 0.8409 (m) cc_final: 0.8069 (t) REVERT: A 129 LYS cc_start: 0.8228 (mttm) cc_final: 0.7933 (mtmm) REVERT: A 164 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7479 (m-40) REVERT: A 175 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.6012 (p90) REVERT: A 188 ARG cc_start: 0.8625 (mtt-85) cc_final: 0.8258 (mpt-90) REVERT: A 206 THR cc_start: 0.8441 (p) cc_final: 0.8227 (p) REVERT: A 281 GLU cc_start: 0.7920 (pm20) cc_final: 0.7607 (pm20) REVERT: A 546 LEU cc_start: 0.8728 (pp) cc_final: 0.8520 (pp) REVERT: A 571 ASP cc_start: 0.7665 (t0) cc_final: 0.7362 (t70) REVERT: A 578 ASP cc_start: 0.8224 (t0) cc_final: 0.8002 (t0) REVERT: A 702 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7284 (mm-30) REVERT: A 745 ASP cc_start: 0.6591 (t0) cc_final: 0.6218 (t70) REVERT: A 773 GLU cc_start: 0.7972 (tt0) cc_final: 0.7681 (tt0) REVERT: A 790 LYS cc_start: 0.8735 (mmmm) cc_final: 0.8423 (mmmm) REVERT: A 808 ASP cc_start: 0.8197 (t0) cc_final: 0.7602 (t0) REVERT: A 954 HIS cc_start: 0.8049 (m-70) cc_final: 0.7687 (m-70) REVERT: A 964 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8622 (mmmm) REVERT: A 988 GLU cc_start: 0.8744 (tp30) cc_final: 0.8429 (tp30) REVERT: A 1002 GLN cc_start: 0.8560 (tt0) cc_final: 0.8300 (tp40) REVERT: A 1019 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7596 (ttm110) REVERT: A 1041 ASP cc_start: 0.8358 (t0) cc_final: 0.8044 (t0) REVERT: B 97 LYS cc_start: 0.8578 (tppp) cc_final: 0.8205 (tppt) REVERT: B 221 SER cc_start: 0.8983 (m) cc_final: 0.8628 (p) REVERT: B 237 ARG cc_start: 0.8565 (mtm180) cc_final: 0.8205 (mtm110) REVERT: B 278 LYS cc_start: 0.9038 (ttpt) cc_final: 0.8549 (ttpt) REVERT: B 304 LYS cc_start: 0.9034 (mptt) cc_final: 0.8811 (mmtp) REVERT: B 338 PHE cc_start: 0.9026 (m-80) cc_final: 0.8802 (m-80) REVERT: B 361 CYS cc_start: 0.6887 (m) cc_final: 0.6526 (m) REVERT: B 380 TYR cc_start: 0.8866 (m-80) cc_final: 0.8661 (m-80) REVERT: B 440 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8231 (ttpt) REVERT: B 574 ASP cc_start: 0.8305 (t0) cc_final: 0.8009 (t0) REVERT: B 764 LYS cc_start: 0.8163 (tmmt) cc_final: 0.7944 (tmmt) REVERT: B 776 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8100 (ttpp) REVERT: B 780 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7767 (mt-10) REVERT: B 816 SER cc_start: 0.8176 (p) cc_final: 0.7926 (t) REVERT: B 825 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8543 (mtmm) REVERT: B 949 GLN cc_start: 0.8557 (tp40) cc_final: 0.8207 (mm-40) REVERT: B 950 ASP cc_start: 0.8308 (t0) cc_final: 0.8041 (t0) REVERT: B 995 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8186 (ptm160) REVERT: C 95 ILE cc_start: 0.8293 (mt) cc_final: 0.7845 (tp) REVERT: C 99 ASN cc_start: 0.7916 (t0) cc_final: 0.7462 (t0) REVERT: C 102 ARG cc_start: 0.7011 (mmm-85) cc_final: 0.6497 (mmm-85) REVERT: C 170 TYR cc_start: 0.7514 (t80) cc_final: 0.7292 (t80) REVERT: C 239 GLN cc_start: 0.8436 (tt0) cc_final: 0.8093 (tt0) REVERT: C 269 TYR cc_start: 0.8341 (m-80) cc_final: 0.7981 (m-80) REVERT: C 281 GLU cc_start: 0.7935 (pm20) cc_final: 0.7391 (pm20) REVERT: C 324 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8012 (mm-30) REVERT: C 518 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7693 (mp) REVERT: C 537 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8339 (ptmm) REVERT: C 558 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8713 (ptpp) REVERT: C 564 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8228 (mm-40) REVERT: C 619 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.4725 (pm20) REVERT: C 690 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7838 (mm110) REVERT: C 710 ASN cc_start: 0.8532 (m-40) cc_final: 0.8186 (m110) REVERT: C 737 ASP cc_start: 0.8334 (t0) cc_final: 0.8105 (t0) REVERT: C 773 GLU cc_start: 0.8619 (tp30) cc_final: 0.8265 (tt0) REVERT: C 790 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8092 (mtmm) REVERT: C 804 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8225 (mm-40) REVERT: C 868 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7377 (tm-30) REVERT: C 869 MET cc_start: 0.8812 (mtt) cc_final: 0.8409 (mtm) REVERT: C 872 GLN cc_start: 0.8472 (mt0) cc_final: 0.8263 (mt0) REVERT: C 970 PHE cc_start: 0.8299 (m-80) cc_final: 0.7954 (m-80) REVERT: C 976 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8115 (m) REVERT: C 995 ARG cc_start: 0.8197 (mtm110) cc_final: 0.7489 (ttp80) REVERT: C 1002 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7780 (tm-30) REVERT: C 1091 ARG cc_start: 0.8807 (ttm-80) cc_final: 0.8498 (ttm170) REVERT: C 1111 GLU cc_start: 0.8708 (tt0) cc_final: 0.8444 (tt0) REVERT: D 34 MET cc_start: 0.6064 (ptp) cc_final: 0.5489 (ptp) REVERT: D 83 MET cc_start: 0.7564 (ptm) cc_final: 0.7199 (pmm) REVERT: E 34 MET cc_start: 0.7884 (mmm) cc_final: 0.7385 (mpp) REVERT: E 35 SER cc_start: 0.8021 (t) cc_final: 0.7404 (p) REVERT: E 37 VAL cc_start: 0.8763 (m) cc_final: 0.8296 (p) REVERT: E 82 MET cc_start: 0.7037 (ptm) cc_final: 0.6719 (ptm) REVERT: E 92 MET cc_start: 0.7410 (mtm) cc_final: 0.6761 (mtm) REVERT: E 94 TYR cc_start: 0.7568 (m-80) cc_final: 0.6952 (m-80) REVERT: F 112 THR cc_start: 0.4473 (OUTLIER) cc_final: 0.4248 (p) REVERT: G 77 MET cc_start: 0.7585 (tpp) cc_final: 0.6885 (ppp) REVERT: H 34 MET cc_start: 0.8285 (ptp) cc_final: 0.7817 (ptp) REVERT: H 59 TYR cc_start: 0.7515 (m-80) cc_final: 0.7206 (m-80) REVERT: H 60 TYR cc_start: 0.7689 (m-80) cc_final: 0.7014 (m-80) REVERT: H 77 ASN cc_start: 0.6753 (t0) cc_final: 0.6232 (t0) REVERT: H 83 MET cc_start: 0.7753 (ptm) cc_final: 0.7268 (ptm) outliers start: 97 outliers final: 84 residues processed: 572 average time/residue: 0.1944 time to fit residues: 173.8692 Evaluate side-chains 586 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 494 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 287 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 331 optimal weight: 1.9990 chunk 360 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 319 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 362 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 955 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** F 73 ASN ** 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 = 0.4103 r_free = 0.4103 target = 0.160613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119469 restraints weight = 48720.814| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.56 r_work: 0.3338 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 29907 Z= 0.258 Angle : 0.701 14.019 40787 Z= 0.351 Chirality : 0.048 0.283 4656 Planarity : 0.005 0.057 5213 Dihedral : 5.727 88.962 4621 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.15 % Allowed : 17.66 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.14), residues: 3639 helix: 1.30 (0.21), residues: 665 sheet: -0.86 (0.16), residues: 927 loop : -1.78 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 983 TYR 0.024 0.002 TYR A 265 PHE 0.032 0.002 PHE C 133 TRP 0.051 0.002 TRP B 64 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00610 (29833) covalent geometry : angle 0.68813 (40611) SS BOND : bond 0.00554 ( 46) SS BOND : angle 2.12217 ( 92) hydrogen bonds : bond 0.04190 ( 910) hydrogen bonds : angle 5.17115 ( 2478) link_NAG-ASN : bond 0.00344 ( 28) link_NAG-ASN : angle 2.19609 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10407.41 seconds wall clock time: 177 minutes 38.48 seconds (10658.48 seconds total)