Starting phenix.real_space_refine on Wed Jun 25 05:01:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whk_32503/06_2025/7whk_32503.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whk_32503/06_2025/7whk_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7whk_32503/06_2025/7whk_32503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whk_32503/06_2025/7whk_32503.map" model { file = "/net/cci-nas-00/data/ceres_data/7whk_32503/06_2025/7whk_32503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whk_32503/06_2025/7whk_32503.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.85s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: 16.91, per 1000 atoms: 0.58 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: 6.90 Conformation dependent library (CDL) restraints added in 3.7 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: 4.32 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: 13.10 Time building geometry restraints manager: 8.24 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 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 26 through 827 or resid 848 through 1147 or resid 1301 thr \ ough 1308)) selection = (chain 'C' and (resid 26 through 177 or resid 182 through 244 or resid 262 throu \ gh 827 or resid 848 through 1147 or resid 1301 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.190 Check model and map are aligned: 0.230 Set scattering table: 0.260 Process input model: 67.260 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.190 ------------------------------------------------------------------------------- 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 : 7.01 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (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 TRP 0.007 0.001 TRP A 886 HIS 0.002 0.000 HIS A 66 PHE 0.018 0.001 PHE A 238 TYR 0.022 0.001 TYR A 265 ARG 0.003 0.000 ARG C 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00846 ( 28) link_NAG-ASN : angle 4.21869 ( 84) hydrogen bonds : bond 0.17121 ( 910) hydrogen bonds : angle 7.30805 ( 2478) SS BOND : bond 0.00316 ( 46) SS BOND : angle 0.72077 ( 92) covalent geometry : bond 0.00397 (29833) covalent geometry : angle 0.69758 (40611) *********************** 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 : 3.045 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7918 (mtt180) REVERT: A 83 VAL cc_start: 0.7382 (OUTLIER) cc_final: 0.7161 (t) REVERT: A 98 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.8068 (p) REVERT: A 99 ASN cc_start: 0.8104 (m-40) cc_final: 0.7191 (t0) REVERT: A 100 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7827 (tp) REVERT: A 115 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6172 (tp40) REVERT: A 116 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7203 (p) REVERT: A 126 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7383 (m) REVERT: A 127 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.7943 (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: 0.6164 (mp0) REVERT: A 135 PHE cc_start: 0.5872 (OUTLIER) cc_final: 0.5363 (m-10) REVERT: A 138 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7303 (t0) REVERT: A 157 PHE cc_start: 0.5886 (OUTLIER) cc_final: 0.5492 (p90) REVERT: A 164 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7201 (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: 0.7798 (mtpt) REVERT: A 206 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8198 (p) REVERT: A 238 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7592 (p90) REVERT: A 287 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6991 (p0) REVERT: A 293 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6966 (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: 0.6944 (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: 0.7201 (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: 0.8035 (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: 0.8116 (mtmm) REVERT: A 976 VAL cc_start: 0.8709 (t) cc_final: 0.8486 (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: 0.7513 (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: 0.6596 (m) REVERT: B 378 LYS cc_start: 0.6602 (OUTLIER) cc_final: 0.6235 (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: 0.7788 (p) REVERT: B 658 ASN cc_start: 0.8306 (p0) cc_final: 0.7624 (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: 0.8128 (t) REVERT: B 935 GLN cc_start: 0.8308 (tt0) cc_final: 0.7832 (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: 0.6288 (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: 0.6672 (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: 0.5843 (pp20) REVERT: C 239 GLN cc_start: 0.7184 (tt0) cc_final: 0.6826 (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: -0.1463 (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: 0.8264 (mm) REVERT: C 619 GLU cc_start: 0.5128 (OUTLIER) cc_final: 0.4440 (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: 0.8498 (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: 0.8007 (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: 0.6782 (tm-30) REVERT: D 34 MET cc_start: 0.5684 (ptp) cc_final: 0.5262 (ptp) REVERT: D 83 MET cc_start: 0.7560 (ptm) cc_final: 0.7139 (pmm) REVERT: E 82 MET cc_start: 0.5929 (ptm) cc_final: 0.5668 (ptm) REVERT: E 92 MET cc_start: 0.6844 (mtm) cc_final: 0.6193 (mtm) REVERT: E 94 TYR cc_start: 0.6954 (m-80) cc_final: 0.6580 (m-80) REVERT: F 69 ILE cc_start: -0.0114 (OUTLIER) cc_final: -0.0346 (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: 49 residues processed: 830 average time/residue: 0.4260 time to fit residues: 550.2844 Evaluate side-chains 612 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 531 time to evaluate : 3.168 ------------------------------------------------------------------------------- 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 100 ILE 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 229 LEU Chi-restraints excluded: chain A residue 237 ARG 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 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 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 308 optimal weight: 0.8980 chunk 276 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 331 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 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 ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 205 HIS 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN 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: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.165791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.124687 restraints weight = 49151.030| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.62 r_work: 0.3398 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 29907 Z= 0.208 Angle : 0.650 9.940 40787 Z= 0.328 Chirality : 0.046 0.278 4656 Planarity : 0.005 0.062 5213 Dihedral : 7.316 92.821 4725 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.28 % Allowed : 12.18 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.13), residues: 3639 helix: 0.78 (0.21), residues: 632 sheet: -1.64 (0.16), residues: 907 loop : -2.72 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 99 HIS 0.006 0.001 HIS A1064 PHE 0.021 0.002 PHE A 515 TYR 0.022 0.002 TYR A 265 ARG 0.009 0.001 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 28) link_NAG-ASN : angle 2.62289 ( 84) hydrogen bonds : bond 0.04047 ( 910) hydrogen bonds : angle 5.42199 ( 2478) SS BOND : bond 0.00680 ( 46) SS BOND : angle 1.99030 ( 92) covalent geometry : bond 0.00477 (29833) covalent geometry : angle 0.63305 (40611) *********************** 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 684 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 548 time to evaluate : 3.079 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 99 ASN cc_start: 0.8419 (m-40) cc_final: 0.7367 (t0) REVERT: A 116 SER cc_start: 0.8423 (m) cc_final: 0.8081 (p) REVERT: A 126 VAL cc_start: 0.7868 (OUTLIER) cc_final: 0.7603 (m) REVERT: A 127 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8296 (p) REVERT: A 129 LYS cc_start: 0.8292 (mttm) cc_final: 0.7764 (mtmm) REVERT: A 132 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6399 (mp0) REVERT: A 138 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.7041 (t70) REVERT: A 157 PHE cc_start: 0.5545 (OUTLIER) cc_final: 0.4757 (p90) REVERT: A 164 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7772 (m-40) REVERT: A 171 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8457 (t) REVERT: A 175 PHE cc_start: 0.6489 (OUTLIER) cc_final: 0.5846 (p90) REVERT: A 206 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8222 (p) REVERT: A 220 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: A 237 ARG cc_start: 0.8500 (mtp180) cc_final: 0.8139 (mtm110) REVERT: A 280 ASN cc_start: 0.8055 (t0) cc_final: 0.7682 (t0) REVERT: A 314 GLN cc_start: 0.8750 (tt0) cc_final: 0.8531 (tp40) REVERT: A 362 VAL cc_start: 0.8916 (t) cc_final: 0.8445 (p) REVERT: A 364 ASP cc_start: 0.8098 (t0) cc_final: 0.7789 (t0) REVERT: A 386 LYS cc_start: 0.8299 (mtmm) cc_final: 0.8081 (mtmm) REVERT: A 537 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8299 (ttpp) REVERT: A 546 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8045 (pp) REVERT: A 578 ASP cc_start: 0.7983 (t0) cc_final: 0.7596 (t0) REVERT: A 643 PHE cc_start: 0.8411 (t80) cc_final: 0.8162 (t80) REVERT: A 750 SER cc_start: 0.8641 (m) cc_final: 0.8367 (m) REVERT: A 756 TYR cc_start: 0.7771 (m-80) cc_final: 0.7515 (m-80) REVERT: A 773 GLU cc_start: 0.7806 (tt0) cc_final: 0.7546 (tt0) REVERT: A 780 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8104 (mm-30) REVERT: A 790 LYS cc_start: 0.8755 (mmmm) cc_final: 0.8308 (mmmt) REVERT: A 796 TYR cc_start: 0.8675 (t80) cc_final: 0.8444 (t80) REVERT: A 907 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8723 (m-40) REVERT: A 933 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8112 (mtmm) REVERT: A 988 GLU cc_start: 0.8392 (tp30) cc_final: 0.7896 (tp30) REVERT: A 1019 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7483 (ttm110) REVERT: B 52 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7734 (tm-30) REVERT: B 64 TRP cc_start: 0.8334 (t60) cc_final: 0.8103 (t60) REVERT: B 97 LYS cc_start: 0.8290 (tppt) cc_final: 0.7918 (tppt) REVERT: B 129 LYS cc_start: 0.8546 (ptpt) cc_final: 0.8310 (ptpt) REVERT: B 173 GLN cc_start: 0.6662 (OUTLIER) cc_final: 0.6161 (tm130) REVERT: B 278 LYS cc_start: 0.9014 (ttpt) cc_final: 0.8678 (ttpt) REVERT: B 764 LYS cc_start: 0.8231 (mmmt) cc_final: 0.7791 (mmmm) REVERT: B 773 GLU cc_start: 0.8041 (tt0) cc_final: 0.7812 (tt0) REVERT: B 776 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8296 (ttmm) REVERT: B 796 TYR cc_start: 0.8388 (t80) cc_final: 0.7885 (t80) REVERT: B 804 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8646 (mm-40) REVERT: B 816 SER cc_start: 0.8131 (p) cc_final: 0.7828 (t) REVERT: B 825 LYS cc_start: 0.8878 (mtpp) cc_final: 0.8419 (mtmm) REVERT: B 949 GLN cc_start: 0.8505 (tp40) cc_final: 0.8108 (mm-40) REVERT: B 950 ASP cc_start: 0.8258 (t0) cc_final: 0.7939 (t0) REVERT: B 973 ILE cc_start: 0.8928 (pt) cc_final: 0.8654 (mt) REVERT: B 979 ASP cc_start: 0.7772 (t70) cc_final: 0.7354 (t0) REVERT: B 983 ARG cc_start: 0.8368 (mtm110) cc_final: 0.7927 (ttp-110) REVERT: B 1123 SER cc_start: 0.8912 (m) cc_final: 0.8617 (p) REVERT: C 96 GLU cc_start: 0.7507 (pp20) cc_final: 0.7258 (pp20) REVERT: C 102 ARG cc_start: 0.6818 (mmm-85) cc_final: 0.6502 (mmm-85) REVERT: C 198 TYR cc_start: 0.8158 (m-80) cc_final: 0.7919 (m-80) REVERT: C 231 ILE cc_start: 0.6669 (tp) cc_final: 0.6294 (tt) REVERT: C 239 GLN cc_start: 0.8521 (tt0) cc_final: 0.8296 (tt0) REVERT: C 305 SER cc_start: 0.9146 (t) cc_final: 0.8848 (p) REVERT: C 324 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7843 (mm-30) REVERT: C 406 GLU cc_start: -0.1404 (OUTLIER) cc_final: -0.1728 (tp30) REVERT: C 518 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7403 (mp) REVERT: C 537 LYS cc_start: 0.8314 (ttpp) cc_final: 0.7904 (tttp) REVERT: C 541 PHE cc_start: 0.8120 (p90) cc_final: 0.7588 (p90) REVERT: C 549 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8155 (m) REVERT: C 555 SER cc_start: 0.8353 (m) cc_final: 0.7377 (p) REVERT: C 619 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.4850 (pm20) REVERT: C 690 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7741 (mm-40) REVERT: C 762 GLN cc_start: 0.8007 (mt0) cc_final: 0.7790 (mt0) REVERT: C 776 LYS cc_start: 0.8845 (ttpt) cc_final: 0.8639 (ttpp) REVERT: C 790 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8311 (mtmt) REVERT: C 811 LYS cc_start: 0.7697 (mppt) cc_final: 0.7458 (mtmt) REVERT: C 900 MET cc_start: 0.8727 (mtp) cc_final: 0.8235 (mtp) REVERT: C 945 LEU cc_start: 0.8807 (mm) cc_final: 0.8575 (mt) REVERT: C 964 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8413 (mtpp) REVERT: C 976 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8238 (m) REVERT: C 1002 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7850 (tm-30) REVERT: C 1111 GLU cc_start: 0.8730 (tt0) cc_final: 0.8496 (tt0) REVERT: D 34 MET cc_start: 0.5931 (ptp) cc_final: 0.5382 (ptp) REVERT: D 83 MET cc_start: 0.7670 (ptm) cc_final: 0.7194 (pmm) REVERT: E 35 SER cc_start: 0.7913 (t) cc_final: 0.7618 (m) REVERT: E 82 MET cc_start: 0.6894 (ptm) cc_final: 0.6567 (ptm) REVERT: E 92 MET cc_start: 0.7554 (mtm) cc_final: 0.6819 (mtm) REVERT: E 94 TYR cc_start: 0.7624 (m-80) cc_final: 0.7093 (m-80) REVERT: G 51 MET cc_start: 0.5227 (OUTLIER) cc_final: 0.4617 (tpt) REVERT: G 77 MET cc_start: 0.7822 (tpp) cc_final: 0.7522 (tpt) REVERT: H 77 ASN cc_start: 0.6876 (t0) cc_final: 0.6092 (t0) outliers start: 136 outliers final: 60 residues processed: 644 average time/residue: 0.4690 time to fit residues: 477.1107 Evaluate side-chains 586 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 507 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 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 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 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 511 VAL 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 934 ILE 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 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 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 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 169 GLU 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 780 GLU Chi-restraints excluded: chain C residue 976 VAL 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 202 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 274 optimal weight: 2.9990 chunk 311 optimal weight: 0.0170 chunk 230 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 335 optimal weight: 8.9990 chunk 151 optimal weight: 0.0980 chunk 173 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.5220 ------------------------------------------------------------------------------- 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 164 ASN A 186 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 804 GLN A 955 ASN A1010 GLN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN 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 = 0.4176 r_free = 0.4176 target = 0.166816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.125762 restraints weight = 49330.215| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.65 r_work: 0.3423 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 29907 Z= 0.120 Angle : 0.590 12.701 40787 Z= 0.294 Chirality : 0.044 0.317 4656 Planarity : 0.004 0.057 5213 Dihedral : 5.867 90.706 4651 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.27 % Allowed : 14.38 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 3639 helix: 1.23 (0.21), residues: 631 sheet: -1.40 (0.16), residues: 911 loop : -2.43 (0.12), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 353 HIS 0.003 0.001 HIS B1064 PHE 0.022 0.001 PHE B 32 TYR 0.025 0.001 TYR E 107 ARG 0.009 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 28) link_NAG-ASN : angle 2.39188 ( 84) hydrogen bonds : bond 0.03411 ( 910) hydrogen bonds : angle 5.11372 ( 2478) SS BOND : bond 0.00451 ( 46) SS BOND : angle 1.63785 ( 92) covalent geometry : bond 0.00282 (29833) covalent geometry : angle 0.57555 (40611) *********************** 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 612 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 508 time to evaluate : 2.996 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 99 ASN cc_start: 0.8322 (m-40) cc_final: 0.7748 (t0) REVERT: A 116 SER cc_start: 0.8374 (m) cc_final: 0.8026 (p) REVERT: A 132 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.5976 (pm20) REVERT: A 171 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8431 (t) REVERT: A 175 PHE cc_start: 0.6425 (OUTLIER) cc_final: 0.6134 (p90) REVERT: A 206 THR cc_start: 0.8535 (p) cc_final: 0.8311 (p) REVERT: A 220 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: A 281 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7152 (pp20) REVERT: A 362 VAL cc_start: 0.8937 (t) cc_final: 0.8404 (p) REVERT: A 364 ASP cc_start: 0.8020 (t0) cc_final: 0.7740 (t0) REVERT: A 386 LYS cc_start: 0.8307 (mtmm) cc_final: 0.8084 (mtmm) REVERT: A 396 TYR cc_start: 0.7626 (m-80) cc_final: 0.7372 (m-80) REVERT: A 537 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8294 (ttpp) REVERT: A 546 LEU cc_start: 0.8351 (pp) cc_final: 0.8033 (pp) REVERT: A 571 ASP cc_start: 0.6820 (t0) cc_final: 0.6606 (t70) REVERT: A 578 ASP cc_start: 0.8014 (t0) cc_final: 0.7700 (t0) REVERT: A 643 PHE cc_start: 0.8407 (t80) cc_final: 0.8129 (t80) REVERT: A 750 SER cc_start: 0.8669 (m) cc_final: 0.8390 (m) REVERT: A 773 GLU cc_start: 0.7701 (tt0) cc_final: 0.7456 (tt0) REVERT: A 790 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8382 (mmmt) REVERT: A 796 TYR cc_start: 0.8652 (t80) cc_final: 0.8422 (t80) REVERT: A 933 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8110 (mtmm) REVERT: A 935 GLN cc_start: 0.8197 (tt0) cc_final: 0.7949 (tt0) REVERT: A 988 GLU cc_start: 0.8521 (tp30) cc_final: 0.8012 (tp30) REVERT: A 1019 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7477 (ttm170) REVERT: B 52 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7543 (tm-30) REVERT: B 64 TRP cc_start: 0.8247 (t60) cc_final: 0.8047 (t60) REVERT: B 97 LYS cc_start: 0.8299 (tppt) cc_final: 0.7903 (tppt) REVERT: B 129 LYS cc_start: 0.8591 (ptpt) cc_final: 0.8347 (ptpt) REVERT: B 170 TYR cc_start: 0.7212 (m-10) cc_final: 0.6986 (m-80) REVERT: B 173 GLN cc_start: 0.6453 (OUTLIER) cc_final: 0.5948 (tm130) REVERT: B 278 LYS cc_start: 0.9050 (ttpt) cc_final: 0.8681 (ttpt) REVERT: B 473 TYR cc_start: 0.8267 (t80) cc_final: 0.7936 (t80) REVERT: B 498 ARG cc_start: 0.7857 (mmm160) cc_final: 0.7095 (mmm160) REVERT: B 619 GLU cc_start: 0.7865 (pm20) cc_final: 0.7457 (pm20) REVERT: B 764 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7760 (mmmm) REVERT: B 776 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8275 (ttpp) REVERT: B 780 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7997 (mt-10) REVERT: B 804 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8678 (mm-40) REVERT: B 816 SER cc_start: 0.8074 (p) cc_final: 0.7848 (t) REVERT: B 949 GLN cc_start: 0.8509 (tp40) cc_final: 0.8149 (mm-40) REVERT: B 950 ASP cc_start: 0.8329 (t0) cc_final: 0.7977 (t0) REVERT: B 973 ILE cc_start: 0.8987 (pt) cc_final: 0.8754 (mt) REVERT: B 979 ASP cc_start: 0.7854 (t70) cc_final: 0.7330 (t0) REVERT: B 983 ARG cc_start: 0.8398 (mtm110) cc_final: 0.8023 (ttp-110) REVERT: B 1123 SER cc_start: 0.8946 (m) cc_final: 0.8614 (p) REVERT: C 41 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8518 (mtpt) REVERT: C 102 ARG cc_start: 0.6776 (mmm-85) cc_final: 0.6453 (mmm-85) REVERT: C 198 TYR cc_start: 0.8268 (m-80) cc_final: 0.8020 (m-80) REVERT: C 239 GLN cc_start: 0.8503 (tt0) cc_final: 0.8257 (tt0) REVERT: C 281 GLU cc_start: 0.7923 (pp20) cc_final: 0.7585 (pp20) REVERT: C 305 SER cc_start: 0.9125 (t) cc_final: 0.8823 (p) REVERT: C 314 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8193 (tm-30) REVERT: C 324 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7726 (mm-30) REVERT: C 518 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7434 (mp) REVERT: C 537 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7903 (tttp) REVERT: C 586 ASP cc_start: 0.8111 (m-30) cc_final: 0.7595 (m-30) REVERT: C 619 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.4947 (pm20) REVERT: C 690 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7905 (mm110) REVERT: C 762 GLN cc_start: 0.7954 (mt0) cc_final: 0.7748 (mt0) REVERT: C 773 GLU cc_start: 0.8409 (tt0) cc_final: 0.8146 (tt0) REVERT: C 776 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8641 (ttpp) REVERT: C 790 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8339 (mtmt) REVERT: C 804 GLN cc_start: 0.8789 (mm-40) cc_final: 0.7976 (mm-40) REVERT: C 945 LEU cc_start: 0.8778 (mm) cc_final: 0.8550 (mt) REVERT: C 964 LYS cc_start: 0.8756 (ttmm) cc_final: 0.8434 (mtpp) REVERT: C 976 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8259 (m) REVERT: C 1002 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7810 (tm-30) REVERT: C 1091 ARG cc_start: 0.8582 (ttm-80) cc_final: 0.8327 (ttm170) REVERT: C 1111 GLU cc_start: 0.8735 (tt0) cc_final: 0.8501 (tt0) REVERT: D 34 MET cc_start: 0.5943 (ptp) cc_final: 0.5375 (ptp) REVERT: D 83 MET cc_start: 0.7671 (ptm) cc_final: 0.7191 (pmm) REVERT: E 58 TYR cc_start: 0.8655 (t80) cc_final: 0.8161 (t80) REVERT: E 82 MET cc_start: 0.6889 (ptm) cc_final: 0.6534 (ptm) REVERT: E 92 MET cc_start: 0.7511 (mtm) cc_final: 0.6727 (mtm) REVERT: E 94 TYR cc_start: 0.7606 (m-80) cc_final: 0.7037 (m-80) REVERT: G 51 MET cc_start: 0.5363 (OUTLIER) cc_final: 0.4121 (tpt) REVERT: G 69 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6368 (tt) REVERT: G 77 MET cc_start: 0.7786 (tpp) cc_final: 0.7471 (tpt) REVERT: H 77 ASN cc_start: 0.6770 (t0) cc_final: 0.6087 (t0) REVERT: H 83 MET cc_start: 0.7859 (ptm) cc_final: 0.7612 (ptm) outliers start: 104 outliers final: 57 residues processed: 589 average time/residue: 0.4167 time to fit residues: 382.9717 Evaluate side-chains 549 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 480 time to evaluate : 3.016 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 186 ASN 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 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 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 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 210 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 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 955 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LYS 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 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE 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 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 1136 THR Chi-restraints excluded: chain C residue 1141 LEU 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 73 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 312 optimal weight: 0.9990 chunk 343 optimal weight: 20.0000 chunk 244 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 556 ASN A 755 GLN A 762 GLN A 901 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 907 ASN B1119 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.163357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121748 restraints weight = 49117.743| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.64 r_work: 0.3355 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 29907 Z= 0.201 Angle : 0.633 16.631 40787 Z= 0.315 Chirality : 0.046 0.275 4656 Planarity : 0.005 0.057 5213 Dihedral : 5.539 89.835 4635 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.06 % Allowed : 13.85 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.13), residues: 3639 helix: 1.27 (0.21), residues: 644 sheet: -1.18 (0.16), residues: 911 loop : -2.22 (0.12), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 64 HIS 0.005 0.001 HIS C1064 PHE 0.031 0.002 PHE A 168 TYR 0.027 0.001 TYR A 265 ARG 0.009 0.001 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 28) link_NAG-ASN : angle 2.46694 ( 84) hydrogen bonds : bond 0.03889 ( 910) hydrogen bonds : angle 5.11810 ( 2478) SS BOND : bond 0.00486 ( 46) SS BOND : angle 1.76346 ( 92) covalent geometry : bond 0.00472 (29833) covalent geometry : angle 0.61824 (40611) *********************** 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 640 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 511 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7874 (OUTLIER) cc_final: 0.7671 (t) REVERT: A 99 ASN cc_start: 0.8466 (m-40) cc_final: 0.7672 (t0) REVERT: A 100 ILE cc_start: 0.8662 (tp) cc_final: 0.8143 (tp) REVERT: A 102 ARG cc_start: 0.8326 (ttm170) cc_final: 0.7865 (ptm160) REVERT: A 116 SER cc_start: 0.8113 (m) cc_final: 0.7726 (p) REVERT: A 171 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8428 (t) REVERT: A 175 PHE cc_start: 0.6498 (OUTLIER) cc_final: 0.6068 (p90) REVERT: A 206 THR cc_start: 0.8603 (p) cc_final: 0.8360 (p) REVERT: A 220 PHE cc_start: 0.8434 (t80) cc_final: 0.8049 (m-80) REVERT: A 280 ASN cc_start: 0.8203 (t0) cc_final: 0.7561 (t0) REVERT: A 281 GLU cc_start: 0.7818 (pp20) cc_final: 0.7528 (pm20) REVERT: A 328 ARG cc_start: 0.8388 (tpp80) cc_final: 0.8160 (tpt-90) REVERT: A 364 ASP cc_start: 0.8072 (t0) cc_final: 0.7799 (t0) REVERT: A 386 LYS cc_start: 0.8309 (mtmm) cc_final: 0.8097 (mtmm) REVERT: A 546 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8229 (pp) REVERT: A 571 ASP cc_start: 0.7276 (t0) cc_final: 0.6996 (t70) REVERT: A 578 ASP cc_start: 0.8178 (t0) cc_final: 0.7897 (t0) REVERT: A 643 PHE cc_start: 0.8473 (t80) cc_final: 0.8264 (t80) REVERT: A 745 ASP cc_start: 0.6574 (t0) cc_final: 0.6150 (t70) REVERT: A 790 LYS cc_start: 0.8808 (mmmm) cc_final: 0.8500 (mmmm) REVERT: A 796 TYR cc_start: 0.8745 (t80) cc_final: 0.8471 (t80) REVERT: A 935 GLN cc_start: 0.8235 (tt0) cc_final: 0.7988 (tt0) REVERT: A 988 GLU cc_start: 0.8652 (tp30) cc_final: 0.8404 (tp30) REVERT: A 1002 GLN cc_start: 0.8548 (tt0) cc_final: 0.8177 (tp-100) REVERT: A 1041 ASP cc_start: 0.8396 (t70) cc_final: 0.8009 (t0) REVERT: A 1111 GLU cc_start: 0.8451 (pt0) cc_final: 0.8131 (pm20) REVERT: B 52 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7533 (tm-30) REVERT: B 64 TRP cc_start: 0.8467 (t60) cc_final: 0.8261 (t60) REVERT: B 97 LYS cc_start: 0.8439 (tppt) cc_final: 0.8051 (tppt) REVERT: B 99 ASN cc_start: 0.7642 (t0) cc_final: 0.7385 (t0) REVERT: B 102 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7789 (ttm170) REVERT: B 173 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.5895 (tm130) REVERT: B 237 ARG cc_start: 0.8625 (mtm180) cc_final: 0.8271 (mtm110) REVERT: B 278 LYS cc_start: 0.9051 (ttpt) cc_final: 0.8700 (ttpt) REVERT: B 304 LYS cc_start: 0.9022 (mptt) cc_final: 0.8813 (mmtp) REVERT: B 326 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8147 (pt) REVERT: B 438 SER cc_start: 0.7669 (p) cc_final: 0.7335 (p) REVERT: B 465 GLU cc_start: 0.7887 (tp30) cc_final: 0.7668 (tp30) REVERT: B 498 ARG cc_start: 0.7993 (mmm160) cc_final: 0.7772 (mmm-85) REVERT: B 619 GLU cc_start: 0.8023 (pm20) cc_final: 0.7819 (pm20) REVERT: B 776 LYS cc_start: 0.8596 (ttpt) cc_final: 0.8377 (ttpp) REVERT: B 804 GLN cc_start: 0.9091 (mt0) cc_final: 0.8845 (mm-40) REVERT: B 816 SER cc_start: 0.8229 (p) cc_final: 0.7952 (t) REVERT: B 825 LYS cc_start: 0.8936 (mtpp) cc_final: 0.8509 (mtmm) REVERT: B 949 GLN cc_start: 0.8575 (tp40) cc_final: 0.8224 (mm-40) REVERT: B 950 ASP cc_start: 0.8300 (t0) cc_final: 0.8002 (t0) REVERT: B 979 ASP cc_start: 0.7876 (t70) cc_final: 0.7608 (t0) REVERT: B 983 ARG cc_start: 0.8376 (mtm110) cc_final: 0.8022 (ttp-110) REVERT: B 1123 SER cc_start: 0.8952 (m) cc_final: 0.8638 (p) REVERT: B 1130 ILE cc_start: 0.8993 (mm) cc_final: 0.8763 (mt) REVERT: C 41 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8556 (mtpt) REVERT: C 64 TRP cc_start: 0.8463 (t60) cc_final: 0.8119 (t60) REVERT: C 99 ASN cc_start: 0.7864 (t0) cc_final: 0.7568 (t0) REVERT: C 102 ARG cc_start: 0.6862 (mmm-85) cc_final: 0.6576 (mmm-85) REVERT: C 239 GLN cc_start: 0.8482 (tt0) cc_final: 0.8197 (tt0) REVERT: C 281 GLU cc_start: 0.8012 (pp20) cc_final: 0.7628 (pp20) REVERT: C 305 SER cc_start: 0.9130 (t) cc_final: 0.8801 (p) REVERT: C 324 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7831 (mm-30) REVERT: C 518 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7497 (mp) REVERT: C 537 LYS cc_start: 0.8495 (ttpp) cc_final: 0.8221 (ptmm) REVERT: C 549 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8189 (m) REVERT: C 558 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8598 (ptpt) REVERT: C 619 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5137 (pm20) REVERT: C 690 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7970 (mm110) REVERT: C 762 GLN cc_start: 0.8087 (mt0) cc_final: 0.7881 (mt0) REVERT: C 776 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8632 (ttpp) REVERT: C 790 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8231 (mtmm) REVERT: C 869 MET cc_start: 0.8840 (mtt) cc_final: 0.8591 (mtm) REVERT: C 900 MET cc_start: 0.8805 (mtp) cc_final: 0.8349 (mtp) REVERT: C 945 LEU cc_start: 0.8841 (mm) cc_final: 0.8602 (mt) REVERT: C 964 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8452 (mtpp) REVERT: C 976 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8267 (m) REVERT: C 1002 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7896 (tm-30) REVERT: C 1091 ARG cc_start: 0.8700 (ttm-80) cc_final: 0.8428 (ttm170) REVERT: C 1111 GLU cc_start: 0.8719 (tt0) cc_final: 0.8469 (tt0) REVERT: D 34 MET cc_start: 0.5926 (ptp) cc_final: 0.5380 (ptp) REVERT: D 83 MET cc_start: 0.7646 (ptm) cc_final: 0.7181 (pmm) REVERT: E 34 MET cc_start: 0.8088 (mmm) cc_final: 0.7573 (mpp) REVERT: E 77 MET cc_start: 0.7001 (mmm) cc_final: 0.6794 (mmm) REVERT: E 82 MET cc_start: 0.7028 (ptm) cc_final: 0.6701 (ptm) REVERT: E 92 MET cc_start: 0.7552 (mtm) cc_final: 0.6843 (mtm) REVERT: E 94 TYR cc_start: 0.7677 (m-80) cc_final: 0.7096 (m-80) REVERT: F 112 THR cc_start: 0.4944 (OUTLIER) cc_final: 0.4710 (p) REVERT: G 77 MET cc_start: 0.7756 (tpp) cc_final: 0.7439 (tpt) REVERT: H 77 ASN cc_start: 0.6816 (t0) cc_final: 0.6256 (t0) outliers start: 129 outliers final: 85 residues processed: 608 average time/residue: 0.4477 time to fit residues: 426.2847 Evaluate side-chains 587 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 490 time to evaluate : 3.098 ------------------------------------------------------------------------------- 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 171 VAL 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 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 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR 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 900 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1136 THR 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 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 358 ILE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 134 GLN 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 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 931 ILE 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 1003 SER Chi-restraints excluded: chain C residue 1114 ILE 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 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 H residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 281 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 321 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 292 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 255 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 762 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 907 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** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.162057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120549 restraints weight = 48710.717| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.61 r_work: 0.3330 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 29907 Z= 0.223 Angle : 0.646 14.380 40787 Z= 0.324 Chirality : 0.047 0.365 4656 Planarity : 0.004 0.059 5213 Dihedral : 5.480 90.108 4624 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.15 % Allowed : 14.83 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 3639 helix: 1.19 (0.21), residues: 658 sheet: -1.16 (0.16), residues: 928 loop : -2.09 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.005 0.001 HIS C1064 PHE 0.035 0.002 PHE B 374 TYR 0.024 0.001 TYR A 265 ARG 0.011 0.001 ARG G 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 28) link_NAG-ASN : angle 2.50037 ( 84) hydrogen bonds : bond 0.03954 ( 910) hydrogen bonds : angle 5.15409 ( 2478) SS BOND : bond 0.00541 ( 46) SS BOND : angle 1.93893 ( 92) covalent geometry : bond 0.00524 (29833) covalent geometry : angle 0.63035 (40611) *********************** 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 652 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 520 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7892 (OUTLIER) cc_final: 0.7690 (t) REVERT: A 99 ASN cc_start: 0.8333 (m-40) cc_final: 0.7672 (t0) REVERT: A 102 ARG cc_start: 0.8302 (ttm170) cc_final: 0.7610 (ptp-110) REVERT: A 116 SER cc_start: 0.8149 (m) cc_final: 0.7675 (p) REVERT: A 129 LYS cc_start: 0.8306 (mttm) cc_final: 0.7982 (mptt) REVERT: A 175 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.6063 (p90) REVERT: A 188 ARG cc_start: 0.8497 (mtt90) cc_final: 0.8286 (mpt-90) REVERT: A 206 THR cc_start: 0.8534 (p) cc_final: 0.8300 (p) REVERT: A 220 PHE cc_start: 0.8474 (t80) cc_final: 0.7971 (m-80) REVERT: A 280 ASN cc_start: 0.8246 (t0) cc_final: 0.7544 (t0) REVERT: A 281 GLU cc_start: 0.7891 (pp20) cc_final: 0.7499 (pm20) REVERT: A 360 ASN cc_start: 0.8460 (p0) cc_final: 0.8230 (p0) REVERT: A 364 ASP cc_start: 0.8070 (t0) cc_final: 0.7822 (t0) REVERT: A 386 LYS cc_start: 0.8308 (mtmm) cc_final: 0.8042 (mtmm) REVERT: A 546 LEU cc_start: 0.8638 (pp) cc_final: 0.8388 (pp) REVERT: A 571 ASP cc_start: 0.7483 (t0) cc_final: 0.7186 (t70) REVERT: A 578 ASP cc_start: 0.8273 (t0) cc_final: 0.7966 (t0) REVERT: A 619 GLU cc_start: 0.7951 (pm20) cc_final: 0.7685 (pm20) REVERT: A 702 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7307 (mm-30) REVERT: A 745 ASP cc_start: 0.6618 (t0) cc_final: 0.6154 (t70) REVERT: A 790 LYS cc_start: 0.8773 (mmmm) cc_final: 0.8466 (mmmm) REVERT: A 796 TYR cc_start: 0.8760 (t80) cc_final: 0.8463 (t80) REVERT: A 988 GLU cc_start: 0.8710 (tp30) cc_final: 0.8365 (tp30) REVERT: A 1002 GLN cc_start: 0.8566 (tt0) cc_final: 0.8174 (tp-100) REVERT: A 1019 ARG cc_start: 0.7889 (ttm110) cc_final: 0.7526 (ttm110) REVERT: A 1041 ASP cc_start: 0.8416 (t70) cc_final: 0.8029 (t0) REVERT: A 1111 GLU cc_start: 0.8508 (pt0) cc_final: 0.8261 (pm20) REVERT: B 29 THR cc_start: 0.8545 (m) cc_final: 0.8261 (m) REVERT: B 52 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7500 (tm-30) REVERT: B 97 LYS cc_start: 0.8474 (tppt) cc_final: 0.8034 (tppt) REVERT: B 173 GLN cc_start: 0.6424 (OUTLIER) cc_final: 0.5972 (tm130) REVERT: B 278 LYS cc_start: 0.9041 (ttpt) cc_final: 0.8615 (ttpt) REVERT: B 304 LYS cc_start: 0.9022 (mptt) cc_final: 0.8767 (mmtp) REVERT: B 326 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8149 (pt) REVERT: B 338 PHE cc_start: 0.9131 (m-80) cc_final: 0.8911 (m-80) REVERT: B 340 GLU cc_start: 0.8233 (pm20) cc_final: 0.7899 (pm20) REVERT: B 438 SER cc_start: 0.7652 (p) cc_final: 0.7326 (p) REVERT: B 465 GLU cc_start: 0.7979 (tp30) cc_final: 0.7657 (tp30) REVERT: B 466 ARG cc_start: 0.8097 (ttp-110) cc_final: 0.7712 (ttm-80) REVERT: B 498 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7655 (mmm-85) REVERT: B 776 LYS cc_start: 0.8566 (ttpt) cc_final: 0.8278 (ttpp) REVERT: B 816 SER cc_start: 0.8213 (p) cc_final: 0.7949 (t) REVERT: B 825 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8686 (mtpp) REVERT: B 949 GLN cc_start: 0.8594 (tp40) cc_final: 0.8261 (mm-40) REVERT: B 950 ASP cc_start: 0.8272 (t0) cc_final: 0.7986 (t0) REVERT: B 979 ASP cc_start: 0.7807 (t70) cc_final: 0.7531 (t0) REVERT: B 983 ARG cc_start: 0.8359 (mtm110) cc_final: 0.8053 (ttp-110) REVERT: B 995 ARG cc_start: 0.8424 (mtp85) cc_final: 0.7859 (ptm160) REVERT: B 1123 SER cc_start: 0.8919 (m) cc_final: 0.8592 (p) REVERT: C 64 TRP cc_start: 0.8578 (t60) cc_final: 0.8275 (t60) REVERT: C 95 ILE cc_start: 0.8522 (mt) cc_final: 0.8156 (tp) REVERT: C 99 ASN cc_start: 0.8050 (t0) cc_final: 0.7712 (t0) REVERT: C 102 ARG cc_start: 0.6924 (mmm-85) cc_final: 0.6574 (mmm-85) REVERT: C 239 GLN cc_start: 0.8484 (tt0) cc_final: 0.8162 (tt0) REVERT: C 281 GLU cc_start: 0.8004 (pp20) cc_final: 0.7731 (pm20) REVERT: C 324 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7840 (mm-30) REVERT: C 518 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7491 (mp) REVERT: C 537 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8343 (ptmm) REVERT: C 558 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8649 (ptpp) REVERT: C 564 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8173 (mm-40) REVERT: C 578 ASP cc_start: 0.7960 (t0) cc_final: 0.7645 (t70) REVERT: C 584 ILE cc_start: 0.8708 (mm) cc_final: 0.8384 (mm) REVERT: C 619 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5302 (pm20) REVERT: C 690 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7886 (mm110) REVERT: C 776 LYS cc_start: 0.8815 (ttpt) cc_final: 0.8580 (ttpp) REVERT: C 790 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8085 (mtmt) REVERT: C 945 LEU cc_start: 0.8855 (mm) cc_final: 0.8621 (mt) REVERT: C 976 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8189 (m) REVERT: C 1002 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7888 (tm-30) REVERT: C 1091 ARG cc_start: 0.8785 (ttm-80) cc_final: 0.8521 (ttm170) REVERT: C 1101 HIS cc_start: 0.8576 (m90) cc_final: 0.8195 (m-70) REVERT: C 1111 GLU cc_start: 0.8731 (tt0) cc_final: 0.8476 (tt0) REVERT: D 34 MET cc_start: 0.5913 (ptp) cc_final: 0.5362 (ptp) REVERT: D 83 MET cc_start: 0.7664 (ptm) cc_final: 0.7212 (pmm) REVERT: E 34 MET cc_start: 0.7974 (mmm) cc_final: 0.7659 (mmm) REVERT: E 35 SER cc_start: 0.7895 (OUTLIER) cc_final: 0.7693 (t) REVERT: E 82 MET cc_start: 0.7046 (ptm) cc_final: 0.6702 (ptm) REVERT: E 92 MET cc_start: 0.7466 (mtm) cc_final: 0.6887 (mtm) REVERT: E 94 TYR cc_start: 0.7629 (m-80) cc_final: 0.7097 (m-80) REVERT: F 112 THR cc_start: 0.4756 (OUTLIER) cc_final: 0.4532 (p) REVERT: G 77 MET cc_start: 0.7745 (tpp) cc_final: 0.7110 (ppp) REVERT: H 34 MET cc_start: 0.8193 (ptp) cc_final: 0.7854 (ptp) REVERT: H 77 ASN cc_start: 0.6751 (t0) cc_final: 0.6234 (t0) REVERT: H 83 MET cc_start: 0.7834 (ptm) cc_final: 0.7538 (ptm) outliers start: 132 outliers final: 91 residues processed: 617 average time/residue: 0.4833 time to fit residues: 467.8864 Evaluate side-chains 603 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 502 time to evaluate : 4.637 ------------------------------------------------------------------------------- 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 83 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 130 VAL 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 227 VAL 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 553 THR 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 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1117 THR 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 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 498 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 532 ASN 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 907 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 126 VAL Chi-restraints excluded: chain C residue 165 ASN 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 556 ASN 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 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 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 H residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 762 GLN A 965 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 955 ASN C 134 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 C1010 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.163098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.121799 restraints weight = 48824.917| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.63 r_work: 0.3355 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29907 Z= 0.152 Angle : 0.616 13.233 40787 Z= 0.308 Chirality : 0.045 0.387 4656 Planarity : 0.004 0.058 5213 Dihedral : 5.442 91.259 4623 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.03 % Allowed : 15.52 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3639 helix: 1.36 (0.21), residues: 658 sheet: -1.06 (0.16), residues: 937 loop : -1.97 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 64 HIS 0.004 0.001 HIS A1088 PHE 0.035 0.001 PHE B 374 TYR 0.022 0.001 TYR A 265 ARG 0.007 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 28) link_NAG-ASN : angle 2.28015 ( 84) hydrogen bonds : bond 0.03576 ( 910) hydrogen bonds : angle 5.07222 ( 2478) SS BOND : bond 0.00467 ( 46) SS BOND : angle 1.84426 ( 92) covalent geometry : bond 0.00360 (29833) covalent geometry : angle 0.60223 (40611) *********************** 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 636 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 508 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8399 (m-40) cc_final: 0.7164 (t0) REVERT: A 102 ARG cc_start: 0.8346 (ttm170) cc_final: 0.7386 (ptp-110) REVERT: A 116 SER cc_start: 0.8195 (m) cc_final: 0.7803 (t) REVERT: A 129 LYS cc_start: 0.8261 (mttm) cc_final: 0.7952 (mptt) REVERT: A 175 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.6101 (p90) REVERT: A 188 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8320 (mpt-90) REVERT: A 206 THR cc_start: 0.8530 (p) cc_final: 0.8297 (p) REVERT: A 220 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8054 (m-80) REVERT: A 280 ASN cc_start: 0.8254 (t0) cc_final: 0.7543 (t0) REVERT: A 281 GLU cc_start: 0.7916 (pp20) cc_final: 0.7486 (pm20) REVERT: A 328 ARG cc_start: 0.8239 (tpp80) cc_final: 0.7871 (tpt-90) REVERT: A 360 ASN cc_start: 0.8469 (p0) cc_final: 0.8257 (p0) REVERT: A 364 ASP cc_start: 0.8030 (t0) cc_final: 0.7815 (t0) REVERT: A 386 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7993 (mtmm) REVERT: A 546 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8420 (pp) REVERT: A 571 ASP cc_start: 0.7508 (t0) cc_final: 0.7228 (t70) REVERT: A 578 ASP cc_start: 0.8233 (t0) cc_final: 0.7910 (t0) REVERT: A 702 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7321 (mm-30) REVERT: A 773 GLU cc_start: 0.7970 (tt0) cc_final: 0.7673 (tt0) REVERT: A 790 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8473 (mmmm) REVERT: A 796 TYR cc_start: 0.8746 (t80) cc_final: 0.8473 (t80) REVERT: A 988 GLU cc_start: 0.8739 (tp30) cc_final: 0.8399 (tp30) REVERT: A 1002 GLN cc_start: 0.8536 (tt0) cc_final: 0.8184 (tp-100) REVERT: A 1041 ASP cc_start: 0.8461 (t70) cc_final: 0.8083 (t0) REVERT: A 1111 GLU cc_start: 0.8506 (pt0) cc_final: 0.8264 (pm20) REVERT: B 29 THR cc_start: 0.8372 (m) cc_final: 0.8058 (m) REVERT: B 52 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7528 (tm-30) REVERT: B 97 LYS cc_start: 0.8474 (tppt) cc_final: 0.8148 (tppt) REVERT: B 173 GLN cc_start: 0.6298 (OUTLIER) cc_final: 0.5836 (tm130) REVERT: B 218 GLN cc_start: 0.8303 (mm-40) cc_final: 0.8102 (mm110) REVERT: B 237 ARG cc_start: 0.8566 (mtm180) cc_final: 0.8258 (mtm110) REVERT: B 278 LYS cc_start: 0.9069 (ttpt) cc_final: 0.8783 (ttpt) REVERT: B 304 LYS cc_start: 0.9025 (mptt) cc_final: 0.8781 (mmtp) REVERT: B 466 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7919 (ttm-80) REVERT: B 498 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7612 (mmm-85) REVERT: B 574 ASP cc_start: 0.8220 (t0) cc_final: 0.7972 (t0) REVERT: B 764 LYS cc_start: 0.8243 (mmmt) cc_final: 0.7999 (tmmt) REVERT: B 776 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8327 (ttpp) REVERT: B 796 TYR cc_start: 0.8356 (t80) cc_final: 0.7984 (t80) REVERT: B 816 SER cc_start: 0.8243 (p) cc_final: 0.7975 (t) REVERT: B 825 LYS cc_start: 0.8909 (mtpp) cc_final: 0.8689 (mtpp) REVERT: B 949 GLN cc_start: 0.8601 (tp40) cc_final: 0.8274 (mm-40) REVERT: B 950 ASP cc_start: 0.8356 (t0) cc_final: 0.8073 (t0) REVERT: B 979 ASP cc_start: 0.7888 (t70) cc_final: 0.7685 (t0) REVERT: B 995 ARG cc_start: 0.8473 (mtp85) cc_final: 0.8194 (ptm160) REVERT: B 1123 SER cc_start: 0.8944 (m) cc_final: 0.8595 (p) REVERT: B 1127 ASP cc_start: 0.8289 (m-30) cc_final: 0.7996 (m-30) REVERT: C 41 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8626 (mtpt) REVERT: C 64 TRP cc_start: 0.8539 (t60) cc_final: 0.8259 (t60) REVERT: C 99 ASN cc_start: 0.8039 (t0) cc_final: 0.7506 (t0) REVERT: C 102 ARG cc_start: 0.6954 (mmm-85) cc_final: 0.6568 (mmm-85) REVERT: C 239 GLN cc_start: 0.8481 (tt0) cc_final: 0.8163 (tt0) REVERT: C 269 TYR cc_start: 0.8376 (m-80) cc_final: 0.8071 (m-80) REVERT: C 281 GLU cc_start: 0.8060 (pp20) cc_final: 0.7745 (pm20) REVERT: C 324 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7873 (mm-30) REVERT: C 537 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8272 (ptmm) REVERT: C 558 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8663 (ptpp) REVERT: C 564 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8172 (mm-40) REVERT: C 578 ASP cc_start: 0.7847 (t0) cc_final: 0.7549 (t70) REVERT: C 619 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5141 (pm20) REVERT: C 690 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7908 (mm110) REVERT: C 773 GLU cc_start: 0.8372 (tt0) cc_final: 0.8162 (tt0) REVERT: C 776 LYS cc_start: 0.8831 (ttpt) cc_final: 0.8603 (ttpp) REVERT: C 790 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8101 (mtmt) REVERT: C 945 LEU cc_start: 0.8850 (mm) cc_final: 0.8616 (mt) REVERT: C 976 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8229 (m) REVERT: C 1002 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7872 (tm-30) REVERT: C 1091 ARG cc_start: 0.8757 (ttm-80) cc_final: 0.8434 (ttm170) REVERT: C 1111 GLU cc_start: 0.8665 (tt0) cc_final: 0.8390 (tt0) REVERT: D 34 MET cc_start: 0.5912 (ptp) cc_final: 0.5352 (ptp) REVERT: D 83 MET cc_start: 0.7639 (ptm) cc_final: 0.7224 (pmm) REVERT: E 34 MET cc_start: 0.7846 (mmm) cc_final: 0.7591 (mmm) REVERT: E 58 TYR cc_start: 0.8747 (t80) cc_final: 0.8390 (t80) REVERT: E 82 MET cc_start: 0.7039 (ptm) cc_final: 0.6687 (ptm) REVERT: E 92 MET cc_start: 0.7463 (mtm) cc_final: 0.6843 (mtm) REVERT: E 94 TYR cc_start: 0.7676 (m-80) cc_final: 0.7063 (m-80) REVERT: F 112 THR cc_start: 0.4780 (OUTLIER) cc_final: 0.4556 (p) REVERT: G 77 MET cc_start: 0.7714 (tpp) cc_final: 0.7149 (ppp) REVERT: H 34 MET cc_start: 0.8179 (ptp) cc_final: 0.7817 (ptp) REVERT: H 59 TYR cc_start: 0.7382 (m-80) cc_final: 0.6698 (m-80) REVERT: H 77 ASN cc_start: 0.6815 (t0) cc_final: 0.6333 (t0) REVERT: H 83 MET cc_start: 0.7785 (ptm) cc_final: 0.7295 (ptm) outliers start: 128 outliers final: 88 residues processed: 605 average time/residue: 0.4309 time to fit residues: 407.9692 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 : 3.049 ------------------------------------------------------------------------------- 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 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 227 VAL 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 546 LEU Chi-restraints excluded: chain A residue 553 THR 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 740 MET Chi-restraints excluded: chain A residue 747 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 A residue 1144 GLU 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 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 378 LYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS 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 907 ASN 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 41 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 126 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 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 732 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1003 SER 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 125 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 301 optimal weight: 0.0470 chunk 124 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 288 optimal weight: 0.8980 chunk 334 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 49 optimal weight: 0.0020 overall best weight: 0.5086 ------------------------------------------------------------------------------- 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 762 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 907 ASN B 955 ASN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.164037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.122795 restraints weight = 48859.177| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.67 r_work: 0.3366 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29907 Z= 0.119 Angle : 0.609 18.526 40787 Z= 0.301 Chirality : 0.044 0.277 4656 Planarity : 0.004 0.057 5213 Dihedral : 5.336 92.004 4622 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.53 % Allowed : 16.49 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3639 helix: 1.59 (0.22), residues: 646 sheet: -1.00 (0.16), residues: 923 loop : -1.87 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 64 HIS 0.003 0.001 HIS A1088 PHE 0.034 0.001 PHE A 168 TYR 0.019 0.001 TYR A 265 ARG 0.008 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 28) link_NAG-ASN : angle 2.04939 ( 84) hydrogen bonds : bond 0.03301 ( 910) hydrogen bonds : angle 4.96127 ( 2478) SS BOND : bond 0.00437 ( 46) SS BOND : angle 1.69376 ( 92) covalent geometry : bond 0.00281 (29833) covalent geometry : angle 0.59790 (40611) *********************** 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 603 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 491 time to evaluate : 3.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8305 (m-40) cc_final: 0.7647 (t0) REVERT: A 102 ARG cc_start: 0.8373 (ttm170) cc_final: 0.7776 (ptp-110) REVERT: A 116 SER cc_start: 0.8191 (m) cc_final: 0.7786 (t) REVERT: A 129 LYS cc_start: 0.8121 (mttm) cc_final: 0.7818 (mptt) REVERT: A 175 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.6040 (p90) REVERT: A 206 THR cc_start: 0.8435 (p) cc_final: 0.8194 (p) REVERT: A 220 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: A 280 ASN cc_start: 0.8255 (t0) cc_final: 0.7608 (t0) REVERT: A 281 GLU cc_start: 0.7912 (pp20) cc_final: 0.7452 (pm20) REVERT: A 328 ARG cc_start: 0.8200 (tpp80) cc_final: 0.7671 (tpt-90) REVERT: A 386 LYS cc_start: 0.8260 (mtmm) cc_final: 0.8013 (mtmm) REVERT: A 546 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8404 (pp) REVERT: A 571 ASP cc_start: 0.7480 (t0) cc_final: 0.7203 (t70) REVERT: A 578 ASP cc_start: 0.8253 (t0) cc_final: 0.7802 (t0) REVERT: A 702 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7554 (mm-30) REVERT: A 773 GLU cc_start: 0.7971 (tt0) cc_final: 0.7701 (tt0) REVERT: A 790 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8495 (mmmm) REVERT: A 796 TYR cc_start: 0.8734 (t80) cc_final: 0.8461 (t80) REVERT: A 988 GLU cc_start: 0.8731 (tp30) cc_final: 0.8387 (tp30) REVERT: A 1002 GLN cc_start: 0.8528 (tt0) cc_final: 0.8183 (tp-100) REVERT: A 1041 ASP cc_start: 0.8452 (t70) cc_final: 0.8075 (t0) REVERT: B 29 THR cc_start: 0.8348 (m) cc_final: 0.8134 (m) REVERT: B 52 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7419 (tm-30) REVERT: B 97 LYS cc_start: 0.8422 (tppt) cc_final: 0.8187 (tppp) REVERT: B 173 GLN cc_start: 0.6302 (OUTLIER) cc_final: 0.5854 (tm130) REVERT: B 278 LYS cc_start: 0.9085 (ttpt) cc_final: 0.8810 (ttpt) REVERT: B 304 LYS cc_start: 0.9033 (mptt) cc_final: 0.8794 (mmtp) REVERT: B 340 GLU cc_start: 0.8261 (pm20) cc_final: 0.7887 (pm20) REVERT: B 466 ARG cc_start: 0.8137 (ttp-110) cc_final: 0.7909 (ttm-80) REVERT: B 498 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7591 (mmm-85) REVERT: B 574 ASP cc_start: 0.8263 (t0) cc_final: 0.7988 (t0) REVERT: B 764 LYS cc_start: 0.8203 (mmmt) cc_final: 0.7975 (tmmt) REVERT: B 776 LYS cc_start: 0.8607 (ttpt) cc_final: 0.8352 (ttpp) REVERT: B 796 TYR cc_start: 0.8340 (t80) cc_final: 0.7912 (t80) REVERT: B 816 SER cc_start: 0.8202 (p) cc_final: 0.7927 (t) REVERT: B 825 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8695 (mtpp) REVERT: B 949 GLN cc_start: 0.8578 (tp40) cc_final: 0.8254 (mm-40) REVERT: B 950 ASP cc_start: 0.8316 (t0) cc_final: 0.8057 (t0) REVERT: B 995 ARG cc_start: 0.8573 (mtp85) cc_final: 0.7928 (ptm160) REVERT: B 1017 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 1019 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7882 (ttp80) REVERT: B 1123 SER cc_start: 0.8980 (m) cc_final: 0.8593 (p) REVERT: C 41 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8628 (mtpt) REVERT: C 64 TRP cc_start: 0.8524 (t60) cc_final: 0.8275 (t60) REVERT: C 99 ASN cc_start: 0.7896 (t0) cc_final: 0.7507 (t0) REVERT: C 102 ARG cc_start: 0.6982 (mmm-85) cc_final: 0.6536 (mmm-85) REVERT: C 239 GLN cc_start: 0.8487 (tt0) cc_final: 0.8155 (tt0) REVERT: C 269 TYR cc_start: 0.8343 (m-80) cc_final: 0.8024 (m-80) REVERT: C 281 GLU cc_start: 0.8064 (pp20) cc_final: 0.7736 (pm20) REVERT: C 305 SER cc_start: 0.9145 (t) cc_final: 0.8814 (p) REVERT: C 324 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7834 (mm-30) REVERT: C 518 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7529 (mp) REVERT: C 537 LYS cc_start: 0.8385 (ttpp) cc_final: 0.8164 (ptmm) REVERT: C 558 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8649 (ptpp) REVERT: C 564 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8139 (mm110) REVERT: C 578 ASP cc_start: 0.7808 (t0) cc_final: 0.7459 (t70) REVERT: C 619 GLU cc_start: 0.6040 (OUTLIER) cc_final: 0.4909 (pm20) REVERT: C 690 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7940 (mm110) REVERT: C 776 LYS cc_start: 0.8860 (ttpt) cc_final: 0.8630 (ttpp) REVERT: C 790 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8104 (mtmm) REVERT: C 872 GLN cc_start: 0.8634 (mt0) cc_final: 0.8324 (mt0) REVERT: C 976 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8256 (m) REVERT: C 1002 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7860 (tm-30) REVERT: C 1091 ARG cc_start: 0.8760 (ttm-80) cc_final: 0.8458 (ttm170) REVERT: C 1111 GLU cc_start: 0.8662 (tt0) cc_final: 0.8390 (tt0) REVERT: D 34 MET cc_start: 0.5950 (ptp) cc_final: 0.5379 (ptp) REVERT: D 83 MET cc_start: 0.7606 (ptm) cc_final: 0.7221 (pmm) REVERT: E 33 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7212 (tm-30) REVERT: E 37 VAL cc_start: 0.8804 (m) cc_final: 0.8291 (p) REVERT: E 58 TYR cc_start: 0.8715 (t80) cc_final: 0.8335 (t80) REVERT: E 82 MET cc_start: 0.7016 (ptm) cc_final: 0.6663 (ptm) REVERT: E 92 MET cc_start: 0.7403 (mtm) cc_final: 0.6719 (mtm) REVERT: E 94 TYR cc_start: 0.7629 (m-80) cc_final: 0.6966 (m-80) REVERT: F 112 THR cc_start: 0.4730 (OUTLIER) cc_final: 0.4505 (p) REVERT: G 77 MET cc_start: 0.7684 (tpp) cc_final: 0.7140 (ppp) REVERT: H 34 MET cc_start: 0.8129 (ptp) cc_final: 0.7758 (ptp) REVERT: H 59 TYR cc_start: 0.7346 (m-80) cc_final: 0.6735 (m-80) REVERT: H 77 ASN cc_start: 0.6805 (t0) cc_final: 0.6349 (t0) REVERT: H 83 MET cc_start: 0.7845 (ptm) cc_final: 0.7342 (ptm) outliers start: 112 outliers final: 81 residues processed: 576 average time/residue: 0.4394 time to fit residues: 395.5901 Evaluate side-chains 574 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 483 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 130 VAL 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 227 VAL 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 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 740 MET Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1144 GLU 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 210 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU 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 498 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 210 VAL 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 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 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 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR 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 234 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 chunk 285 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 chunk 249 optimal weight: 7.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- 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 762 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 907 ASN B 955 ASN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN ** D 43 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.163647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.122367 restraints weight = 48768.464| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.64 r_work: 0.3357 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 29907 Z= 0.138 Angle : 0.625 18.221 40787 Z= 0.309 Chirality : 0.045 0.258 4656 Planarity : 0.004 0.056 5213 Dihedral : 5.291 91.277 4622 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.65 % Allowed : 16.68 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3639 helix: 1.52 (0.21), residues: 655 sheet: -0.91 (0.16), residues: 946 loop : -1.82 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 64 HIS 0.004 0.001 HIS A1088 PHE 0.028 0.001 PHE A 168 TYR 0.020 0.001 TYR A 265 ARG 0.007 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 28) link_NAG-ASN : angle 2.00286 ( 84) hydrogen bonds : bond 0.03367 ( 910) hydrogen bonds : angle 4.94884 ( 2478) SS BOND : bond 0.00539 ( 46) SS BOND : angle 1.84192 ( 92) covalent geometry : bond 0.00326 (29833) covalent geometry : angle 0.61306 (40611) *********************** 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 614 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 498 time to evaluate : 3.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8327 (m-40) cc_final: 0.7751 (t0) REVERT: A 102 ARG cc_start: 0.8378 (ttm170) cc_final: 0.7879 (ptp-110) REVERT: A 116 SER cc_start: 0.8169 (m) cc_final: 0.7739 (t) REVERT: A 129 LYS cc_start: 0.8110 (mttm) cc_final: 0.7770 (mptt) REVERT: A 175 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.6143 (p90) REVERT: A 206 THR cc_start: 0.8387 (p) cc_final: 0.8147 (p) REVERT: A 220 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8056 (m-80) REVERT: A 280 ASN cc_start: 0.8248 (t0) cc_final: 0.7641 (t0) REVERT: A 281 GLU cc_start: 0.7931 (pp20) cc_final: 0.7473 (pm20) REVERT: A 546 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8416 (pp) REVERT: A 571 ASP cc_start: 0.7536 (t0) cc_final: 0.7281 (t70) REVERT: A 578 ASP cc_start: 0.8219 (t0) cc_final: 0.7988 (t0) REVERT: A 643 PHE cc_start: 0.8430 (t80) cc_final: 0.8200 (t80) REVERT: A 702 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7298 (mm-30) REVERT: A 773 GLU cc_start: 0.7977 (tt0) cc_final: 0.7671 (tt0) REVERT: A 790 LYS cc_start: 0.8782 (mmmm) cc_final: 0.8479 (mmmm) REVERT: A 796 TYR cc_start: 0.8727 (t80) cc_final: 0.8446 (t80) REVERT: A 988 GLU cc_start: 0.8692 (tp30) cc_final: 0.8390 (tp30) REVERT: A 1019 ARG cc_start: 0.8049 (ttm110) cc_final: 0.7742 (ttp-170) REVERT: A 1041 ASP cc_start: 0.8449 (t70) cc_final: 0.8088 (t0) REVERT: A 1111 GLU cc_start: 0.8459 (pt0) cc_final: 0.8190 (pm20) REVERT: B 52 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7408 (tm-30) REVERT: B 97 LYS cc_start: 0.8407 (tppt) cc_final: 0.8171 (tppp) REVERT: B 173 GLN cc_start: 0.6250 (OUTLIER) cc_final: 0.5813 (tm130) REVERT: B 237 ARG cc_start: 0.8508 (mtm180) cc_final: 0.8156 (mtm110) REVERT: B 278 LYS cc_start: 0.9104 (ttpt) cc_final: 0.8799 (ttpt) REVERT: B 298 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7350 (tt0) REVERT: B 304 LYS cc_start: 0.9032 (mptt) cc_final: 0.8808 (mmtp) REVERT: B 324 GLU cc_start: 0.8477 (pt0) cc_final: 0.8149 (pm20) REVERT: B 340 GLU cc_start: 0.8210 (pm20) cc_final: 0.7783 (pm20) REVERT: B 361 CYS cc_start: 0.7125 (m) cc_final: 0.6849 (m) REVERT: B 406 GLU cc_start: 0.8046 (tt0) cc_final: 0.7814 (tt0) REVERT: B 466 ARG cc_start: 0.8140 (ttp-110) cc_final: 0.7918 (ttm-80) REVERT: B 574 ASP cc_start: 0.8277 (t0) cc_final: 0.7975 (t0) REVERT: B 764 LYS cc_start: 0.8281 (mmmt) cc_final: 0.7998 (ttpt) REVERT: B 776 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8274 (ttpp) REVERT: B 796 TYR cc_start: 0.8299 (t80) cc_final: 0.7863 (t80) REVERT: B 816 SER cc_start: 0.8204 (p) cc_final: 0.7972 (t) REVERT: B 825 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8664 (mtpp) REVERT: B 949 GLN cc_start: 0.8543 (tp40) cc_final: 0.8218 (mm-40) REVERT: B 950 ASP cc_start: 0.8269 (t0) cc_final: 0.8015 (t0) REVERT: B 983 ARG cc_start: 0.8466 (mtm110) cc_final: 0.8190 (ttp-110) REVERT: B 1019 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7782 (ttp80) REVERT: B 1123 SER cc_start: 0.8979 (m) cc_final: 0.8568 (p) REVERT: C 41 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8641 (mtpt) REVERT: C 64 TRP cc_start: 0.8541 (t60) cc_final: 0.8305 (t60) REVERT: C 99 ASN cc_start: 0.7971 (t0) cc_final: 0.7533 (t0) REVERT: C 102 ARG cc_start: 0.6964 (mmm-85) cc_final: 0.6459 (mmm-85) REVERT: C 239 GLN cc_start: 0.8450 (tt0) cc_final: 0.8108 (tt0) REVERT: C 269 TYR cc_start: 0.8366 (m-80) cc_final: 0.8090 (m-80) REVERT: C 281 GLU cc_start: 0.8062 (pp20) cc_final: 0.7724 (pm20) REVERT: C 305 SER cc_start: 0.9148 (t) cc_final: 0.8802 (p) REVERT: C 324 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7847 (mm-30) REVERT: C 518 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7472 (mp) REVERT: C 537 LYS cc_start: 0.8435 (ttpp) cc_final: 0.8202 (ptmm) REVERT: C 558 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8667 (ptpp) REVERT: C 564 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8150 (mm110) REVERT: C 578 ASP cc_start: 0.7842 (t0) cc_final: 0.7534 (t70) REVERT: C 619 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.4932 (pm20) REVERT: C 675 GLN cc_start: 0.8097 (mt0) cc_final: 0.7834 (mm-40) REVERT: C 690 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7941 (mm110) REVERT: C 776 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8537 (ttpp) REVERT: C 790 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8036 (mtmm) REVERT: C 872 GLN cc_start: 0.8596 (mt0) cc_final: 0.8332 (mt0) REVERT: C 957 GLN cc_start: 0.8263 (tm-30) cc_final: 0.8036 (tt0) REVERT: C 976 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8209 (m) REVERT: C 995 ARG cc_start: 0.8128 (ptp-110) cc_final: 0.7725 (ttp80) REVERT: C 1002 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7847 (tm-30) REVERT: C 1091 ARG cc_start: 0.8770 (ttm-80) cc_final: 0.8469 (ttm170) REVERT: C 1111 GLU cc_start: 0.8668 (tt0) cc_final: 0.8396 (tt0) REVERT: D 34 MET cc_start: 0.6012 (ptp) cc_final: 0.5403 (ptp) REVERT: D 83 MET cc_start: 0.7566 (ptm) cc_final: 0.7163 (pmm) REVERT: E 34 MET cc_start: 0.7736 (mmm) cc_final: 0.7370 (mmt) REVERT: E 37 VAL cc_start: 0.8744 (m) cc_final: 0.8254 (p) REVERT: E 58 TYR cc_start: 0.8730 (t80) cc_final: 0.8321 (t80) REVERT: E 82 MET cc_start: 0.7018 (ptm) cc_final: 0.6660 (ptm) REVERT: E 92 MET cc_start: 0.7382 (mtm) cc_final: 0.6674 (mtm) REVERT: E 94 TYR cc_start: 0.7521 (m-80) cc_final: 0.6893 (m-80) REVERT: F 112 THR cc_start: 0.4781 (OUTLIER) cc_final: 0.4559 (p) REVERT: G 77 MET cc_start: 0.7620 (tpp) cc_final: 0.7060 (ppp) REVERT: H 34 MET cc_start: 0.8138 (ptp) cc_final: 0.7762 (ptp) REVERT: H 59 TYR cc_start: 0.7357 (m-80) cc_final: 0.6817 (m-80) REVERT: H 77 ASN cc_start: 0.6815 (t0) cc_final: 0.6398 (t0) REVERT: H 83 MET cc_start: 0.7795 (ptm) cc_final: 0.7293 (ptm) outliers start: 116 outliers final: 92 residues processed: 579 average time/residue: 0.4302 time to fit residues: 388.0267 Evaluate side-chains 586 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 485 time to evaluate : 3.303 ------------------------------------------------------------------------------- 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 100 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 130 VAL 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 227 VAL Chi-restraints excluded: chain A residue 267 VAL 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 537 LYS 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 740 MET 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 1144 GLU 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 210 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU 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 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 549 THR 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 907 ASN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 210 VAL 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 532 ASN 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 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 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 177 optimal weight: 0.3980 chunk 40 optimal weight: 20.0000 chunk 163 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 306 optimal weight: 0.4980 chunk 353 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 250 optimal weight: 50.0000 chunk 237 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 762 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 907 ASN B 955 ASN B 957 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** 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 = 0.4138 r_free = 0.4138 target = 0.163700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.122652 restraints weight = 48816.742| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.61 r_work: 0.3360 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29907 Z= 0.138 Angle : 0.622 16.161 40787 Z= 0.309 Chirality : 0.045 0.243 4656 Planarity : 0.004 0.056 5213 Dihedral : 5.219 91.226 4618 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.37 % Allowed : 17.15 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3639 helix: 1.50 (0.21), residues: 667 sheet: -0.87 (0.16), residues: 941 loop : -1.73 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 64 HIS 0.006 0.001 HIS A 954 PHE 0.035 0.001 PHE A 168 TYR 0.020 0.001 TYR A 265 ARG 0.008 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 28) link_NAG-ASN : angle 1.95015 ( 84) hydrogen bonds : bond 0.03353 ( 910) hydrogen bonds : angle 4.93168 ( 2478) SS BOND : bond 0.00454 ( 46) SS BOND : angle 1.69951 ( 92) covalent geometry : bond 0.00327 (29833) covalent geometry : angle 0.61127 (40611) *********************** 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 596 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 489 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8347 (m-40) cc_final: 0.7756 (t0) REVERT: A 102 ARG cc_start: 0.8360 (ttm170) cc_final: 0.7899 (ptp-110) REVERT: A 116 SER cc_start: 0.8298 (m) cc_final: 0.7874 (t) REVERT: A 129 LYS cc_start: 0.8109 (mttm) cc_final: 0.7816 (mptt) REVERT: A 175 PHE cc_start: 0.6649 (OUTLIER) cc_final: 0.6122 (p90) REVERT: A 188 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.8175 (mpt-90) REVERT: A 206 THR cc_start: 0.8397 (p) cc_final: 0.8157 (p) REVERT: A 220 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: A 280 ASN cc_start: 0.8267 (t0) cc_final: 0.7690 (t0) REVERT: A 281 GLU cc_start: 0.7938 (pp20) cc_final: 0.7489 (pm20) REVERT: A 546 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8458 (pp) REVERT: A 571 ASP cc_start: 0.7545 (t0) cc_final: 0.7286 (t70) REVERT: A 578 ASP cc_start: 0.8291 (t0) cc_final: 0.8045 (t0) REVERT: A 643 PHE cc_start: 0.8464 (t80) cc_final: 0.8231 (t80) REVERT: A 702 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7327 (mm-30) REVERT: A 773 GLU cc_start: 0.7969 (tt0) cc_final: 0.7609 (tt0) REVERT: A 790 LYS cc_start: 0.8797 (mmmm) cc_final: 0.8498 (mmmm) REVERT: A 796 TYR cc_start: 0.8722 (t80) cc_final: 0.8426 (t80) REVERT: A 954 HIS cc_start: 0.8165 (m-70) cc_final: 0.7668 (m90) REVERT: A 988 GLU cc_start: 0.8670 (tp30) cc_final: 0.8319 (tp30) REVERT: A 1002 GLN cc_start: 0.8538 (tt0) cc_final: 0.8199 (tp-100) REVERT: A 1019 ARG cc_start: 0.8033 (ttm110) cc_final: 0.7679 (ttm110) REVERT: A 1041 ASP cc_start: 0.8416 (t70) cc_final: 0.8065 (t0) REVERT: A 1111 GLU cc_start: 0.8445 (pt0) cc_final: 0.8221 (pm20) REVERT: B 52 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7370 (tm-30) REVERT: B 97 LYS cc_start: 0.8406 (tppt) cc_final: 0.8181 (tppp) REVERT: B 118 LEU cc_start: 0.8795 (tp) cc_final: 0.8572 (tt) REVERT: B 173 GLN cc_start: 0.6289 (OUTLIER) cc_final: 0.5875 (tm130) REVERT: B 237 ARG cc_start: 0.8508 (mtm180) cc_final: 0.8216 (mtm110) REVERT: B 278 LYS cc_start: 0.9080 (ttpt) cc_final: 0.8804 (ttpt) REVERT: B 304 LYS cc_start: 0.9034 (mptt) cc_final: 0.8814 (mmtp) REVERT: B 340 GLU cc_start: 0.8230 (pm20) cc_final: 0.7794 (pm20) REVERT: B 361 CYS cc_start: 0.7102 (m) cc_final: 0.6878 (m) REVERT: B 466 ARG cc_start: 0.8176 (ttp-110) cc_final: 0.7959 (ttm-80) REVERT: B 574 ASP cc_start: 0.8276 (t0) cc_final: 0.7976 (t0) REVERT: B 764 LYS cc_start: 0.8268 (mmmt) cc_final: 0.8003 (ttpt) REVERT: B 776 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8327 (ttpp) REVERT: B 796 TYR cc_start: 0.8321 (t80) cc_final: 0.7898 (t80) REVERT: B 816 SER cc_start: 0.8257 (p) cc_final: 0.8002 (t) REVERT: B 825 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8666 (mtpp) REVERT: B 949 GLN cc_start: 0.8568 (tp40) cc_final: 0.8241 (mm-40) REVERT: B 950 ASP cc_start: 0.8313 (t0) cc_final: 0.8022 (t0) REVERT: B 1123 SER cc_start: 0.8972 (m) cc_final: 0.8563 (p) REVERT: C 64 TRP cc_start: 0.8555 (t60) cc_final: 0.8305 (t60) REVERT: C 99 ASN cc_start: 0.7957 (t0) cc_final: 0.7539 (t0) REVERT: C 102 ARG cc_start: 0.6966 (mmm-85) cc_final: 0.6458 (mmm-85) REVERT: C 239 GLN cc_start: 0.8448 (tt0) cc_final: 0.8121 (tt0) REVERT: C 269 TYR cc_start: 0.8370 (m-80) cc_final: 0.8074 (m-80) REVERT: C 305 SER cc_start: 0.9166 (t) cc_final: 0.8833 (p) REVERT: C 324 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7865 (mm-30) REVERT: C 518 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7565 (mp) REVERT: C 537 LYS cc_start: 0.8421 (ttpp) cc_final: 0.8206 (ptmm) REVERT: C 558 LYS cc_start: 0.8912 (mtmt) cc_final: 0.8672 (ptpp) REVERT: C 564 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8160 (mm110) REVERT: C 578 ASP cc_start: 0.7839 (t0) cc_final: 0.7535 (t70) REVERT: C 619 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.4726 (pm20) REVERT: C 675 GLN cc_start: 0.8102 (mt0) cc_final: 0.7879 (mm-40) REVERT: C 690 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7976 (mm110) REVERT: C 776 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8681 (ttpp) REVERT: C 790 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8135 (mtmm) REVERT: C 872 GLN cc_start: 0.8603 (mt0) cc_final: 0.8315 (mt0) REVERT: C 976 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8259 (m) REVERT: C 1002 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7854 (tm-30) REVERT: C 1091 ARG cc_start: 0.8759 (ttm-80) cc_final: 0.8466 (ttm170) REVERT: C 1111 GLU cc_start: 0.8653 (tt0) cc_final: 0.8393 (tt0) REVERT: D 34 MET cc_start: 0.6004 (ptp) cc_final: 0.5407 (ptp) REVERT: D 83 MET cc_start: 0.7567 (ptm) cc_final: 0.7191 (pmm) REVERT: E 34 MET cc_start: 0.7861 (mmm) cc_final: 0.7541 (mmt) REVERT: E 37 VAL cc_start: 0.8752 (m) cc_final: 0.8281 (p) REVERT: E 58 TYR cc_start: 0.8727 (t80) cc_final: 0.8375 (t80) REVERT: E 82 MET cc_start: 0.7012 (ptm) cc_final: 0.6665 (ptm) REVERT: E 92 MET cc_start: 0.7381 (mtm) cc_final: 0.6690 (mtm) REVERT: E 94 TYR cc_start: 0.7558 (m-80) cc_final: 0.6930 (m-80) REVERT: F 112 THR cc_start: 0.4669 (OUTLIER) cc_final: 0.4445 (p) REVERT: G 82 MET cc_start: 0.8396 (tmm) cc_final: 0.8120 (tmm) REVERT: H 59 TYR cc_start: 0.7397 (m-80) cc_final: 0.6881 (m-80) REVERT: H 77 ASN cc_start: 0.6827 (t0) cc_final: 0.6428 (t0) REVERT: H 83 MET cc_start: 0.7767 (ptm) cc_final: 0.7279 (ptm) outliers start: 107 outliers final: 95 residues processed: 565 average time/residue: 0.4491 time to fit residues: 394.1682 Evaluate side-chains 582 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 479 time to evaluate : 3.063 ------------------------------------------------------------------------------- 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 100 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 130 VAL 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 227 VAL 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 537 LYS 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 740 MET 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 1144 GLU 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 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 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 549 THR 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 907 ASN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 973 ILE 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 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 210 VAL 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 532 ASN 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 641 ASN Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 716 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 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 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 290 optimal weight: 2.9990 chunk 351 optimal weight: 8.9990 chunk 311 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 chunk 268 optimal weight: 0.0970 chunk 329 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 363 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 955 ASN B 957 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.161693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120164 restraints weight = 48353.352| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.63 r_work: 0.3353 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 29907 Z= 0.206 Angle : 0.665 15.173 40787 Z= 0.332 Chirality : 0.046 0.260 4656 Planarity : 0.004 0.056 5213 Dihedral : 5.381 90.449 4618 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.46 % Allowed : 17.19 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 3639 helix: 1.37 (0.21), residues: 671 sheet: -0.88 (0.16), residues: 950 loop : -1.74 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 64 HIS 0.006 0.001 HIS A 954 PHE 0.029 0.002 PHE B 32 TYR 0.022 0.001 TYR B1067 ARG 0.012 0.001 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 28) link_NAG-ASN : angle 2.08888 ( 84) hydrogen bonds : bond 0.03811 ( 910) hydrogen bonds : angle 5.03145 ( 2478) SS BOND : bond 0.00511 ( 46) SS BOND : angle 1.91548 ( 92) covalent geometry : bond 0.00488 (29833) covalent geometry : angle 0.65375 (40611) ********************** 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 606 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 496 time to evaluate : 3.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8387 (m-40) cc_final: 0.7709 (t0) REVERT: A 102 ARG cc_start: 0.8400 (ttm170) cc_final: 0.7951 (ptp-110) REVERT: A 116 SER cc_start: 0.8354 (m) cc_final: 0.7960 (t) REVERT: A 129 LYS cc_start: 0.8363 (mttm) cc_final: 0.8067 (mptt) REVERT: A 175 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6129 (p90) REVERT: A 188 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.8133 (mpt-90) REVERT: A 206 THR cc_start: 0.8429 (p) cc_final: 0.8188 (p) REVERT: A 280 ASN cc_start: 0.8256 (t0) cc_final: 0.7722 (t0) REVERT: A 281 GLU cc_start: 0.7955 (pp20) cc_final: 0.7468 (pm20) REVERT: A 546 LEU cc_start: 0.8813 (pp) cc_final: 0.8568 (pp) REVERT: A 571 ASP cc_start: 0.7676 (t0) cc_final: 0.7397 (t70) REVERT: A 578 ASP cc_start: 0.8328 (t0) cc_final: 0.8087 (t0) REVERT: A 619 GLU cc_start: 0.7841 (pm20) cc_final: 0.7530 (pm20) REVERT: A 643 PHE cc_start: 0.8513 (t80) cc_final: 0.8301 (t80) REVERT: A 702 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7286 (mm-30) REVERT: A 773 GLU cc_start: 0.8028 (tt0) cc_final: 0.7772 (tt0) REVERT: A 790 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8440 (mmmm) REVERT: A 988 GLU cc_start: 0.8756 (tp30) cc_final: 0.8455 (tp30) REVERT: A 1002 GLN cc_start: 0.8560 (tt0) cc_final: 0.8188 (tp-100) REVERT: A 1019 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7702 (ttp-170) REVERT: A 1041 ASP cc_start: 0.8399 (t70) cc_final: 0.8051 (t0) REVERT: A 1111 GLU cc_start: 0.8569 (pt0) cc_final: 0.8253 (pm20) REVERT: B 52 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7397 (tm-30) REVERT: B 118 LEU cc_start: 0.8828 (tp) cc_final: 0.8610 (tt) REVERT: B 224 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7631 (mm-30) REVERT: B 237 ARG cc_start: 0.8525 (mtm180) cc_final: 0.8206 (mtm110) REVERT: B 278 LYS cc_start: 0.9029 (ttpt) cc_final: 0.8726 (ttpt) REVERT: B 304 LYS cc_start: 0.9057 (mptt) cc_final: 0.8828 (mmtp) REVERT: B 326 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8125 (pt) REVERT: B 340 GLU cc_start: 0.8227 (pm20) cc_final: 0.7774 (pm20) REVERT: B 361 CYS cc_start: 0.7057 (m) cc_final: 0.6786 (m) REVERT: B 466 ARG cc_start: 0.8158 (ttp-110) cc_final: 0.7911 (ttm-80) REVERT: B 574 ASP cc_start: 0.8310 (t0) cc_final: 0.7986 (t0) REVERT: B 764 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7961 (mtmt) REVERT: B 776 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8262 (ttpp) REVERT: B 816 SER cc_start: 0.8284 (p) cc_final: 0.8015 (t) REVERT: B 825 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8660 (mtpp) REVERT: B 921 LYS cc_start: 0.8712 (mmtt) cc_final: 0.8382 (tppt) REVERT: B 949 GLN cc_start: 0.8595 (tp40) cc_final: 0.8263 (mm-40) REVERT: B 950 ASP cc_start: 0.8306 (t0) cc_final: 0.8034 (t0) REVERT: B 995 ARG cc_start: 0.8598 (mtp85) cc_final: 0.8241 (ptm160) REVERT: B 1019 ARG cc_start: 0.8216 (ttp-110) cc_final: 0.7989 (ttp80) REVERT: B 1038 LYS cc_start: 0.9017 (mttm) cc_final: 0.8773 (mmtm) REVERT: B 1123 SER cc_start: 0.8946 (m) cc_final: 0.8529 (p) REVERT: C 99 ASN cc_start: 0.8088 (t0) cc_final: 0.7599 (t0) REVERT: C 102 ARG cc_start: 0.7050 (mmm-85) cc_final: 0.6543 (mmm-85) REVERT: C 239 GLN cc_start: 0.8435 (tt0) cc_final: 0.8091 (tt0) REVERT: C 269 TYR cc_start: 0.8414 (m-80) cc_final: 0.8214 (m-80) REVERT: C 281 GLU cc_start: 0.7917 (pm20) cc_final: 0.7698 (pm20) REVERT: C 324 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7935 (mm-30) REVERT: C 518 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7498 (mp) REVERT: C 558 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8711 (ptpp) REVERT: C 564 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8214 (mm110) REVERT: C 619 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.4939 (pm20) REVERT: C 675 GLN cc_start: 0.8120 (mt0) cc_final: 0.7894 (mm-40) REVERT: C 690 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7917 (mm110) REVERT: C 773 GLU cc_start: 0.8694 (tp30) cc_final: 0.8459 (tt0) REVERT: C 776 LYS cc_start: 0.8816 (ttpt) cc_final: 0.8595 (ttpp) REVERT: C 790 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8100 (mtmm) REVERT: C 795 LYS cc_start: 0.8311 (mmtm) cc_final: 0.8060 (mmtm) REVERT: C 872 GLN cc_start: 0.8582 (mt0) cc_final: 0.8274 (mt0) REVERT: C 976 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8189 (m) REVERT: C 995 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.7906 (ttp80) REVERT: C 1002 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7832 (tm-30) REVERT: C 1091 ARG cc_start: 0.8817 (ttm-80) cc_final: 0.8512 (ttm170) REVERT: C 1101 HIS cc_start: 0.8573 (m90) cc_final: 0.8218 (m-70) REVERT: C 1111 GLU cc_start: 0.8687 (tt0) cc_final: 0.8433 (tt0) REVERT: D 34 MET cc_start: 0.6005 (ptp) cc_final: 0.5427 (ptp) REVERT: D 83 MET cc_start: 0.7560 (ptm) cc_final: 0.7147 (pmm) REVERT: E 29 PHE cc_start: 0.7765 (t80) cc_final: 0.7275 (t80) REVERT: E 34 MET cc_start: 0.7894 (mmm) cc_final: 0.7358 (mmt) REVERT: E 37 VAL cc_start: 0.8764 (m) cc_final: 0.8313 (p) REVERT: E 46 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7971 (mm-30) REVERT: E 58 TYR cc_start: 0.8785 (t80) cc_final: 0.8480 (t80) REVERT: E 82 MET cc_start: 0.7031 (ptm) cc_final: 0.6687 (ptm) REVERT: E 92 MET cc_start: 0.7426 (mtm) cc_final: 0.6745 (mtm) REVERT: E 94 TYR cc_start: 0.7579 (m-80) cc_final: 0.6958 (m-80) REVERT: F 112 THR cc_start: 0.4675 (OUTLIER) cc_final: 0.4451 (p) REVERT: G 77 MET cc_start: 0.7228 (tpp) cc_final: 0.6422 (tmm) REVERT: G 82 MET cc_start: 0.8491 (tmm) cc_final: 0.8230 (tmm) REVERT: H 34 MET cc_start: 0.8233 (ptp) cc_final: 0.7781 (ptp) REVERT: H 59 TYR cc_start: 0.7522 (m-80) cc_final: 0.7146 (m-80) REVERT: H 60 TYR cc_start: 0.7943 (m-80) cc_final: 0.7026 (m-80) REVERT: H 77 ASN cc_start: 0.6969 (t0) cc_final: 0.6613 (t0) REVERT: H 83 MET cc_start: 0.7719 (ptm) cc_final: 0.7247 (ptm) outliers start: 110 outliers final: 96 residues processed: 571 average time/residue: 0.6625 time to fit residues: 597.1932 Evaluate side-chains 592 residues out of total 3228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 490 time to evaluate : 6.284 ------------------------------------------------------------------------------- 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 100 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 130 VAL 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 227 VAL 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 537 LYS 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 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 29 THR 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 210 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU 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 510 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 549 THR 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 907 ASN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 973 ILE 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 126 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 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 641 ASN Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 716 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 994 ASP 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 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 73 optimal weight: 0.8980 chunk 319 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 240 optimal weight: 20.0000 chunk 344 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 311 optimal weight: 7.9990 chunk 312 optimal weight: 6.9990 chunk 322 optimal weight: 0.8980 chunk 226 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 762 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 955 ASN B 957 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.161345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120058 restraints weight = 48096.427| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.63 r_work: 0.3369 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29907 Z= 0.177 Angle : 0.655 14.564 40787 Z= 0.326 Chirality : 0.046 0.249 4656 Planarity : 0.004 0.057 5213 Dihedral : 5.318 90.997 4615 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.43 % Allowed : 17.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 3639 helix: 1.40 (0.21), residues: 677 sheet: -0.80 (0.16), residues: 938 loop : -1.72 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 64 HIS 0.009 0.001 HIS A 954 PHE 0.029 0.002 PHE B 32 TYR 0.021 0.001 TYR B1067 ARG 0.011 0.001 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 28) link_NAG-ASN : angle 2.02890 ( 84) hydrogen bonds : bond 0.03651 ( 910) hydrogen bonds : angle 5.02864 ( 2478) SS BOND : bond 0.00500 ( 46) SS BOND : angle 1.82333 ( 92) covalent geometry : bond 0.00420 (29833) covalent geometry : angle 0.64430 (40611) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26455.66 seconds wall clock time: 462 minutes 42.64 seconds (27762.64 seconds total)