Starting phenix.real_space_refine on Wed Jun 25 18:31:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wor_32656/06_2025/7wor_32656.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wor_32656/06_2025/7wor_32656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wor_32656/06_2025/7wor_32656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wor_32656/06_2025/7wor_32656.map" model { file = "/net/cci-nas-00/data/ceres_data/7wor_32656/06_2025/7wor_32656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wor_32656/06_2025/7wor_32656.cif" } resolution = 3.7 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= 0.023 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 134 5.16 5 C 18904 2.51 5 N 4911 2.21 5 O 5721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.56s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29670 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7989 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "E" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "F" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 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 Time building chain proxies: 16.65, per 1000 atoms: 0.56 Number of scatterers: 29670 At special positions: 0 Unit cell: (146.832, 161.728, 203.224, 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 134 16.00 O 5721 8.00 N 4911 7.00 C 18904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 221 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 146 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 221 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1098 " " NAG A1307 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 616 " " 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 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " Time building additional restraints: 6.79 Conformation dependent library (CDL) restraints added in 3.6 seconds 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7038 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 57 sheets defined 18.3% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 367 through 371 removed outlier: 4.054A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 444 through 448 removed outlier: 3.815A pdb=" N GLY A 447 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.545A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 783 removed outlier: 3.814A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.084A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.544A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 910 " --> pdb=" O PHE A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 930 through 941 removed outlier: 3.537A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.604A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.093A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.984A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 336 through 341 removed outlier: 4.102A pdb=" N ASP B 339 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.701A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.563A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 781 removed outlier: 3.564A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.659A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 939 removed outlier: 4.337A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.540A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.548A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 removed outlier: 3.862A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1143 through 1147' Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 336 through 341 removed outlier: 4.122A pdb=" N ASP C 339 " --> pdb=" O CYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.941A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.590A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.872A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 780 removed outlier: 3.657A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.631A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.072A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 980 removed outlier: 3.605A pdb=" N ASP C 979 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 980 " --> pdb=" O LEU C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 980' Processing helix chain 'C' and resid 985 through 993 removed outlier: 4.427A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1033 removed outlier: 3.670A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.902A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 152 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.670A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.676A pdb=" N ARG B 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.359A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.707A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 93 removed outlier: 3.557A pdb=" N VAL A 191 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 203 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 224 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 5.492A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.955A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.783A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.525A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.762A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.633A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.902A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 229 removed outlier: 3.702A pdb=" N LEU B 226 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASP B 228 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N PHE B 199 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 120 through 122 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.686A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.522A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.736A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 718 removed outlier: 7.066A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 721 through 728 removed outlier: 7.113A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.808A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.935A pdb=" N SER C 94 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN C 186 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 192 through 194 removed outlier: 7.495A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU C 224 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.999A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.524A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.716A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AE6, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AE7, first strand: chain 'C' and resid 721 through 728 removed outlier: 3.782A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.812A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.126A pdb=" N LEU D 48 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN D 39 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 68 through 69 Processing sheet with id=AF4, first strand: chain 'D' and resid 172 through 177 removed outlier: 6.088A pdb=" N TRP D 173 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG D 164 " --> pdb=" O TRP D 173 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 177 " --> pdb=" O MET D 160 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET D 160 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 21 through 23 Processing sheet with id=AF6, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.006A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.006A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR E 87 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 130 through 131 removed outlier: 3.557A pdb=" N SER E 131 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 182 through 184 removed outlier: 6.648A pdb=" N TRP E 160 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL E 174 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 47 through 50 removed outlier: 6.138A pdb=" N LEU F 48 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN F 39 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 64 through 69 removed outlier: 5.373A pdb=" N SER F 65 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER F 67 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 172 through 176 removed outlier: 6.082A pdb=" N TRP F 173 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG F 164 " --> pdb=" O TRP F 173 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 2136 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: 12.12 Time building geometry restraints manager: 8.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7896 1.33 - 1.45: 5888 1.45 - 1.57: 16409 1.57 - 1.69: 0 1.69 - 1.82: 172 Bond restraints: 30365 Sorted by residual: bond pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.23e-02 6.61e+03 4.74e+01 bond pdb=" CA ASN C1134 " pdb=" C ASN C1134 " ideal model delta sigma weight residual 1.523 1.459 0.065 1.19e-02 7.06e+03 2.95e+01 bond pdb=" CA TYR B 707 " pdb=" C TYR B 707 " ideal model delta sigma weight residual 1.525 1.465 0.060 1.28e-02 6.10e+03 2.17e+01 bond pdb=" CA ASN B 801 " pdb=" C ASN B 801 " ideal model delta sigma weight residual 1.522 1.475 0.047 1.08e-02 8.57e+03 1.87e+01 bond pdb=" CA ASN C 280 " pdb=" C ASN C 280 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.34e-02 5.57e+03 1.67e+01 ... (remaining 30360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 40772 2.07 - 4.14: 500 4.14 - 6.22: 51 6.22 - 8.29: 5 8.29 - 10.36: 1 Bond angle restraints: 41329 Sorted by residual: angle pdb=" N ASN A 616 " pdb=" CA ASN A 616 " pdb=" C ASN A 616 " ideal model delta sigma weight residual 112.93 107.19 5.74 1.12e+00 7.97e-01 2.63e+01 angle pdb=" N GLU A 281 " pdb=" CA GLU A 281 " pdb=" C GLU A 281 " ideal model delta sigma weight residual 111.71 106.00 5.71 1.15e+00 7.56e-01 2.47e+01 angle pdb=" N ASN B1134 " pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 109.24 101.31 7.93 1.63e+00 3.76e-01 2.37e+01 angle pdb=" N ALA C 27 " pdb=" CA ALA C 27 " pdb=" C ALA C 27 " ideal model delta sigma weight residual 110.80 100.44 10.36 2.13e+00 2.20e-01 2.37e+01 angle pdb=" N ILE B 418 " pdb=" CA ILE B 418 " pdb=" C ILE B 418 " ideal model delta sigma weight residual 113.53 108.78 4.75 9.80e-01 1.04e+00 2.35e+01 ... (remaining 41324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 17451 16.86 - 33.72: 712 33.72 - 50.58: 124 50.58 - 67.45: 35 67.45 - 84.31: 4 Dihedral angle restraints: 18326 sinusoidal: 7335 harmonic: 10991 Sorted by residual: dihedral pdb=" CA ALA C 27 " pdb=" C ALA C 27 " pdb=" N TYR C 28 " pdb=" CA TYR C 28 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR C 28 " pdb=" C TYR C 28 " pdb=" N THR C 29 " pdb=" CA THR C 29 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA CYS B 336 " pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " ideal model delta sinusoidal sigma weight residual 79.00 20.41 58.59 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 18323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 4707 0.294 - 0.588: 2 0.588 - 0.881: 1 0.881 - 1.175: 0 1.175 - 1.469: 1 Chirality restraints: 4711 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-01 2.50e+01 5.39e+01 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.43e+00 ... (remaining 4708 not shown) Planarity restraints: 5356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " 0.357 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG C1304 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " 0.131 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1307 " 0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C1307 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C1307 " 0.088 2.00e-02 2.50e+03 pdb=" N2 NAG C1307 " -0.536 2.00e-02 2.50e+03 pdb=" O7 NAG C1307 " 0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1308 " -0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C1308 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG C1308 " -0.089 2.00e-02 2.50e+03 pdb=" N2 NAG C1308 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG C1308 " -0.178 2.00e-02 2.50e+03 ... (remaining 5353 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3132 2.75 - 3.29: 29561 3.29 - 3.83: 48424 3.83 - 4.36: 55090 4.36 - 4.90: 95448 Nonbonded interactions: 231655 Sorted by model distance: nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.216 3.040 nonbonded pdb=" OG SER F 91 " pdb=" OE1 GLN F 227 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR C 719 " pdb=" O VAL C1068 " model vdw 2.236 3.040 nonbonded pdb=" OG SER D 91 " pdb=" OE1 GLN D 227 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR B 719 " pdb=" O VAL B1068 " model vdw 2.240 3.040 ... (remaining 231650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 243 or resid 262 through 1147 or resid 1301 thr \ ough 1307)) selection = (chain 'B' and (resid 26 through 243 or resid 262 through 1147 or resid 1301 thr \ ough 1307)) selection = (chain 'C' and (resid 26 through 1147 or resid 1301 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 65.180 Find NCS groups from input model: 1.660 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 30432 Z= 0.199 Angle : 0.540 10.359 41486 Z= 0.294 Chirality : 0.049 1.469 4711 Planarity : 0.014 0.307 5333 Dihedral : 9.284 84.306 11156 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.68 % Favored : 92.22 % Rotamer: Outliers : 5.34 % Allowed : 8.31 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.11), residues: 3739 helix: -0.58 (0.19), residues: 658 sheet: -2.46 (0.18), residues: 630 loop : -3.61 (0.10), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 98 HIS 0.001 0.000 HIS A 519 PHE 0.011 0.001 PHE A 375 TYR 0.011 0.001 TYR A1067 ARG 0.002 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00816 ( 23) link_NAG-ASN : angle 3.06291 ( 69) hydrogen bonds : bond 0.14024 ( 800) hydrogen bonds : angle 6.13493 ( 2136) SS BOND : bond 0.00126 ( 44) SS BOND : angle 0.50492 ( 88) covalent geometry : bond 0.00311 (30365) covalent geometry : angle 0.52557 (41329) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 628 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7238 (m-10) cc_final: 0.6995 (m-10) REVERT: A 223 LEU cc_start: 0.7206 (mp) cc_final: 0.6891 (mp) REVERT: A 300 LYS cc_start: 0.8346 (mtmt) cc_final: 0.8004 (mttm) REVERT: A 307 THR cc_start: 0.7835 (m) cc_final: 0.7491 (p) REVERT: A 364 ASP cc_start: 0.8201 (t0) cc_final: 0.7814 (t0) REVERT: A 396 TYR cc_start: 0.5889 (m-80) cc_final: 0.5032 (m-80) REVERT: A 516 GLU cc_start: 0.5249 (pt0) cc_final: 0.4200 (pt0) REVERT: A 546 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8298 (tt) REVERT: A 556 ASN cc_start: 0.8009 (p0) cc_final: 0.7408 (p0) REVERT: A 562 PHE cc_start: 0.7058 (p90) cc_final: 0.6636 (p90) REVERT: A 592 PHE cc_start: 0.6818 (p90) cc_final: 0.6205 (p90) REVERT: A 602 THR cc_start: 0.7836 (m) cc_final: 0.7164 (p) REVERT: A 615 VAL cc_start: 0.8413 (t) cc_final: 0.8107 (m) REVERT: A 732 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8527 (p) REVERT: A 737 ASP cc_start: 0.7069 (t0) cc_final: 0.6219 (t0) REVERT: A 776 LYS cc_start: 0.8282 (tmmt) cc_final: 0.7871 (tptp) REVERT: A 821 LEU cc_start: 0.8392 (tp) cc_final: 0.8037 (mt) REVERT: A 864 LEU cc_start: 0.8707 (tp) cc_final: 0.8419 (tt) REVERT: A 914 ASN cc_start: 0.7830 (p0) cc_final: 0.7602 (p0) REVERT: A 921 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7768 (mmmt) REVERT: A 954 HIS cc_start: 0.6810 (m-70) cc_final: 0.6534 (m170) REVERT: A 960 ASN cc_start: 0.7426 (m-40) cc_final: 0.7128 (m-40) REVERT: A 964 LYS cc_start: 0.8511 (tmtm) cc_final: 0.8215 (tppt) REVERT: A 969 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7617 (mppt) REVERT: A 980 ILE cc_start: 0.8796 (mt) cc_final: 0.8536 (pt) REVERT: A 984 LEU cc_start: 0.8961 (mt) cc_final: 0.8137 (mt) REVERT: A 988 GLU cc_start: 0.7638 (tp30) cc_final: 0.6757 (tp30) REVERT: A 1002 GLN cc_start: 0.7056 (tp-100) cc_final: 0.6611 (tp-100) REVERT: A 1057 PRO cc_start: 0.8968 (Cg_exo) cc_final: 0.8689 (Cg_endo) REVERT: A 1081 ILE cc_start: 0.8517 (pt) cc_final: 0.8065 (mm) REVERT: A 1111 GLU cc_start: 0.6842 (tt0) cc_final: 0.6595 (tt0) REVERT: B 33 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8931 (p) REVERT: B 41 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7302 (mttt) REVERT: B 44 ARG cc_start: 0.8044 (mtt90) cc_final: 0.7668 (mtt180) REVERT: B 132 GLU cc_start: 0.3624 (pt0) cc_final: 0.3314 (pm20) REVERT: B 177 MET cc_start: 0.5805 (mtt) cc_final: 0.5312 (mtt) REVERT: B 186 ASN cc_start: 0.6148 (p0) cc_final: 0.5429 (p0) REVERT: B 188 ARG cc_start: 0.7213 (mtt-85) cc_final: 0.6550 (mtm-85) REVERT: B 189 GLU cc_start: 0.7070 (pm20) cc_final: 0.6468 (pm20) REVERT: B 193 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7771 (ttmt) REVERT: B 200 LYS cc_start: 0.8562 (mttt) cc_final: 0.8262 (mptt) REVERT: B 267 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.8076 (p) REVERT: B 278 LYS cc_start: 0.8359 (ttmp) cc_final: 0.8152 (ttmm) REVERT: B 286 THR cc_start: 0.7724 (p) cc_final: 0.7486 (p) REVERT: B 307 THR cc_start: 0.7885 (m) cc_final: 0.7480 (p) REVERT: B 329 PHE cc_start: 0.5966 (m-10) cc_final: 0.5620 (m-10) REVERT: B 403 ARG cc_start: 0.5596 (mtm-85) cc_final: 0.5038 (ttm170) REVERT: B 524 VAL cc_start: -0.0245 (OUTLIER) cc_final: -0.1091 (t) REVERT: B 698 SER cc_start: 0.8138 (t) cc_final: 0.7801 (p) REVERT: B 759 PHE cc_start: 0.7276 (t80) cc_final: 0.6739 (t80) REVERT: B 768 THR cc_start: 0.8457 (m) cc_final: 0.8236 (p) REVERT: B 776 LYS cc_start: 0.8122 (ttpm) cc_final: 0.7797 (ttpp) REVERT: B 821 LEU cc_start: 0.8883 (tt) cc_final: 0.8649 (tp) REVERT: B 851 CYS cc_start: 0.7973 (t) cc_final: 0.7490 (p) REVERT: B 856 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8640 (tppp) REVERT: B 914 ASN cc_start: 0.8005 (p0) cc_final: 0.7568 (p0) REVERT: B 965 GLN cc_start: 0.6910 (mt0) cc_final: 0.6619 (mm110) REVERT: B 979 ASP cc_start: 0.8106 (m-30) cc_final: 0.7851 (m-30) REVERT: B 1019 ARG cc_start: 0.7717 (ttm110) cc_final: 0.7409 (ttm170) REVERT: C 28 TYR cc_start: 0.7470 (m-80) cc_final: 0.6850 (m-10) REVERT: C 92 PHE cc_start: 0.7450 (t80) cc_final: 0.7180 (t80) REVERT: C 118 LEU cc_start: 0.8597 (mp) cc_final: 0.8180 (mm) REVERT: C 129 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7613 (tptt) REVERT: C 188 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5597 (tpp80) REVERT: C 560 LEU cc_start: 0.8477 (mt) cc_final: 0.8172 (mm) REVERT: C 602 THR cc_start: 0.8612 (m) cc_final: 0.8400 (m) REVERT: C 616 ASN cc_start: 0.5482 (t0) cc_final: 0.5078 (t0) REVERT: C 707 TYR cc_start: 0.7943 (t80) cc_final: 0.7313 (t80) REVERT: C 759 PHE cc_start: 0.6811 (m-80) cc_final: 0.6468 (m-80) REVERT: C 816 SER cc_start: 0.8284 (p) cc_final: 0.8083 (p) REVERT: C 819 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7047 (mt-10) REVERT: C 850 ILE cc_start: 0.8807 (mm) cc_final: 0.8598 (tp) REVERT: C 851 CYS cc_start: 0.8041 (t) cc_final: 0.7521 (p) REVERT: C 914 ASN cc_start: 0.7751 (p0) cc_final: 0.7122 (p0) REVERT: C 922 LEU cc_start: 0.7954 (tp) cc_final: 0.7716 (tp) REVERT: C 950 ASP cc_start: 0.7005 (t70) cc_final: 0.6594 (t0) REVERT: C 953 ASN cc_start: 0.8247 (m-40) cc_final: 0.8031 (m-40) REVERT: C 978 ASN cc_start: 0.8284 (m-40) cc_final: 0.7957 (m-40) REVERT: C 985 ASP cc_start: 0.7750 (p0) cc_final: 0.7547 (p0) REVERT: C 991 VAL cc_start: 0.8827 (t) cc_final: 0.7893 (p) REVERT: C 1031 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7308 (mt-10) REVERT: C 1097 SER cc_start: 0.9166 (t) cc_final: 0.8680 (p) REVERT: C 1136 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8579 (p) REVERT: D 6 GLN cc_start: -0.0341 (OUTLIER) cc_final: -0.1228 (tp-100) REVERT: D 35 VAL cc_start: 0.2299 (OUTLIER) cc_final: 0.2006 (p) REVERT: D 111 LEU cc_start: 0.5380 (OUTLIER) cc_final: 0.4978 (tm) REVERT: D 144 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5697 (tm) REVERT: D 193 PHE cc_start: -0.1356 (OUTLIER) cc_final: -0.1613 (p90) REVERT: E 174 VAL cc_start: 0.4147 (OUTLIER) cc_final: 0.3885 (t) REVERT: F 128 VAL cc_start: -0.3221 (OUTLIER) cc_final: -0.3633 (p) REVERT: F 160 MET cc_start: -0.0689 (ptp) cc_final: -0.1815 (mmm) outliers start: 173 outliers final: 60 residues processed: 773 average time/residue: 0.4228 time to fit residues: 513.4413 Evaluate side-chains 567 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 491 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 20.0000 chunk 285 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 295 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 chunk 342 optimal weight: 50.0000 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 49 HIS A 87 ASN A 173 GLN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 422 ASN A 540 ASN A 564 GLN A 613 GLN A 690 GLN A 784 GLN A 853 GLN A 901 GLN A1002 GLN A1005 GLN A1011 GLN A1048 HIS A1101 HIS B 173 GLN B 181 GLN B 245 HIS B 321 GLN B 354 ASN B 370 ASN B 388 ASN B 448 ASN B 477 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 607 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 901 GLN B 914 ASN B 926 GLN B 957 GLN B1010 GLN B1048 HIS B1054 GLN B1119 ASN C 49 HIS C 99 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 205 HIS C 218 GLN C 271 GLN C 321 GLN C 354 ASN C 370 ASN C 388 ASN C 409 GLN C 422 ASN C 448 ASN C 477 ASN C 487 ASN C 540 ASN C 580 GLN C 613 GLN C 641 ASN C 784 GLN C 853 GLN C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 914 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN C1048 HIS C1119 ASN C1125 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 39 GLN D 40 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 202 ASN D 207 GLN D 209 ASN E 80 GLN E 97 ASN E 137 GLN E 201 ASN E 206 GLN F 33 ASN F 39 GLN F 40 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN F 202 ASN F 207 GLN Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.201724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148957 restraints weight = 54538.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.152568 restraints weight = 24700.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.154191 restraints weight = 13253.378| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 30432 Z= 0.199 Angle : 0.671 13.090 41486 Z= 0.329 Chirality : 0.048 0.613 4711 Planarity : 0.005 0.106 5333 Dihedral : 7.200 80.095 4735 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 4.88 % Allowed : 13.37 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.12), residues: 3739 helix: 0.15 (0.20), residues: 686 sheet: -2.11 (0.18), residues: 668 loop : -3.24 (0.11), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 64 HIS 0.007 0.001 HIS A1064 PHE 0.028 0.002 PHE B 106 TYR 0.026 0.001 TYR B1067 ARG 0.010 0.001 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 23) link_NAG-ASN : angle 3.22560 ( 69) hydrogen bonds : bond 0.03810 ( 800) hydrogen bonds : angle 4.88540 ( 2136) SS BOND : bond 0.00377 ( 44) SS BOND : angle 2.39781 ( 88) covalent geometry : bond 0.00438 (30365) covalent geometry : angle 0.64971 (41329) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 511 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8101 (p0) cc_final: 0.7870 (p0) REVERT: A 64 TRP cc_start: 0.7791 (t60) cc_final: 0.7558 (t-100) REVERT: A 88 ASP cc_start: 0.5477 (p0) cc_final: 0.5127 (p0) REVERT: A 300 LYS cc_start: 0.8285 (mtmt) cc_final: 0.8016 (mtmm) REVERT: A 307 THR cc_start: 0.7945 (m) cc_final: 0.7633 (p) REVERT: A 396 TYR cc_start: 0.5970 (m-80) cc_final: 0.5274 (m-80) REVERT: A 516 GLU cc_start: 0.5757 (pt0) cc_final: 0.4818 (pt0) REVERT: A 546 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8311 (tt) REVERT: A 556 ASN cc_start: 0.8072 (p0) cc_final: 0.7647 (t0) REVERT: A 562 PHE cc_start: 0.7269 (p90) cc_final: 0.6876 (p90) REVERT: A 596 SER cc_start: 0.8814 (m) cc_final: 0.8589 (p) REVERT: A 602 THR cc_start: 0.7958 (m) cc_final: 0.7454 (p) REVERT: A 604 THR cc_start: 0.6843 (t) cc_final: 0.6160 (m) REVERT: A 615 VAL cc_start: 0.8536 (t) cc_final: 0.8306 (m) REVERT: A 674 TYR cc_start: 0.8174 (t80) cc_final: 0.7942 (t80) REVERT: A 737 ASP cc_start: 0.7013 (t0) cc_final: 0.6638 (t0) REVERT: A 790 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8173 (ptpp) REVERT: A 820 ASP cc_start: 0.7992 (m-30) cc_final: 0.7731 (t0) REVERT: A 856 LYS cc_start: 0.8065 (tppt) cc_final: 0.7651 (tppt) REVERT: A 864 LEU cc_start: 0.8679 (tp) cc_final: 0.8466 (tt) REVERT: A 921 LYS cc_start: 0.8432 (mmmt) cc_final: 0.7821 (mmmt) REVERT: A 950 ASP cc_start: 0.7206 (t70) cc_final: 0.6346 (t70) REVERT: A 954 HIS cc_start: 0.7104 (m-70) cc_final: 0.6721 (m170) REVERT: A 955 ASN cc_start: 0.8397 (t0) cc_final: 0.8173 (t0) REVERT: A 964 LYS cc_start: 0.8695 (tmtm) cc_final: 0.8492 (tppt) REVERT: A 983 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7412 (ttp80) REVERT: A 984 LEU cc_start: 0.8844 (mt) cc_final: 0.8535 (mt) REVERT: A 988 GLU cc_start: 0.7764 (tp30) cc_final: 0.7087 (tp30) REVERT: A 1057 PRO cc_start: 0.8918 (Cg_exo) cc_final: 0.8610 (Cg_endo) REVERT: A 1081 ILE cc_start: 0.8517 (pt) cc_final: 0.8287 (mm) REVERT: B 41 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7228 (mtpt) REVERT: B 62 VAL cc_start: 0.8135 (t) cc_final: 0.7833 (m) REVERT: B 105 ILE cc_start: 0.8391 (mm) cc_final: 0.7810 (tp) REVERT: B 106 PHE cc_start: 0.7139 (m-80) cc_final: 0.6900 (m-80) REVERT: B 186 ASN cc_start: 0.6693 (p0) cc_final: 0.5658 (p0) REVERT: B 188 ARG cc_start: 0.7529 (mtt-85) cc_final: 0.7035 (mtt-85) REVERT: B 193 LYS cc_start: 0.8152 (ttpt) cc_final: 0.7802 (ttmm) REVERT: B 200 LYS cc_start: 0.8605 (mttt) cc_final: 0.8307 (mttt) REVERT: B 267 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8191 (p) REVERT: B 307 THR cc_start: 0.8028 (m) cc_final: 0.7593 (p) REVERT: B 329 PHE cc_start: 0.5922 (m-10) cc_final: 0.5651 (m-10) REVERT: B 403 ARG cc_start: 0.6153 (mtm-85) cc_final: 0.5545 (ttm170) REVERT: B 563 GLN cc_start: 0.6668 (pt0) cc_final: 0.6381 (pt0) REVERT: B 592 PHE cc_start: 0.7425 (p90) cc_final: 0.5220 (p90) REVERT: B 602 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8192 (p) REVERT: B 698 SER cc_start: 0.8411 (t) cc_final: 0.7869 (p) REVERT: B 726 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8171 (mp) REVERT: B 773 GLU cc_start: 0.6751 (tp30) cc_final: 0.6411 (tp30) REVERT: B 776 LYS cc_start: 0.8273 (ttpm) cc_final: 0.7995 (ttpp) REVERT: B 780 GLU cc_start: 0.7376 (tp30) cc_final: 0.6992 (tp30) REVERT: B 851 CYS cc_start: 0.8315 (t) cc_final: 0.7759 (p) REVERT: B 856 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8897 (tppp) REVERT: B 957 GLN cc_start: 0.7085 (tm-30) cc_final: 0.6726 (tm-30) REVERT: B 964 LYS cc_start: 0.8355 (tmmt) cc_final: 0.7516 (tmmt) REVERT: B 977 LEU cc_start: 0.8442 (mp) cc_final: 0.8212 (mt) REVERT: B 1019 ARG cc_start: 0.7984 (ttm110) cc_final: 0.7659 (ttp80) REVERT: C 55 PHE cc_start: 0.7059 (m-10) cc_final: 0.5418 (m-10) REVERT: C 104 TRP cc_start: 0.7019 (m-90) cc_final: 0.6770 (m-10) REVERT: C 118 LEU cc_start: 0.8668 (mp) cc_final: 0.8418 (mm) REVERT: C 129 LYS cc_start: 0.8287 (ttmt) cc_final: 0.7633 (tptt) REVERT: C 224 GLU cc_start: 0.7000 (pm20) cc_final: 0.6716 (pm20) REVERT: C 269 TYR cc_start: 0.6861 (m-10) cc_final: 0.6528 (m-80) REVERT: C 303 LEU cc_start: 0.8301 (tp) cc_final: 0.7958 (tp) REVERT: C 361 CYS cc_start: 0.6078 (OUTLIER) cc_final: 0.3029 (p) REVERT: C 362 VAL cc_start: 0.7552 (OUTLIER) cc_final: 0.7013 (m) REVERT: C 537 LYS cc_start: 0.7981 (tttp) cc_final: 0.7778 (tptm) REVERT: C 557 LYS cc_start: 0.8709 (mttm) cc_final: 0.8501 (mttm) REVERT: C 558 LYS cc_start: 0.8475 (mttt) cc_final: 0.8251 (mtmt) REVERT: C 707 TYR cc_start: 0.8120 (t80) cc_final: 0.7544 (t80) REVERT: C 718 PHE cc_start: 0.7753 (p90) cc_final: 0.7334 (p90) REVERT: C 754 LEU cc_start: 0.8605 (tp) cc_final: 0.8352 (tt) REVERT: C 776 LYS cc_start: 0.8337 (ttpp) cc_final: 0.8058 (ttpp) REVERT: C 820 ASP cc_start: 0.7674 (t70) cc_final: 0.7340 (t0) REVERT: C 821 LEU cc_start: 0.8894 (tp) cc_final: 0.8653 (tt) REVERT: C 851 CYS cc_start: 0.8084 (t) cc_final: 0.7675 (p) REVERT: C 854 LYS cc_start: 0.8188 (tmtt) cc_final: 0.7974 (tmtt) REVERT: C 868 GLU cc_start: 0.7488 (tp30) cc_final: 0.7286 (tp30) REVERT: C 914 ASN cc_start: 0.7757 (p0) cc_final: 0.7484 (p0) REVERT: C 950 ASP cc_start: 0.7326 (t70) cc_final: 0.6829 (t0) REVERT: C 978 ASN cc_start: 0.8497 (m-40) cc_final: 0.8102 (m-40) REVERT: C 1029 MET cc_start: 0.8502 (tpp) cc_final: 0.8187 (ttm) REVERT: C 1084 ASP cc_start: 0.7757 (t0) cc_final: 0.7459 (t0) REVERT: C 1086 LYS cc_start: 0.8387 (mmmt) cc_final: 0.8060 (mmmt) REVERT: C 1097 SER cc_start: 0.9027 (t) cc_final: 0.8449 (p) REVERT: C 1136 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8591 (p) REVERT: D 6 GLN cc_start: -0.0531 (OUTLIER) cc_final: -0.1332 (tp-100) REVERT: D 35 VAL cc_start: 0.2041 (OUTLIER) cc_final: 0.1728 (p) REVERT: D 90 CYS cc_start: 0.6007 (OUTLIER) cc_final: 0.5633 (t) REVERT: D 111 LEU cc_start: 0.5338 (OUTLIER) cc_final: 0.4923 (tm) REVERT: D 234 MET cc_start: -0.3844 (pmt) cc_final: -0.4442 (pmt) REVERT: F 160 MET cc_start: -0.0701 (ptp) cc_final: -0.1697 (mmm) outliers start: 158 outliers final: 83 residues processed: 636 average time/residue: 0.4044 time to fit residues: 409.2659 Evaluate side-chains 567 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 470 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 357 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 298 optimal weight: 0.5980 chunk 337 optimal weight: 5.9990 chunk 268 optimal weight: 0.9990 chunk 330 optimal weight: 50.0000 chunk 256 optimal weight: 0.0270 chunk 196 optimal weight: 0.0070 chunk 218 optimal weight: 2.9990 chunk 279 optimal weight: 0.5980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 935 GLN A1005 GLN A1101 HIS B 422 ASN B 563 GLN B 607 GLN B 690 GLN B 804 GLN B 926 GLN B 965 GLN C 563 GLN C 613 GLN C 641 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.202900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.151961 restraints weight = 54948.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.153082 restraints weight = 27536.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155267 restraints weight = 15791.042| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 30432 Z= 0.108 Angle : 0.600 15.480 41486 Z= 0.291 Chirality : 0.045 0.410 4711 Planarity : 0.004 0.054 5333 Dihedral : 6.679 80.377 4706 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.45 % Allowed : 15.10 % Favored : 80.46 % 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: -3.01 (0.13), residues: 3739 helix: 0.71 (0.21), residues: 670 sheet: -2.00 (0.20), residues: 596 loop : -3.00 (0.11), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.008 0.001 HIS A 519 PHE 0.024 0.001 PHE B 92 TYR 0.027 0.001 TYR A 170 ARG 0.009 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 23) link_NAG-ASN : angle 2.52140 ( 69) hydrogen bonds : bond 0.03109 ( 800) hydrogen bonds : angle 4.71487 ( 2136) SS BOND : bond 0.00184 ( 44) SS BOND : angle 1.74327 ( 88) covalent geometry : bond 0.00245 (30365) covalent geometry : angle 0.58658 (41329) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 479 time to evaluate : 3.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.6964 (m-10) cc_final: 0.6658 (m-10) REVERT: A 64 TRP cc_start: 0.7834 (t60) cc_final: 0.7631 (t60) REVERT: A 88 ASP cc_start: 0.5491 (p0) cc_final: 0.5148 (p0) REVERT: A 118 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5965 (pp) REVERT: A 223 LEU cc_start: 0.7396 (mp) cc_final: 0.6758 (mp) REVERT: A 307 THR cc_start: 0.7912 (m) cc_final: 0.7533 (p) REVERT: A 308 VAL cc_start: 0.8582 (p) cc_final: 0.8364 (m) REVERT: A 319 ARG cc_start: 0.7720 (ttm170) cc_final: 0.7512 (ttm-80) REVERT: A 396 TYR cc_start: 0.6109 (m-80) cc_final: 0.5468 (m-80) REVERT: A 516 GLU cc_start: 0.5813 (pt0) cc_final: 0.5036 (pt0) REVERT: A 546 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8276 (tt) REVERT: A 556 ASN cc_start: 0.8042 (p0) cc_final: 0.7489 (t0) REVERT: A 560 LEU cc_start: 0.7789 (tp) cc_final: 0.7452 (tp) REVERT: A 562 PHE cc_start: 0.7271 (p90) cc_final: 0.6943 (p90) REVERT: A 596 SER cc_start: 0.8786 (m) cc_final: 0.8565 (p) REVERT: A 602 THR cc_start: 0.7869 (m) cc_final: 0.7352 (p) REVERT: A 604 THR cc_start: 0.6993 (t) cc_final: 0.6355 (m) REVERT: A 615 VAL cc_start: 0.8392 (t) cc_final: 0.8142 (m) REVERT: A 643 PHE cc_start: 0.7248 (t80) cc_final: 0.7032 (t80) REVERT: A 674 TYR cc_start: 0.8099 (t80) cc_final: 0.7871 (t80) REVERT: A 790 LYS cc_start: 0.8488 (ptpp) cc_final: 0.8101 (ptpp) REVERT: A 856 LYS cc_start: 0.8282 (tppt) cc_final: 0.8005 (tppt) REVERT: A 864 LEU cc_start: 0.8574 (tp) cc_final: 0.8311 (tt) REVERT: A 921 LYS cc_start: 0.8405 (mmmt) cc_final: 0.7816 (mmmt) REVERT: A 950 ASP cc_start: 0.7111 (t70) cc_final: 0.6217 (t70) REVERT: A 954 HIS cc_start: 0.7095 (m-70) cc_final: 0.6691 (m170) REVERT: A 955 ASN cc_start: 0.8387 (t0) cc_final: 0.7946 (t0) REVERT: A 959 LEU cc_start: 0.8538 (mt) cc_final: 0.8316 (mt) REVERT: A 964 LYS cc_start: 0.8714 (tmtm) cc_final: 0.8501 (tppt) REVERT: A 983 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7640 (ttp80) REVERT: A 984 LEU cc_start: 0.8857 (mt) cc_final: 0.8495 (mt) REVERT: A 988 GLU cc_start: 0.7530 (tp30) cc_final: 0.7022 (tp30) REVERT: A 1057 PRO cc_start: 0.8839 (Cg_exo) cc_final: 0.8508 (Cg_endo) REVERT: A 1111 GLU cc_start: 0.7030 (tt0) cc_final: 0.6812 (tt0) REVERT: A 1138 TYR cc_start: 0.7708 (t80) cc_final: 0.7443 (t80) REVERT: B 62 VAL cc_start: 0.8170 (t) cc_final: 0.7871 (p) REVERT: B 105 ILE cc_start: 0.8461 (mm) cc_final: 0.8025 (tp) REVERT: B 186 ASN cc_start: 0.6569 (p0) cc_final: 0.6210 (p0) REVERT: B 189 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6264 (pm20) REVERT: B 193 LYS cc_start: 0.8101 (ttpt) cc_final: 0.7764 (ttmm) REVERT: B 200 LYS cc_start: 0.8590 (mttt) cc_final: 0.8129 (mttp) REVERT: B 201 ILE cc_start: 0.9029 (mp) cc_final: 0.8777 (pt) REVERT: B 204 LYS cc_start: 0.7716 (tppp) cc_final: 0.6822 (tptt) REVERT: B 220 PHE cc_start: 0.7499 (t80) cc_final: 0.7201 (t80) REVERT: B 271 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 307 THR cc_start: 0.7877 (m) cc_final: 0.7506 (p) REVERT: B 329 PHE cc_start: 0.5903 (m-10) cc_final: 0.5622 (m-10) REVERT: B 403 ARG cc_start: 0.6021 (mtm-85) cc_final: 0.5388 (ttm170) REVERT: B 592 PHE cc_start: 0.7148 (p90) cc_final: 0.6845 (p90) REVERT: B 602 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8100 (p) REVERT: B 698 SER cc_start: 0.8295 (t) cc_final: 0.7817 (p) REVERT: B 776 LYS cc_start: 0.8209 (ttpm) cc_final: 0.7678 (ttpp) REVERT: B 780 GLU cc_start: 0.7464 (tp30) cc_final: 0.6916 (tp30) REVERT: B 851 CYS cc_start: 0.8354 (t) cc_final: 0.7725 (p) REVERT: B 856 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8973 (tppp) REVERT: B 957 GLN cc_start: 0.7089 (tm-30) cc_final: 0.6657 (tm-30) REVERT: B 964 LYS cc_start: 0.8295 (tmmt) cc_final: 0.8040 (tmmt) REVERT: B 965 GLN cc_start: 0.7383 (mm110) cc_final: 0.6425 (mm-40) REVERT: B 1019 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7559 (ttp80) REVERT: C 106 PHE cc_start: 0.8145 (m-80) cc_final: 0.7873 (m-10) REVERT: C 118 LEU cc_start: 0.8831 (mp) cc_final: 0.8532 (mm) REVERT: C 129 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7604 (tptt) REVERT: C 229 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7336 (pp) REVERT: C 237 ARG cc_start: 0.7440 (mtp85) cc_final: 0.7022 (mtp85) REVERT: C 269 TYR cc_start: 0.6754 (m-10) cc_final: 0.6458 (m-80) REVERT: C 281 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6652 (mt-10) REVERT: C 303 LEU cc_start: 0.8309 (tp) cc_final: 0.7899 (tp) REVERT: C 361 CYS cc_start: 0.5626 (OUTLIER) cc_final: 0.3344 (p) REVERT: C 557 LYS cc_start: 0.8708 (mttm) cc_final: 0.8498 (mttm) REVERT: C 558 LYS cc_start: 0.8533 (mttt) cc_final: 0.8265 (mttt) REVERT: C 707 TYR cc_start: 0.8085 (t80) cc_final: 0.7491 (t80) REVERT: C 718 PHE cc_start: 0.7687 (p90) cc_final: 0.7178 (p90) REVERT: C 754 LEU cc_start: 0.8530 (tp) cc_final: 0.8288 (tt) REVERT: C 821 LEU cc_start: 0.8907 (tp) cc_final: 0.8641 (tt) REVERT: C 851 CYS cc_start: 0.8021 (t) cc_final: 0.7777 (p) REVERT: C 868 GLU cc_start: 0.7445 (tp30) cc_final: 0.7244 (tp30) REVERT: C 914 ASN cc_start: 0.7741 (p0) cc_final: 0.7482 (p0) REVERT: C 950 ASP cc_start: 0.7345 (t70) cc_final: 0.6802 (t0) REVERT: C 978 ASN cc_start: 0.8142 (m-40) cc_final: 0.7940 (m-40) REVERT: C 1029 MET cc_start: 0.8267 (tpp) cc_final: 0.8045 (ttm) REVERT: C 1084 ASP cc_start: 0.7867 (t0) cc_final: 0.7500 (t0) REVERT: C 1086 LYS cc_start: 0.8408 (mmmt) cc_final: 0.8155 (mmmt) REVERT: C 1097 SER cc_start: 0.9043 (t) cc_final: 0.8531 (p) REVERT: C 1136 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8526 (p) REVERT: D 6 GLN cc_start: -0.0646 (OUTLIER) cc_final: -0.1402 (tp-100) REVERT: D 35 VAL cc_start: 0.2226 (OUTLIER) cc_final: 0.1913 (p) REVERT: D 90 CYS cc_start: 0.5904 (OUTLIER) cc_final: 0.5413 (t) REVERT: D 111 LEU cc_start: 0.5283 (OUTLIER) cc_final: 0.4890 (tm) REVERT: D 208 MET cc_start: 0.2779 (tmm) cc_final: 0.2416 (tmm) REVERT: D 234 MET cc_start: -0.3733 (pmt) cc_final: -0.4301 (pmt) REVERT: E 174 VAL cc_start: 0.5138 (OUTLIER) cc_final: 0.4872 (t) REVERT: F 160 MET cc_start: -0.1019 (ptp) cc_final: -0.1888 (mmm) outliers start: 144 outliers final: 85 residues processed: 589 average time/residue: 0.4328 time to fit residues: 405.1862 Evaluate side-chains 542 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 444 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 195 optimal weight: 1.9990 chunk 332 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 244 optimal weight: 0.0060 chunk 249 optimal weight: 40.0000 chunk 367 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 311 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1101 HIS B 422 ASN B 607 GLN B 644 GLN B1010 GLN B1101 HIS C 81 ASN C 99 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.198064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145379 restraints weight = 54877.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.147949 restraints weight = 26464.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150624 restraints weight = 14010.187| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 30432 Z= 0.214 Angle : 0.637 9.932 41486 Z= 0.317 Chirality : 0.046 0.408 4711 Planarity : 0.005 0.064 5333 Dihedral : 6.772 80.333 4693 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 5.03 % Allowed : 15.71 % Favored : 79.25 % 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: -2.91 (0.13), residues: 3739 helix: 0.69 (0.21), residues: 667 sheet: -1.82 (0.19), residues: 660 loop : -2.94 (0.11), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.010 0.002 HIS A 66 PHE 0.025 0.002 PHE C 562 TYR 0.024 0.001 TYR B1067 ARG 0.009 0.001 ARG C 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 23) link_NAG-ASN : angle 2.55194 ( 69) hydrogen bonds : bond 0.03805 ( 800) hydrogen bonds : angle 4.89706 ( 2136) SS BOND : bond 0.00684 ( 44) SS BOND : angle 1.97943 ( 88) covalent geometry : bond 0.00475 (30365) covalent geometry : angle 0.62251 (41329) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 476 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7041 (m-10) cc_final: 0.6688 (m-10) REVERT: A 64 TRP cc_start: 0.7691 (t60) cc_final: 0.7480 (t60) REVERT: A 106 PHE cc_start: 0.7492 (m-80) cc_final: 0.6751 (m-80) REVERT: A 118 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6194 (pp) REVERT: A 177 MET cc_start: 0.4203 (tpp) cc_final: 0.3979 (tpp) REVERT: A 223 LEU cc_start: 0.7479 (mp) cc_final: 0.7261 (mp) REVERT: A 307 THR cc_start: 0.8078 (m) cc_final: 0.7800 (p) REVERT: A 308 VAL cc_start: 0.8751 (p) cc_final: 0.8538 (m) REVERT: A 396 TYR cc_start: 0.6240 (m-80) cc_final: 0.5698 (m-80) REVERT: A 433 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7395 (m) REVERT: A 516 GLU cc_start: 0.6044 (pt0) cc_final: 0.5300 (pt0) REVERT: A 546 LEU cc_start: 0.8739 (tm) cc_final: 0.8364 (tt) REVERT: A 560 LEU cc_start: 0.8167 (tp) cc_final: 0.7742 (tp) REVERT: A 562 PHE cc_start: 0.7343 (p90) cc_final: 0.6988 (p90) REVERT: A 596 SER cc_start: 0.8894 (m) cc_final: 0.8629 (p) REVERT: A 602 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7607 (p) REVERT: A 615 VAL cc_start: 0.8551 (t) cc_final: 0.8298 (m) REVERT: A 921 LYS cc_start: 0.8425 (mmmt) cc_final: 0.7849 (mmmt) REVERT: A 950 ASP cc_start: 0.7460 (t70) cc_final: 0.6083 (t0) REVERT: A 954 HIS cc_start: 0.7150 (m-70) cc_final: 0.6462 (m170) REVERT: A 955 ASN cc_start: 0.8388 (t0) cc_final: 0.8004 (t0) REVERT: A 969 LYS cc_start: 0.7669 (mppt) cc_final: 0.7452 (mptt) REVERT: A 983 ARG cc_start: 0.7868 (ttp80) cc_final: 0.7637 (ttp80) REVERT: A 984 LEU cc_start: 0.8749 (mt) cc_final: 0.8292 (mt) REVERT: A 988 GLU cc_start: 0.7522 (tp30) cc_final: 0.7134 (tp30) REVERT: A 1005 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7758 (tp40) REVERT: A 1057 PRO cc_start: 0.8955 (Cg_exo) cc_final: 0.8639 (Cg_endo) REVERT: B 62 VAL cc_start: 0.8303 (t) cc_final: 0.8080 (p) REVERT: B 105 ILE cc_start: 0.8447 (mm) cc_final: 0.8115 (tp) REVERT: B 106 PHE cc_start: 0.7114 (m-80) cc_final: 0.6880 (m-80) REVERT: B 188 ARG cc_start: 0.7567 (mtt-85) cc_final: 0.6909 (mtt-85) REVERT: B 189 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: B 193 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7716 (ttmt) REVERT: B 200 LYS cc_start: 0.8676 (mttt) cc_final: 0.8222 (mttp) REVERT: B 201 ILE cc_start: 0.9002 (mp) cc_final: 0.8756 (pt) REVERT: B 205 HIS cc_start: 0.7116 (t-170) cc_final: 0.6527 (t70) REVERT: B 224 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6663 (mp0) REVERT: B 271 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7613 (tm-30) REVERT: B 281 GLU cc_start: 0.7461 (tp30) cc_final: 0.7133 (tp30) REVERT: B 307 THR cc_start: 0.7999 (m) cc_final: 0.7609 (p) REVERT: B 329 PHE cc_start: 0.6327 (m-10) cc_final: 0.6085 (m-10) REVERT: B 403 ARG cc_start: 0.6610 (mtm-85) cc_final: 0.6072 (ttm170) REVERT: B 602 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8239 (p) REVERT: B 725 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6781 (tm-30) REVERT: B 773 GLU cc_start: 0.7349 (tp30) cc_final: 0.6930 (tp30) REVERT: B 776 LYS cc_start: 0.8108 (ttpm) cc_final: 0.7836 (ttpp) REVERT: B 780 GLU cc_start: 0.7678 (tp30) cc_final: 0.7302 (tp30) REVERT: B 803 SER cc_start: 0.8582 (m) cc_final: 0.8178 (p) REVERT: B 851 CYS cc_start: 0.8373 (t) cc_final: 0.7882 (t) REVERT: B 856 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8913 (tppp) REVERT: B 933 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7871 (mtmt) REVERT: B 957 GLN cc_start: 0.7046 (tm-30) cc_final: 0.6747 (tm-30) REVERT: B 964 LYS cc_start: 0.8338 (tmmt) cc_final: 0.7954 (tmmt) REVERT: B 965 GLN cc_start: 0.7503 (mm110) cc_final: 0.6350 (mm-40) REVERT: B 1019 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7680 (ttp80) REVERT: B 1101 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.7027 (m90) REVERT: B 1130 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8393 (tp) REVERT: C 104 TRP cc_start: 0.7395 (m-90) cc_final: 0.7175 (m-10) REVERT: C 118 LEU cc_start: 0.8763 (mp) cc_final: 0.8489 (mm) REVERT: C 129 LYS cc_start: 0.8403 (ttmt) cc_final: 0.7796 (tptt) REVERT: C 190 PHE cc_start: 0.7218 (m-80) cc_final: 0.6974 (m-80) REVERT: C 193 LYS cc_start: 0.7547 (ptpp) cc_final: 0.7279 (ptmt) REVERT: C 229 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7492 (pp) REVERT: C 269 TYR cc_start: 0.6783 (m-10) cc_final: 0.6318 (m-80) REVERT: C 274 THR cc_start: 0.8554 (p) cc_final: 0.8219 (m) REVERT: C 281 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6749 (mt-10) REVERT: C 303 LEU cc_start: 0.8312 (tp) cc_final: 0.7909 (tp) REVERT: C 361 CYS cc_start: 0.5430 (OUTLIER) cc_final: 0.3884 (p) REVERT: C 362 VAL cc_start: 0.7491 (OUTLIER) cc_final: 0.7190 (m) REVERT: C 537 LYS cc_start: 0.8343 (tttp) cc_final: 0.8097 (tptt) REVERT: C 558 LYS cc_start: 0.8629 (mttt) cc_final: 0.8317 (mtmt) REVERT: C 707 TYR cc_start: 0.8088 (t80) cc_final: 0.7542 (t80) REVERT: C 820 ASP cc_start: 0.7658 (t70) cc_final: 0.7328 (t0) REVERT: C 821 LEU cc_start: 0.8965 (tp) cc_final: 0.8665 (tt) REVERT: C 859 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7987 (p) REVERT: C 869 MET cc_start: 0.7869 (mmm) cc_final: 0.7602 (mtp) REVERT: C 1086 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8335 (mmmt) REVERT: C 1097 SER cc_start: 0.9001 (t) cc_final: 0.8472 (p) REVERT: C 1136 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8467 (p) REVERT: D 6 GLN cc_start: -0.0474 (OUTLIER) cc_final: -0.1212 (tp-100) REVERT: D 35 VAL cc_start: 0.2275 (OUTLIER) cc_final: 0.1929 (p) REVERT: D 90 CYS cc_start: 0.5948 (OUTLIER) cc_final: 0.5336 (t) REVERT: D 111 LEU cc_start: 0.5185 (OUTLIER) cc_final: 0.4798 (tm) REVERT: D 234 MET cc_start: -0.3750 (pmt) cc_final: -0.4307 (pmt) REVERT: F 160 MET cc_start: -0.1116 (ptp) cc_final: -0.1916 (mmm) outliers start: 163 outliers final: 107 residues processed: 599 average time/residue: 0.3992 time to fit residues: 382.3160 Evaluate side-chains 574 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 450 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 370 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 267 optimal weight: 0.8980 chunk 50 optimal weight: 0.0970 chunk 167 optimal weight: 0.3980 chunk 270 optimal weight: 0.2980 chunk 308 optimal weight: 40.0000 chunk 240 optimal weight: 30.0000 chunk 47 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 935 GLN A1002 GLN A1101 HIS B 422 ASN B 607 GLN B 641 ASN B1002 GLN B1101 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.200178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.149195 restraints weight = 54377.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.151273 restraints weight = 24771.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.152192 restraints weight = 14256.784| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30432 Z= 0.115 Angle : 0.590 9.856 41486 Z= 0.291 Chirality : 0.045 0.400 4711 Planarity : 0.005 0.148 5333 Dihedral : 6.465 80.230 4683 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.75 % Allowed : 16.73 % Favored : 78.51 % 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: -2.68 (0.13), residues: 3739 helix: 0.93 (0.21), residues: 672 sheet: -1.69 (0.19), residues: 635 loop : -2.80 (0.11), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 64 HIS 0.007 0.001 HIS B1101 PHE 0.028 0.001 PHE A 329 TYR 0.023 0.001 TYR A 170 ARG 0.010 0.000 ARG C 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 23) link_NAG-ASN : angle 2.30321 ( 69) hydrogen bonds : bond 0.03202 ( 800) hydrogen bonds : angle 4.80999 ( 2136) SS BOND : bond 0.00261 ( 44) SS BOND : angle 1.58212 ( 88) covalent geometry : bond 0.00261 (30365) covalent geometry : angle 0.57936 (41329) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 461 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7020 (m-10) cc_final: 0.6644 (m-10) REVERT: A 64 TRP cc_start: 0.7736 (t60) cc_final: 0.7526 (t60) REVERT: A 106 PHE cc_start: 0.7483 (m-80) cc_final: 0.6995 (m-80) REVERT: A 177 MET cc_start: 0.4338 (tpp) cc_final: 0.4080 (tpp) REVERT: A 223 LEU cc_start: 0.7584 (mp) cc_final: 0.6941 (mp) REVERT: A 307 THR cc_start: 0.8019 (m) cc_final: 0.7715 (p) REVERT: A 308 VAL cc_start: 0.8740 (p) cc_final: 0.8469 (m) REVERT: A 396 TYR cc_start: 0.6277 (m-80) cc_final: 0.5739 (m-80) REVERT: A 516 GLU cc_start: 0.5859 (pt0) cc_final: 0.5249 (pt0) REVERT: A 546 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8376 (tt) REVERT: A 560 LEU cc_start: 0.8052 (tp) cc_final: 0.7695 (tp) REVERT: A 562 PHE cc_start: 0.7373 (p90) cc_final: 0.7019 (p90) REVERT: A 596 SER cc_start: 0.8899 (m) cc_final: 0.8654 (p) REVERT: A 602 THR cc_start: 0.7932 (m) cc_final: 0.7428 (p) REVERT: A 615 VAL cc_start: 0.8467 (t) cc_final: 0.8168 (m) REVERT: A 644 GLN cc_start: 0.7798 (tp40) cc_final: 0.7283 (tp40) REVERT: A 743 CYS cc_start: 0.6415 (OUTLIER) cc_final: 0.5413 (t) REVERT: A 921 LYS cc_start: 0.8451 (mmmt) cc_final: 0.7855 (mmmt) REVERT: A 950 ASP cc_start: 0.7287 (t70) cc_final: 0.5917 (t0) REVERT: A 954 HIS cc_start: 0.7142 (m-70) cc_final: 0.6390 (m170) REVERT: A 955 ASN cc_start: 0.8399 (t0) cc_final: 0.8044 (t0) REVERT: A 983 ARG cc_start: 0.7867 (ttp80) cc_final: 0.7597 (ttp80) REVERT: A 984 LEU cc_start: 0.8733 (mt) cc_final: 0.8166 (mt) REVERT: A 988 GLU cc_start: 0.7515 (tp30) cc_final: 0.7033 (tp30) REVERT: A 1002 GLN cc_start: 0.7137 (tp-100) cc_final: 0.6859 (tp-100) REVERT: A 1057 PRO cc_start: 0.8885 (Cg_exo) cc_final: 0.8540 (Cg_endo) REVERT: B 106 PHE cc_start: 0.7045 (m-80) cc_final: 0.6838 (m-80) REVERT: B 188 ARG cc_start: 0.7406 (mtt-85) cc_final: 0.6560 (mtm-85) REVERT: B 193 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7715 (ttmt) REVERT: B 200 LYS cc_start: 0.8668 (mttt) cc_final: 0.8183 (mttp) REVERT: B 201 ILE cc_start: 0.9084 (mp) cc_final: 0.8745 (pt) REVERT: B 204 LYS cc_start: 0.7829 (tptt) cc_final: 0.7597 (tptt) REVERT: B 205 HIS cc_start: 0.6820 (t-170) cc_final: 0.6483 (t70) REVERT: B 224 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6755 (mp0) REVERT: B 226 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7451 (tp) REVERT: B 271 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7579 (tm-30) REVERT: B 307 THR cc_start: 0.7974 (m) cc_final: 0.7613 (p) REVERT: B 329 PHE cc_start: 0.6441 (m-10) cc_final: 0.6167 (m-10) REVERT: B 403 ARG cc_start: 0.6389 (mtm-85) cc_final: 0.5818 (ttm170) REVERT: B 602 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8159 (p) REVERT: B 644 GLN cc_start: 0.8291 (tp-100) cc_final: 0.7919 (tp40) REVERT: B 773 GLU cc_start: 0.7320 (tp30) cc_final: 0.6842 (tp30) REVERT: B 776 LYS cc_start: 0.8049 (ttpm) cc_final: 0.7704 (ttpp) REVERT: B 780 GLU cc_start: 0.7671 (tp30) cc_final: 0.7279 (tp30) REVERT: B 803 SER cc_start: 0.8506 (m) cc_final: 0.8146 (p) REVERT: B 851 CYS cc_start: 0.8423 (t) cc_final: 0.7788 (p) REVERT: B 856 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8938 (tppp) REVERT: B 955 ASN cc_start: 0.8290 (m-40) cc_final: 0.7881 (m110) REVERT: B 957 GLN cc_start: 0.7089 (tm-30) cc_final: 0.6586 (tm-30) REVERT: B 964 LYS cc_start: 0.8358 (tmmt) cc_final: 0.8035 (tmmt) REVERT: B 965 GLN cc_start: 0.7417 (mm110) cc_final: 0.6427 (mm-40) REVERT: B 1002 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7756 (tp40) REVERT: B 1019 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7592 (ttp80) REVERT: C 129 LYS cc_start: 0.8378 (ttmt) cc_final: 0.7748 (tptt) REVERT: C 169 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7750 (tm-30) REVERT: C 190 PHE cc_start: 0.7246 (m-80) cc_final: 0.6946 (m-80) REVERT: C 193 LYS cc_start: 0.7397 (ptpp) cc_final: 0.7184 (ptmt) REVERT: C 229 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7396 (pp) REVERT: C 303 LEU cc_start: 0.8320 (tp) cc_final: 0.7899 (tp) REVERT: C 361 CYS cc_start: 0.5240 (OUTLIER) cc_final: 0.4022 (p) REVERT: C 537 LYS cc_start: 0.8271 (tttp) cc_final: 0.7979 (tptt) REVERT: C 558 LYS cc_start: 0.8611 (mttt) cc_final: 0.8348 (mtmt) REVERT: C 707 TYR cc_start: 0.8084 (t80) cc_final: 0.7523 (t80) REVERT: C 820 ASP cc_start: 0.7682 (t70) cc_final: 0.7350 (t0) REVERT: C 821 LEU cc_start: 0.8947 (tp) cc_final: 0.8680 (tt) REVERT: C 869 MET cc_start: 0.7939 (mmm) cc_final: 0.7619 (mtp) REVERT: C 1029 MET cc_start: 0.8442 (tpp) cc_final: 0.8172 (ttm) REVERT: C 1031 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7694 (mt-10) REVERT: C 1097 SER cc_start: 0.8987 (t) cc_final: 0.8468 (p) REVERT: C 1136 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8498 (p) REVERT: D 6 GLN cc_start: -0.0583 (OUTLIER) cc_final: -0.1302 (tp-100) REVERT: D 85 GLU cc_start: 0.3106 (OUTLIER) cc_final: 0.2759 (pm20) REVERT: D 111 LEU cc_start: 0.5199 (OUTLIER) cc_final: 0.4824 (tm) REVERT: D 208 MET cc_start: 0.2593 (tmm) cc_final: 0.2238 (tmm) REVERT: D 234 MET cc_start: -0.3741 (pmt) cc_final: -0.4179 (pmt) REVERT: F 160 MET cc_start: -0.1165 (ptp) cc_final: -0.1922 (mmm) outliers start: 154 outliers final: 100 residues processed: 577 average time/residue: 0.4113 time to fit residues: 381.6446 Evaluate side-chains 559 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 448 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 271 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 302 optimal weight: 0.0370 chunk 356 optimal weight: 0.9990 chunk 343 optimal weight: 50.0000 chunk 197 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 290 optimal weight: 0.4980 chunk 277 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 317 optimal weight: 10.0000 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 935 GLN A1005 GLN B 607 GLN B 641 ASN C 183 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.199871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.147595 restraints weight = 54579.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149883 restraints weight = 27118.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.153134 restraints weight = 14185.075| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30432 Z= 0.123 Angle : 0.586 9.856 41486 Z= 0.287 Chirality : 0.045 0.401 4711 Planarity : 0.004 0.080 5333 Dihedral : 6.373 80.092 4674 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.54 % Allowed : 17.38 % Favored : 78.08 % 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: -2.57 (0.13), residues: 3739 helix: 0.95 (0.21), residues: 669 sheet: -1.61 (0.19), residues: 676 loop : -2.71 (0.11), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 104 HIS 0.005 0.001 HIS C 205 PHE 0.044 0.001 PHE A 643 TYR 0.018 0.001 TYR A 655 ARG 0.007 0.000 ARG D 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 23) link_NAG-ASN : angle 2.21194 ( 69) hydrogen bonds : bond 0.03169 ( 800) hydrogen bonds : angle 4.78599 ( 2136) SS BOND : bond 0.00295 ( 44) SS BOND : angle 1.56637 ( 88) covalent geometry : bond 0.00283 (30365) covalent geometry : angle 0.57544 (41329) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 455 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.6958 (m-10) cc_final: 0.6573 (m-10) REVERT: A 64 TRP cc_start: 0.7757 (t60) cc_final: 0.7542 (t60) REVERT: A 106 PHE cc_start: 0.7543 (m-80) cc_final: 0.7098 (m-80) REVERT: A 223 LEU cc_start: 0.7516 (mp) cc_final: 0.6926 (mp) REVERT: A 234 ASN cc_start: 0.6392 (t0) cc_final: 0.6192 (t0) REVERT: A 307 THR cc_start: 0.8037 (m) cc_final: 0.7740 (p) REVERT: A 308 VAL cc_start: 0.8756 (p) cc_final: 0.8493 (m) REVERT: A 396 TYR cc_start: 0.6299 (m-80) cc_final: 0.5772 (m-80) REVERT: A 516 GLU cc_start: 0.5937 (pt0) cc_final: 0.5306 (pt0) REVERT: A 546 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8470 (tt) REVERT: A 560 LEU cc_start: 0.8103 (tp) cc_final: 0.7756 (tp) REVERT: A 562 PHE cc_start: 0.7414 (p90) cc_final: 0.7028 (p90) REVERT: A 563 GLN cc_start: 0.6853 (tp-100) cc_final: 0.6615 (tp-100) REVERT: A 596 SER cc_start: 0.8884 (m) cc_final: 0.8625 (p) REVERT: A 602 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7516 (p) REVERT: A 644 GLN cc_start: 0.7853 (tp40) cc_final: 0.7534 (tp40) REVERT: A 743 CYS cc_start: 0.6493 (OUTLIER) cc_final: 0.5527 (t) REVERT: A 825 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8457 (tttt) REVERT: A 921 LYS cc_start: 0.8465 (mmmt) cc_final: 0.7860 (mmmt) REVERT: A 950 ASP cc_start: 0.7315 (t70) cc_final: 0.5966 (t0) REVERT: A 954 HIS cc_start: 0.7142 (m-70) cc_final: 0.6403 (m170) REVERT: A 955 ASN cc_start: 0.8375 (t0) cc_final: 0.8016 (t0) REVERT: A 969 LYS cc_start: 0.7665 (mppt) cc_final: 0.7299 (mmtm) REVERT: A 983 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7633 (ttp80) REVERT: A 984 LEU cc_start: 0.8627 (mt) cc_final: 0.8180 (mt) REVERT: A 988 GLU cc_start: 0.7432 (tp30) cc_final: 0.7058 (tp30) REVERT: A 1002 GLN cc_start: 0.7351 (tp-100) cc_final: 0.6970 (tp-100) REVERT: A 1057 PRO cc_start: 0.8916 (Cg_exo) cc_final: 0.8602 (Cg_endo) REVERT: B 106 PHE cc_start: 0.7137 (m-80) cc_final: 0.6886 (m-80) REVERT: B 188 ARG cc_start: 0.7489 (mtt-85) cc_final: 0.6773 (mtm-85) REVERT: B 193 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7791 (ttmt) REVERT: B 200 LYS cc_start: 0.8688 (mttt) cc_final: 0.8205 (mttp) REVERT: B 201 ILE cc_start: 0.9067 (mp) cc_final: 0.8757 (pt) REVERT: B 204 LYS cc_start: 0.7891 (tptt) cc_final: 0.7334 (tptt) REVERT: B 205 HIS cc_start: 0.6928 (t-170) cc_final: 0.6615 (t70) REVERT: B 224 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6731 (mp0) REVERT: B 226 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7571 (tp) REVERT: B 271 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7846 (tm-30) REVERT: B 307 THR cc_start: 0.7989 (m) cc_final: 0.7622 (p) REVERT: B 329 PHE cc_start: 0.6522 (m-10) cc_final: 0.6240 (m-10) REVERT: B 403 ARG cc_start: 0.6381 (mtm-85) cc_final: 0.5805 (ttm170) REVERT: B 602 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8176 (p) REVERT: B 644 GLN cc_start: 0.8279 (tp-100) cc_final: 0.7899 (tp40) REVERT: B 773 GLU cc_start: 0.7365 (tp30) cc_final: 0.6818 (tp30) REVERT: B 776 LYS cc_start: 0.8106 (ttpm) cc_final: 0.7734 (ttpp) REVERT: B 780 GLU cc_start: 0.7681 (tp30) cc_final: 0.7262 (tp30) REVERT: B 803 SER cc_start: 0.8586 (m) cc_final: 0.8246 (p) REVERT: B 851 CYS cc_start: 0.8368 (t) cc_final: 0.7838 (p) REVERT: B 856 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8915 (tppp) REVERT: B 957 GLN cc_start: 0.7078 (tm-30) cc_final: 0.6614 (tm-30) REVERT: B 965 GLN cc_start: 0.7422 (mm110) cc_final: 0.7205 (mm-40) REVERT: B 1002 GLN cc_start: 0.8081 (tp-100) cc_final: 0.7580 (mm-40) REVERT: B 1019 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7666 (ttp80) REVERT: B 1107 ARG cc_start: 0.6869 (mpt180) cc_final: 0.6572 (mtt90) REVERT: C 129 LYS cc_start: 0.8401 (ttmt) cc_final: 0.7737 (tptt) REVERT: C 169 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7786 (tm-30) REVERT: C 193 LYS cc_start: 0.7303 (ptpp) cc_final: 0.7093 (ptmt) REVERT: C 229 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7419 (pp) REVERT: C 303 LEU cc_start: 0.8288 (tp) cc_final: 0.7876 (tp) REVERT: C 361 CYS cc_start: 0.5023 (OUTLIER) cc_final: 0.3863 (p) REVERT: C 537 LYS cc_start: 0.8305 (tttp) cc_final: 0.8001 (tptt) REVERT: C 558 LYS cc_start: 0.8570 (mttt) cc_final: 0.8347 (mtmt) REVERT: C 564 GLN cc_start: 0.7955 (mt0) cc_final: 0.7653 (mt0) REVERT: C 675 GLN cc_start: 0.7714 (mm110) cc_final: 0.7494 (mm110) REVERT: C 707 TYR cc_start: 0.8109 (t80) cc_final: 0.7532 (t80) REVERT: C 820 ASP cc_start: 0.7683 (t70) cc_final: 0.7348 (t0) REVERT: C 821 LEU cc_start: 0.8965 (tp) cc_final: 0.8716 (tt) REVERT: C 869 MET cc_start: 0.7923 (mmm) cc_final: 0.7551 (mtp) REVERT: C 1002 GLN cc_start: 0.7251 (tp40) cc_final: 0.6669 (tp40) REVERT: C 1029 MET cc_start: 0.8446 (tpp) cc_final: 0.8150 (ttm) REVERT: C 1031 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7663 (mt-10) REVERT: C 1097 SER cc_start: 0.8989 (t) cc_final: 0.8438 (p) REVERT: C 1136 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8513 (p) REVERT: D 6 GLN cc_start: -0.0645 (OUTLIER) cc_final: -0.1352 (tp-100) REVERT: D 85 GLU cc_start: 0.3095 (OUTLIER) cc_final: 0.2771 (pm20) REVERT: D 111 LEU cc_start: 0.5176 (OUTLIER) cc_final: 0.4797 (tm) REVERT: D 208 MET cc_start: 0.2791 (tmm) cc_final: 0.2386 (tmm) REVERT: D 234 MET cc_start: -0.3999 (pmt) cc_final: -0.4222 (pmt) REVERT: F 160 MET cc_start: -0.1170 (ptp) cc_final: -0.1920 (mmm) outliers start: 147 outliers final: 105 residues processed: 568 average time/residue: 0.4156 time to fit residues: 377.6410 Evaluate side-chains 552 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 435 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 272 optimal weight: 0.8980 chunk 47 optimal weight: 0.0770 chunk 38 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 196 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 365 optimal weight: 30.0000 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 935 GLN A1005 GLN B 607 GLN B 641 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.199722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147127 restraints weight = 54634.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.149951 restraints weight = 25970.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.152442 restraints weight = 13608.434| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30432 Z= 0.126 Angle : 0.597 9.980 41486 Z= 0.293 Chirality : 0.045 0.401 4711 Planarity : 0.004 0.068 5333 Dihedral : 6.419 79.962 4674 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 4.45 % Allowed : 17.44 % Favored : 78.11 % 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: -2.50 (0.13), residues: 3739 helix: 1.00 (0.21), residues: 668 sheet: -1.57 (0.19), residues: 699 loop : -2.66 (0.12), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP C 104 HIS 0.006 0.001 HIS A 519 PHE 0.039 0.001 PHE A 643 TYR 0.022 0.001 TYR A 655 ARG 0.007 0.000 ARG D 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 23) link_NAG-ASN : angle 2.15907 ( 69) hydrogen bonds : bond 0.03132 ( 800) hydrogen bonds : angle 4.79293 ( 2136) SS BOND : bond 0.00309 ( 44) SS BOND : angle 1.62509 ( 88) covalent geometry : bond 0.00289 (30365) covalent geometry : angle 0.58667 (41329) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 455 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.6980 (m-10) cc_final: 0.6484 (m-10) REVERT: A 106 PHE cc_start: 0.7501 (m-80) cc_final: 0.7066 (m-80) REVERT: A 177 MET cc_start: 0.3796 (tpp) cc_final: 0.3381 (tpp) REVERT: A 190 PHE cc_start: 0.7278 (m-80) cc_final: 0.6925 (m-10) REVERT: A 223 LEU cc_start: 0.7497 (mp) cc_final: 0.6878 (mp) REVERT: A 234 ASN cc_start: 0.6476 (t0) cc_final: 0.6269 (t0) REVERT: A 307 THR cc_start: 0.8025 (m) cc_final: 0.7725 (p) REVERT: A 308 VAL cc_start: 0.8738 (p) cc_final: 0.8458 (m) REVERT: A 396 TYR cc_start: 0.6336 (m-80) cc_final: 0.5789 (m-80) REVERT: A 516 GLU cc_start: 0.5958 (pt0) cc_final: 0.5366 (pt0) REVERT: A 546 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8492 (tt) REVERT: A 562 PHE cc_start: 0.7454 (p90) cc_final: 0.7040 (p90) REVERT: A 596 SER cc_start: 0.8855 (m) cc_final: 0.8620 (p) REVERT: A 602 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7475 (p) REVERT: A 644 GLN cc_start: 0.7746 (tp40) cc_final: 0.7410 (tp40) REVERT: A 675 GLN cc_start: 0.7355 (pp30) cc_final: 0.7138 (tm-30) REVERT: A 743 CYS cc_start: 0.6559 (OUTLIER) cc_final: 0.5555 (t) REVERT: A 825 LYS cc_start: 0.8808 (mtpp) cc_final: 0.8480 (tttt) REVERT: A 921 LYS cc_start: 0.8403 (mmmt) cc_final: 0.7828 (mmmt) REVERT: A 950 ASP cc_start: 0.7339 (t70) cc_final: 0.5965 (t0) REVERT: A 954 HIS cc_start: 0.7154 (m-70) cc_final: 0.6383 (m170) REVERT: A 955 ASN cc_start: 0.8384 (t0) cc_final: 0.8012 (t0) REVERT: A 969 LYS cc_start: 0.7661 (mppt) cc_final: 0.7284 (mmtm) REVERT: A 983 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7581 (ttp80) REVERT: A 984 LEU cc_start: 0.8637 (tt) cc_final: 0.8161 (mt) REVERT: A 988 GLU cc_start: 0.7433 (tp30) cc_final: 0.7060 (tp30) REVERT: A 1002 GLN cc_start: 0.7372 (tp-100) cc_final: 0.6960 (tp-100) REVERT: A 1057 PRO cc_start: 0.8914 (Cg_exo) cc_final: 0.8596 (Cg_endo) REVERT: B 106 PHE cc_start: 0.7160 (m-80) cc_final: 0.6935 (m-80) REVERT: B 188 ARG cc_start: 0.7635 (mtt-85) cc_final: 0.6806 (mtm-85) REVERT: B 193 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7859 (ttmt) REVERT: B 200 LYS cc_start: 0.8706 (mttt) cc_final: 0.8321 (mptp) REVERT: B 224 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6812 (mp0) REVERT: B 271 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7923 (tm-30) REVERT: B 307 THR cc_start: 0.8012 (m) cc_final: 0.7640 (p) REVERT: B 329 PHE cc_start: 0.6598 (m-10) cc_final: 0.6317 (m-10) REVERT: B 403 ARG cc_start: 0.6476 (mtm-85) cc_final: 0.5897 (ttm170) REVERT: B 602 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8147 (p) REVERT: B 644 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7913 (tp40) REVERT: B 773 GLU cc_start: 0.7371 (tp30) cc_final: 0.6727 (tp30) REVERT: B 776 LYS cc_start: 0.8131 (ttpm) cc_final: 0.7845 (ttpp) REVERT: B 780 GLU cc_start: 0.7679 (tp30) cc_final: 0.7273 (tp30) REVERT: B 803 SER cc_start: 0.8576 (m) cc_final: 0.8238 (p) REVERT: B 851 CYS cc_start: 0.8387 (t) cc_final: 0.7826 (p) REVERT: B 856 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8904 (tppp) REVERT: B 957 GLN cc_start: 0.7031 (tm-30) cc_final: 0.6575 (tm-30) REVERT: B 1002 GLN cc_start: 0.8063 (tp-100) cc_final: 0.7547 (mm-40) REVERT: B 1019 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7775 (ttp80) REVERT: C 129 LYS cc_start: 0.8361 (ttmt) cc_final: 0.7778 (tptt) REVERT: C 190 PHE cc_start: 0.7571 (m-80) cc_final: 0.7169 (m-80) REVERT: C 193 LYS cc_start: 0.7318 (ptpp) cc_final: 0.7061 (ptpt) REVERT: C 229 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7425 (pp) REVERT: C 273 ARG cc_start: 0.6883 (mmm-85) cc_final: 0.6680 (mtt180) REVERT: C 303 LEU cc_start: 0.8289 (tp) cc_final: 0.7897 (tp) REVERT: C 355 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6528 (tmt90) REVERT: C 558 LYS cc_start: 0.8585 (mttt) cc_final: 0.8369 (mttt) REVERT: C 564 GLN cc_start: 0.7995 (mt0) cc_final: 0.7665 (mt0) REVERT: C 675 GLN cc_start: 0.7711 (mm110) cc_final: 0.7430 (mm110) REVERT: C 707 TYR cc_start: 0.8111 (t80) cc_final: 0.7538 (t80) REVERT: C 755 GLN cc_start: 0.7369 (mm-40) cc_final: 0.7152 (mm-40) REVERT: C 820 ASP cc_start: 0.7676 (t70) cc_final: 0.7329 (t0) REVERT: C 821 LEU cc_start: 0.8963 (tp) cc_final: 0.8707 (tt) REVERT: C 869 MET cc_start: 0.7949 (mmm) cc_final: 0.7666 (mmm) REVERT: C 990 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: C 1002 GLN cc_start: 0.7253 (tp40) cc_final: 0.6767 (tp40) REVERT: C 1029 MET cc_start: 0.8431 (tpp) cc_final: 0.8110 (ttm) REVERT: C 1031 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7488 (mt-10) REVERT: C 1076 THR cc_start: 0.9071 (m) cc_final: 0.8843 (p) REVERT: C 1136 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8534 (p) REVERT: D 6 GLN cc_start: -0.0731 (OUTLIER) cc_final: -0.1411 (tp-100) REVERT: D 85 GLU cc_start: 0.3103 (OUTLIER) cc_final: 0.2778 (pm20) REVERT: D 111 LEU cc_start: 0.5184 (OUTLIER) cc_final: 0.4802 (tm) REVERT: D 234 MET cc_start: -0.4056 (pmt) cc_final: -0.4296 (pmt) REVERT: F 160 MET cc_start: -0.1226 (ptp) cc_final: -0.1961 (mmm) outliers start: 144 outliers final: 111 residues processed: 563 average time/residue: 0.4252 time to fit residues: 382.8203 Evaluate side-chains 571 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 448 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 346 optimal weight: 20.0000 chunk 220 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 359 optimal weight: 50.0000 chunk 305 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 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 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 607 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.196650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144020 restraints weight = 54698.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146606 restraints weight = 26043.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.149387 restraints weight = 13972.137| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 30432 Z= 0.211 Angle : 0.672 24.418 41486 Z= 0.332 Chirality : 0.047 0.419 4711 Planarity : 0.005 0.097 5333 Dihedral : 6.686 79.835 4670 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 4.29 % Allowed : 18.18 % Favored : 77.52 % 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: -2.54 (0.13), residues: 3739 helix: 0.89 (0.21), residues: 669 sheet: -1.47 (0.19), residues: 715 loop : -2.71 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C 104 HIS 0.007 0.001 HIS A1083 PHE 0.031 0.002 PHE C 855 TYR 0.023 0.001 TYR B1067 ARG 0.015 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 23) link_NAG-ASN : angle 2.31599 ( 69) hydrogen bonds : bond 0.03817 ( 800) hydrogen bonds : angle 4.99436 ( 2136) SS BOND : bond 0.00710 ( 44) SS BOND : angle 2.17216 ( 88) covalent geometry : bond 0.00469 (30365) covalent geometry : angle 0.65928 (41329) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 465 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7560 (m-80) cc_final: 0.7131 (m-80) REVERT: A 177 MET cc_start: 0.4066 (tpp) cc_final: 0.3681 (tpp) REVERT: A 190 PHE cc_start: 0.7484 (m-80) cc_final: 0.6919 (m-80) REVERT: A 223 LEU cc_start: 0.7544 (mp) cc_final: 0.7169 (mp) REVERT: A 307 THR cc_start: 0.8134 (m) cc_final: 0.7849 (p) REVERT: A 308 VAL cc_start: 0.8742 (p) cc_final: 0.8483 (m) REVERT: A 396 TYR cc_start: 0.6422 (m-80) cc_final: 0.5792 (m-80) REVERT: A 516 GLU cc_start: 0.5971 (pt0) cc_final: 0.5317 (pt0) REVERT: A 596 SER cc_start: 0.8875 (m) cc_final: 0.8577 (p) REVERT: A 602 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7640 (p) REVERT: A 644 GLN cc_start: 0.7546 (tp-100) cc_final: 0.7040 (tp40) REVERT: A 737 ASP cc_start: 0.7564 (m-30) cc_final: 0.7034 (p0) REVERT: A 743 CYS cc_start: 0.6593 (OUTLIER) cc_final: 0.5718 (t) REVERT: A 921 LYS cc_start: 0.8459 (mmmt) cc_final: 0.7860 (mmmt) REVERT: A 950 ASP cc_start: 0.7450 (t70) cc_final: 0.6732 (t0) REVERT: A 954 HIS cc_start: 0.7133 (m-70) cc_final: 0.6718 (m170) REVERT: A 955 ASN cc_start: 0.8414 (t0) cc_final: 0.8051 (t0) REVERT: A 969 LYS cc_start: 0.7812 (mppt) cc_final: 0.7384 (mmtp) REVERT: A 984 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8273 (mt) REVERT: A 988 GLU cc_start: 0.7544 (tp30) cc_final: 0.7205 (tp30) REVERT: A 1002 GLN cc_start: 0.7513 (tp-100) cc_final: 0.7071 (tp-100) REVERT: A 1057 PRO cc_start: 0.8981 (Cg_exo) cc_final: 0.8651 (Cg_endo) REVERT: B 105 ILE cc_start: 0.8574 (mm) cc_final: 0.8300 (pt) REVERT: B 188 ARG cc_start: 0.7521 (mtt-85) cc_final: 0.7305 (mtm-85) REVERT: B 193 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7834 (ttmt) REVERT: B 200 LYS cc_start: 0.8678 (mttt) cc_final: 0.8330 (mptp) REVERT: B 224 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6836 (mp0) REVERT: B 271 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7966 (tm-30) REVERT: B 307 THR cc_start: 0.8265 (m) cc_final: 0.7840 (p) REVERT: B 329 PHE cc_start: 0.6839 (m-10) cc_final: 0.6575 (m-10) REVERT: B 403 ARG cc_start: 0.6814 (mtm-85) cc_final: 0.6222 (ttm170) REVERT: B 602 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8310 (p) REVERT: B 644 GLN cc_start: 0.8172 (tp-100) cc_final: 0.7710 (tp40) REVERT: B 773 GLU cc_start: 0.7386 (tp30) cc_final: 0.7029 (tp30) REVERT: B 803 SER cc_start: 0.8758 (m) cc_final: 0.8425 (p) REVERT: B 851 CYS cc_start: 0.8405 (t) cc_final: 0.7872 (t) REVERT: B 856 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8933 (tppp) REVERT: B 933 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7830 (mtmt) REVERT: B 957 GLN cc_start: 0.7043 (tm-30) cc_final: 0.6591 (tm-30) REVERT: B 964 LYS cc_start: 0.8361 (tmmt) cc_final: 0.8108 (ttmt) REVERT: B 994 ASP cc_start: 0.6856 (t0) cc_final: 0.6601 (t0) REVERT: B 1002 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7851 (mm-40) REVERT: B 1019 ARG cc_start: 0.8076 (ttm110) cc_final: 0.7814 (ttp80) REVERT: C 41 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8293 (mtmt) REVERT: C 129 LYS cc_start: 0.8414 (ttmt) cc_final: 0.8050 (tptt) REVERT: C 169 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7527 (tm-30) REVERT: C 190 PHE cc_start: 0.7566 (m-80) cc_final: 0.7242 (m-80) REVERT: C 193 LYS cc_start: 0.7416 (ptpp) cc_final: 0.7118 (ptpt) REVERT: C 229 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7485 (pp) REVERT: C 269 TYR cc_start: 0.6900 (m-10) cc_final: 0.6524 (m-80) REVERT: C 303 LEU cc_start: 0.8275 (tp) cc_final: 0.7867 (tp) REVERT: C 355 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6499 (tmt90) REVERT: C 362 VAL cc_start: 0.7552 (OUTLIER) cc_final: 0.7336 (m) REVERT: C 537 LYS cc_start: 0.8504 (tttp) cc_final: 0.8248 (tptt) REVERT: C 558 LYS cc_start: 0.8581 (mttt) cc_final: 0.8371 (mttt) REVERT: C 564 GLN cc_start: 0.8152 (mt0) cc_final: 0.7797 (mt0) REVERT: C 707 TYR cc_start: 0.8133 (t80) cc_final: 0.7577 (t80) REVERT: C 773 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6354 (tm-30) REVERT: C 820 ASP cc_start: 0.7736 (t70) cc_final: 0.7399 (t0) REVERT: C 821 LEU cc_start: 0.8980 (tp) cc_final: 0.8763 (tt) REVERT: C 869 MET cc_start: 0.8056 (mmm) cc_final: 0.7660 (mmm) REVERT: C 979 ASP cc_start: 0.7504 (t0) cc_final: 0.7085 (t0) REVERT: C 1050 MET cc_start: 0.7605 (mtm) cc_final: 0.7385 (mtp) REVERT: C 1136 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8494 (p) REVERT: D 6 GLN cc_start: -0.0789 (OUTLIER) cc_final: -0.1529 (tp-100) REVERT: D 85 GLU cc_start: 0.3125 (OUTLIER) cc_final: 0.2802 (pm20) REVERT: D 90 CYS cc_start: 0.6035 (OUTLIER) cc_final: 0.5498 (t) REVERT: D 111 LEU cc_start: 0.5076 (OUTLIER) cc_final: 0.4702 (tm) REVERT: D 234 MET cc_start: -0.3753 (pmt) cc_final: -0.4195 (pmt) REVERT: F 160 MET cc_start: -0.1359 (ptp) cc_final: -0.1972 (mmm) outliers start: 139 outliers final: 108 residues processed: 563 average time/residue: 0.4203 time to fit residues: 375.8542 Evaluate side-chains 571 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 450 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 265 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 336 optimal weight: 9.9990 chunk 374 optimal weight: 6.9990 chunk 108 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 278 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 194 ASN A 317 ASN A 394 ASN B 205 HIS B 607 GLN B 644 GLN B 935 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.198413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147783 restraints weight = 54249.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.148756 restraints weight = 27768.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.150379 restraints weight = 15465.345| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30432 Z= 0.130 Angle : 0.653 21.836 41486 Z= 0.321 Chirality : 0.046 0.479 4711 Planarity : 0.005 0.054 5333 Dihedral : 6.525 79.771 4669 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 4.11 % Allowed : 18.93 % Favored : 76.97 % 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: -2.39 (0.13), residues: 3739 helix: 1.02 (0.21), residues: 660 sheet: -1.43 (0.19), residues: 703 loop : -2.57 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP C 104 HIS 0.007 0.001 HIS A 519 PHE 0.028 0.001 PHE A 643 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG D 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 23) link_NAG-ASN : angle 2.17580 ( 69) hydrogen bonds : bond 0.03256 ( 800) hydrogen bonds : angle 4.92440 ( 2136) SS BOND : bond 0.00585 ( 44) SS BOND : angle 2.19101 ( 88) covalent geometry : bond 0.00297 (30365) covalent geometry : angle 0.64060 (41329) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 452 time to evaluate : 3.310 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 106 PHE cc_start: 0.7454 (m-80) cc_final: 0.7056 (m-80) REVERT: A 177 MET cc_start: 0.4156 (tpp) cc_final: 0.3833 (tpp) REVERT: A 190 PHE cc_start: 0.7447 (m-80) cc_final: 0.6895 (m-80) REVERT: A 223 LEU cc_start: 0.7528 (mp) cc_final: 0.6908 (mp) REVERT: A 307 THR cc_start: 0.8079 (m) cc_final: 0.7801 (p) REVERT: A 396 TYR cc_start: 0.6350 (m-80) cc_final: 0.5778 (m-80) REVERT: A 516 GLU cc_start: 0.6015 (pt0) cc_final: 0.5493 (pt0) REVERT: A 596 SER cc_start: 0.8951 (m) cc_final: 0.8642 (p) REVERT: A 602 THR cc_start: 0.8035 (m) cc_final: 0.7486 (p) REVERT: A 644 GLN cc_start: 0.7470 (tp-100) cc_final: 0.7149 (tp40) REVERT: A 737 ASP cc_start: 0.7501 (m-30) cc_final: 0.7002 (p0) REVERT: A 743 CYS cc_start: 0.6761 (OUTLIER) cc_final: 0.5604 (t) REVERT: A 921 LYS cc_start: 0.8436 (mmmt) cc_final: 0.7841 (mmmt) REVERT: A 950 ASP cc_start: 0.7412 (t70) cc_final: 0.6652 (t0) REVERT: A 954 HIS cc_start: 0.7067 (m-70) cc_final: 0.6654 (m170) REVERT: A 955 ASN cc_start: 0.8356 (t0) cc_final: 0.7973 (t0) REVERT: A 969 LYS cc_start: 0.7573 (mppt) cc_final: 0.7229 (mmtm) REVERT: A 983 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7629 (ttp80) REVERT: A 984 LEU cc_start: 0.8609 (mt) cc_final: 0.8170 (mt) REVERT: A 988 GLU cc_start: 0.7618 (tp30) cc_final: 0.7170 (tp30) REVERT: A 1002 GLN cc_start: 0.7342 (tp-100) cc_final: 0.7009 (tp-100) REVERT: A 1057 PRO cc_start: 0.8909 (Cg_exo) cc_final: 0.8569 (Cg_endo) REVERT: B 81 ASN cc_start: 0.6514 (p0) cc_final: 0.6180 (t0) REVERT: B 105 ILE cc_start: 0.8535 (mm) cc_final: 0.8319 (pt) REVERT: B 193 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7798 (ttmt) REVERT: B 200 LYS cc_start: 0.8670 (mttt) cc_final: 0.8317 (mptp) REVERT: B 201 ILE cc_start: 0.9092 (mp) cc_final: 0.8736 (pt) REVERT: B 224 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6731 (mp0) REVERT: B 228 ASP cc_start: 0.7611 (t70) cc_final: 0.7360 (t0) REVERT: B 271 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7950 (tm-30) REVERT: B 307 THR cc_start: 0.8121 (m) cc_final: 0.7743 (p) REVERT: B 329 PHE cc_start: 0.6816 (m-10) cc_final: 0.6590 (m-10) REVERT: B 403 ARG cc_start: 0.6603 (mtm-85) cc_final: 0.6040 (ttm170) REVERT: B 602 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8200 (p) REVERT: B 644 GLN cc_start: 0.8136 (tp40) cc_final: 0.7767 (tp40) REVERT: B 773 GLU cc_start: 0.7398 (tp30) cc_final: 0.6965 (tp30) REVERT: B 803 SER cc_start: 0.8663 (m) cc_final: 0.8329 (p) REVERT: B 851 CYS cc_start: 0.8399 (t) cc_final: 0.7781 (p) REVERT: B 856 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8875 (tppp) REVERT: B 907 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8216 (t0) REVERT: B 933 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7511 (ttmm) REVERT: B 957 GLN cc_start: 0.7011 (tm-30) cc_final: 0.6556 (tm-30) REVERT: B 964 LYS cc_start: 0.8364 (tmmt) cc_final: 0.8133 (ttmt) REVERT: B 965 GLN cc_start: 0.7579 (mm110) cc_final: 0.7071 (mp10) REVERT: B 1002 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7823 (mm-40) REVERT: B 1019 ARG cc_start: 0.7990 (ttm110) cc_final: 0.7644 (ttp80) REVERT: C 41 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8230 (mtmt) REVERT: C 129 LYS cc_start: 0.8450 (ttmt) cc_final: 0.8102 (tptt) REVERT: C 169 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7509 (tm-30) REVERT: C 229 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7401 (pp) REVERT: C 303 LEU cc_start: 0.8247 (tp) cc_final: 0.7769 (tt) REVERT: C 355 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6432 (tmt90) REVERT: C 558 LYS cc_start: 0.8605 (mttt) cc_final: 0.8314 (mttt) REVERT: C 564 GLN cc_start: 0.8006 (mt0) cc_final: 0.7740 (mt0) REVERT: C 707 TYR cc_start: 0.8117 (t80) cc_final: 0.7547 (t80) REVERT: C 820 ASP cc_start: 0.7691 (t70) cc_final: 0.7349 (t0) REVERT: C 869 MET cc_start: 0.8022 (mmm) cc_final: 0.7642 (mmm) REVERT: C 1029 MET cc_start: 0.8491 (tpp) cc_final: 0.8121 (ttm) REVERT: C 1031 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7533 (mt-10) REVERT: C 1050 MET cc_start: 0.7598 (mtm) cc_final: 0.7374 (mtp) REVERT: C 1136 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8522 (p) REVERT: D 6 GLN cc_start: -0.0946 (OUTLIER) cc_final: -0.1679 (tp-100) REVERT: D 85 GLU cc_start: 0.3065 (OUTLIER) cc_final: 0.2726 (pm20) REVERT: D 90 CYS cc_start: 0.5942 (OUTLIER) cc_final: 0.5413 (t) REVERT: D 111 LEU cc_start: 0.5170 (OUTLIER) cc_final: 0.4786 (tm) REVERT: D 234 MET cc_start: -0.3724 (pmt) cc_final: -0.4155 (pmt) REVERT: F 160 MET cc_start: -0.1155 (ptp) cc_final: -0.1903 (mmm) outliers start: 133 outliers final: 101 residues processed: 551 average time/residue: 0.4289 time to fit residues: 375.6099 Evaluate side-chains 553 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 441 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 281 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 318 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 287 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 121 optimal weight: 0.0980 chunk 278 optimal weight: 1.9990 chunk 329 optimal weight: 30.0000 chunk 326 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 644 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.197189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144539 restraints weight = 54511.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.147754 restraints weight = 26193.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.150370 restraints weight = 13364.837| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 30432 Z= 0.173 Angle : 0.673 17.216 41486 Z= 0.332 Chirality : 0.047 0.410 4711 Planarity : 0.005 0.052 5333 Dihedral : 6.571 79.662 4667 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.74 % Allowed : 19.17 % Favored : 77.09 % 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: -2.37 (0.13), residues: 3739 helix: 0.98 (0.21), residues: 657 sheet: -1.40 (0.19), residues: 699 loop : -2.55 (0.12), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP C 104 HIS 0.006 0.001 HIS A 519 PHE 0.032 0.002 PHE C 190 TYR 0.028 0.001 TYR A 265 ARG 0.010 0.000 ARG B 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 23) link_NAG-ASN : angle 2.21814 ( 69) hydrogen bonds : bond 0.03513 ( 800) hydrogen bonds : angle 4.96444 ( 2136) SS BOND : bond 0.00516 ( 44) SS BOND : angle 2.19912 ( 88) covalent geometry : bond 0.00391 (30365) covalent geometry : angle 0.66086 (41329) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 449 time to evaluate : 2.914 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 106 PHE cc_start: 0.7544 (m-80) cc_final: 0.7044 (m-80) REVERT: A 177 MET cc_start: 0.4278 (tpp) cc_final: 0.3985 (tpp) REVERT: A 190 PHE cc_start: 0.7487 (m-80) cc_final: 0.6870 (m-80) REVERT: A 223 LEU cc_start: 0.7526 (mp) cc_final: 0.6861 (mp) REVERT: A 307 THR cc_start: 0.8274 (m) cc_final: 0.8024 (p) REVERT: A 357 ARG cc_start: 0.6662 (ttp80) cc_final: 0.6462 (ttp80) REVERT: A 396 TYR cc_start: 0.6288 (m-80) cc_final: 0.5921 (m-80) REVERT: A 596 SER cc_start: 0.8933 (m) cc_final: 0.8590 (p) REVERT: A 602 THR cc_start: 0.8289 (m) cc_final: 0.7859 (p) REVERT: A 644 GLN cc_start: 0.7727 (tp40) cc_final: 0.7473 (tp40) REVERT: A 743 CYS cc_start: 0.6688 (OUTLIER) cc_final: 0.5761 (t) REVERT: A 868 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6913 (mm-30) REVERT: A 921 LYS cc_start: 0.8447 (mmmt) cc_final: 0.7842 (mmmt) REVERT: A 950 ASP cc_start: 0.7422 (t70) cc_final: 0.6682 (t0) REVERT: A 954 HIS cc_start: 0.7091 (m-70) cc_final: 0.6640 (m170) REVERT: A 955 ASN cc_start: 0.8425 (t0) cc_final: 0.8065 (t0) REVERT: A 969 LYS cc_start: 0.7727 (mppt) cc_final: 0.7405 (mmtm) REVERT: A 983 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7681 (ttp80) REVERT: A 984 LEU cc_start: 0.8618 (tt) cc_final: 0.8155 (mt) REVERT: A 988 GLU cc_start: 0.7517 (tp30) cc_final: 0.7188 (tp30) REVERT: A 1002 GLN cc_start: 0.7437 (tp-100) cc_final: 0.7013 (tp-100) REVERT: A 1057 PRO cc_start: 0.8967 (Cg_exo) cc_final: 0.8654 (Cg_endo) REVERT: A 1072 GLU cc_start: 0.8068 (pm20) cc_final: 0.7742 (pm20) REVERT: B 105 ILE cc_start: 0.8535 (mm) cc_final: 0.8265 (pt) REVERT: B 193 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7836 (ttmt) REVERT: B 200 LYS cc_start: 0.8722 (mttt) cc_final: 0.8283 (mptp) REVERT: B 201 ILE cc_start: 0.9072 (mp) cc_final: 0.8767 (pt) REVERT: B 205 HIS cc_start: 0.7388 (t-90) cc_final: 0.7091 (t-170) REVERT: B 224 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: B 271 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 307 THR cc_start: 0.8253 (m) cc_final: 0.7856 (p) REVERT: B 329 PHE cc_start: 0.6869 (m-10) cc_final: 0.6595 (m-10) REVERT: B 403 ARG cc_start: 0.6775 (mtm-85) cc_final: 0.6160 (ttm170) REVERT: B 602 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8284 (p) REVERT: B 644 GLN cc_start: 0.8144 (tp40) cc_final: 0.7860 (tp40) REVERT: B 719 THR cc_start: 0.7886 (m) cc_final: 0.7600 (p) REVERT: B 765 ARG cc_start: 0.7331 (mtp85) cc_final: 0.7034 (mmm-85) REVERT: B 773 GLU cc_start: 0.7498 (tp30) cc_final: 0.7041 (tp30) REVERT: B 803 SER cc_start: 0.8727 (m) cc_final: 0.8399 (p) REVERT: B 851 CYS cc_start: 0.8334 (t) cc_final: 0.7769 (p) REVERT: B 856 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8873 (tppp) REVERT: B 933 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7805 (mtmt) REVERT: B 957 GLN cc_start: 0.7041 (tm-30) cc_final: 0.6586 (tm-30) REVERT: B 964 LYS cc_start: 0.8375 (tmmt) cc_final: 0.8127 (ttmt) REVERT: B 965 GLN cc_start: 0.7602 (mm110) cc_final: 0.7100 (mp10) REVERT: B 1019 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7709 (ttp80) REVERT: C 41 LYS cc_start: 0.8504 (mtmt) cc_final: 0.8300 (mtmt) REVERT: C 129 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8093 (tptt) REVERT: C 169 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7450 (tm-30) REVERT: C 229 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7468 (pp) REVERT: C 303 LEU cc_start: 0.8261 (tp) cc_final: 0.7988 (tp) REVERT: C 355 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6538 (tmt90) REVERT: C 558 LYS cc_start: 0.8576 (mttt) cc_final: 0.8321 (mttt) REVERT: C 564 GLN cc_start: 0.8126 (mt0) cc_final: 0.7858 (mt0) REVERT: C 707 TYR cc_start: 0.8130 (t80) cc_final: 0.7571 (t80) REVERT: C 773 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6451 (tm-30) REVERT: C 820 ASP cc_start: 0.7739 (t70) cc_final: 0.7402 (t0) REVERT: C 859 THR cc_start: 0.8164 (p) cc_final: 0.7952 (p) REVERT: C 1050 MET cc_start: 0.7609 (mtm) cc_final: 0.7400 (mtp) REVERT: C 1136 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8502 (p) REVERT: D 6 GLN cc_start: -0.0843 (OUTLIER) cc_final: -0.1651 (tp-100) REVERT: D 90 CYS cc_start: 0.6002 (OUTLIER) cc_final: 0.5349 (t) REVERT: D 111 LEU cc_start: 0.5050 (OUTLIER) cc_final: 0.4682 (tm) REVERT: D 234 MET cc_start: -0.3763 (pmt) cc_final: -0.4187 (pmt) REVERT: F 160 MET cc_start: -0.1260 (ptp) cc_final: -0.1925 (mmm) outliers start: 121 outliers final: 104 residues processed: 541 average time/residue: 0.4322 time to fit residues: 370.9649 Evaluate side-chains 551 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 437 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 74 optimal weight: 0.8980 chunk 300 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 330 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 309 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 186 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 641 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.197796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.145311 restraints weight = 54458.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.148344 restraints weight = 26636.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.150964 restraints weight = 13616.525| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30432 Z= 0.147 Angle : 0.666 17.173 41486 Z= 0.329 Chirality : 0.046 0.386 4711 Planarity : 0.005 0.055 5333 Dihedral : 6.535 79.619 4667 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.86 % Allowed : 19.27 % Favored : 76.88 % 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: -2.34 (0.13), residues: 3739 helix: 0.96 (0.21), residues: 665 sheet: -1.44 (0.19), residues: 714 loop : -2.50 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP C 104 HIS 0.006 0.001 HIS A 519 PHE 0.031 0.001 PHE C 190 TYR 0.019 0.001 TYR A 265 ARG 0.009 0.000 ARG B 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 23) link_NAG-ASN : angle 2.15156 ( 69) hydrogen bonds : bond 0.03343 ( 800) hydrogen bonds : angle 4.96188 ( 2136) SS BOND : bond 0.00509 ( 44) SS BOND : angle 2.16092 ( 88) covalent geometry : bond 0.00334 (30365) covalent geometry : angle 0.65361 (41329) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11351.19 seconds wall clock time: 197 minutes 14.64 seconds (11834.64 seconds total)