Starting phenix.real_space_refine on Sun Jun 29 21:57:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wov_32660/06_2025/7wov_32660.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wov_32660/06_2025/7wov_32660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wov_32660/06_2025/7wov_32660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wov_32660/06_2025/7wov_32660.map" model { file = "/net/cci-nas-00/data/ceres_data/7wov_32660/06_2025/7wov_32660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wov_32660/06_2025/7wov_32660.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 22148 2.51 5 N 5802 2.21 5 O 6778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34884 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'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: "G" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "H" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "I" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 19.09, per 1000 atoms: 0.55 Number of scatterers: 34884 At special positions: 0 Unit cell: (144.704, 164.92, 212.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 6778 8.00 N 5802 7.00 C 22148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 221 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 146 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 221 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 146 " - pdb=" SG CYS G 220 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 221 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 146 " - pdb=" SG CYS I 220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A 717 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 717 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B1134 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C1098 " " NAG C1307 " - " ASN C1134 " Time building additional restraints: 8.72 Conformation dependent library (CDL) restraints added in 5.5 seconds 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8268 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 72 sheets defined 16.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.749A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.781A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.627A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.819A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 783 removed outlier: 3.514A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.060A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.866A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 910 " --> pdb=" O PHE A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 930 through 941 removed outlier: 3.928A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.674A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.272A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.952A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.711A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.712A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.590A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 756 Processing helix chain 'B' and resid 761 through 782 removed outlier: 3.528A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 906 Processing helix chain 'B' and resid 907 through 909 No H-bonds generated for 'chain 'B' and resid 907 through 909' Processing helix chain 'B' and resid 912 through 939 removed outlier: 4.404A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.615A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.206A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B1001 " --> pdb=" O ILE B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 removed outlier: 3.864A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1143 through 1147' Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.792A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.605A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 755 removed outlier: 4.018A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 778 removed outlier: 3.586A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.628A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 882 Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.610A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 removed outlier: 3.594A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.597A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.517A pdb=" N ASP C 979 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE C 980 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N PHE C 981 " --> pdb=" O ASN C 978 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 982 " --> pdb=" O ASP C 979 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 983 " --> pdb=" O ILE C 980 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 983' Processing helix chain 'C' and resid 985 through 993 removed outlier: 4.178A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1033 removed outlier: 3.664A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.971A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'G' and resid 152 through 156 Processing helix chain 'I' and resid 80 through 84 Processing helix chain 'I' and resid 152 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 3.933A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.799A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.812A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 93 removed outlier: 3.596A pdb=" N VAL A 191 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 203 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 224 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.514A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.674A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.443A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.461A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 removed outlier: 5.738A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.721A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.533A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.906A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 90 through 94 removed outlier: 3.523A pdb=" N VAL B 191 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B 198 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 229 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 201 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 227 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER B 203 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 120 through 122 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.763A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.820A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.478A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.674A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.821A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 712 through 718 removed outlier: 6.945A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 721 through 728 removed outlier: 7.248A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD6, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.724A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.335A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 224 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.759A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.873A pdb=" N SER C 94 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.979A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.656A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.404A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.697A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.780A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AE9, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AF1, first strand: chain 'C' and resid 721 through 728 removed outlier: 3.693A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.592A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF5, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.208A pdb=" N LEU D 48 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN D 39 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D 88 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR D 106 " --> pdb=" O TYR D 88 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 64 through 69 removed outlier: 5.278A pdb=" N SER D 65 " --> pdb=" O THR D 76 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER D 67 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 172 through 176 removed outlier: 6.007A pdb=" N TRP D 173 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG D 164 " --> pdb=" O TRP D 173 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 21 through 23 Processing sheet with id=AF9, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.025A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.025A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR E 87 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 143 through 144 Processing sheet with id=AG3, first strand: chain 'E' and resid 182 through 184 removed outlier: 6.610A pdb=" N TRP E 160 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL E 174 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N MET E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 47 through 50 removed outlier: 6.836A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR F 88 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR F 106 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 66 through 69 removed outlier: 3.707A pdb=" N SER F 67 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 172 through 176 removed outlier: 6.023A pdb=" N TRP F 173 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG F 164 " --> pdb=" O TRP F 173 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 21 through 23 Processing sheet with id=AG8, first strand: chain 'G' and resid 46 through 49 removed outlier: 5.031A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN G 97 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 130 through 131 Processing sheet with id=AH1, first strand: chain 'G' and resid 182 through 184 removed outlier: 6.589A pdb=" N TRP G 160 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL G 174 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N MET G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 47 through 50 removed outlier: 6.210A pdb=" N LEU H 48 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN H 39 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR H 88 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR H 106 " --> pdb=" O TYR H 88 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 66 through 69 removed outlier: 3.706A pdb=" N SER H 67 " --> pdb=" O SER H 74 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 172 through 177 removed outlier: 5.992A pdb=" N TRP H 173 " --> pdb=" O ARG H 164 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG H 164 " --> pdb=" O TRP H 173 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE H 177 " --> pdb=" O MET H 160 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET H 160 " --> pdb=" O ILE H 177 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 21 through 23 Processing sheet with id=AH6, first strand: chain 'I' and resid 46 through 49 removed outlier: 5.019A pdb=" N LEU I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLN I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN I 97 " --> pdb=" O ASP I 93 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 46 through 49 removed outlier: 5.019A pdb=" N LEU I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLN I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR I 87 " --> pdb=" O THR I 104 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 143 through 144 Processing sheet with id=AH9, first strand: chain 'I' and resid 182 through 184 removed outlier: 6.618A pdb=" N TRP I 160 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL I 174 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET I 158 " --> pdb=" O VAL I 174 " (cutoff:3.500A) 915 hydrogen bonds defined for protein. 2379 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.38 Time building geometry restraints manager: 10.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6382 1.33 - 1.45: 9725 1.45 - 1.57: 19390 1.57 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 35701 Sorted by residual: bond pdb=" CA THR A 33 " pdb=" C THR A 33 " ideal model delta sigma weight residual 1.524 1.450 0.075 8.80e-03 1.29e+04 7.19e+01 bond pdb=" CA ARG A 34 " pdb=" C ARG A 34 " ideal model delta sigma weight residual 1.527 1.429 0.098 1.41e-02 5.03e+03 4.86e+01 bond pdb=" CA ASN B1134 " pdb=" C ASN B1134 " ideal model delta sigma weight residual 1.526 1.453 0.073 1.28e-02 6.10e+03 3.24e+01 bond pdb=" CA ASN A 801 " pdb=" C ASN A 801 " ideal model delta sigma weight residual 1.526 1.458 0.068 1.30e-02 5.92e+03 2.74e+01 bond pdb=" CA ASN A 717 " pdb=" C ASN A 717 " ideal model delta sigma weight residual 1.522 1.461 0.062 1.20e-02 6.94e+03 2.64e+01 ... (remaining 35696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 47472 1.51 - 3.03: 909 3.03 - 4.54: 162 4.54 - 6.06: 22 6.06 - 7.57: 15 Bond angle restraints: 48580 Sorted by residual: angle pdb=" O SER A 708 " pdb=" C SER A 708 " pdb=" N ASN A 709 " ideal model delta sigma weight residual 122.81 115.24 7.57 1.23e+00 6.61e-01 3.79e+01 angle pdb=" CA SER A 708 " pdb=" C SER A 708 " pdb=" N ASN A 709 " ideal model delta sigma weight residual 115.56 123.05 -7.49 1.30e+00 5.92e-01 3.32e+01 angle pdb=" C ILE B 233 " pdb=" N ASN B 234 " pdb=" CA ASN B 234 " ideal model delta sigma weight residual 122.30 116.06 6.24 1.35e+00 5.49e-01 2.14e+01 angle pdb=" C SER A 708 " pdb=" N ASN A 709 " pdb=" CA ASN A 709 " ideal model delta sigma weight residual 120.31 113.29 7.02 1.52e+00 4.33e-01 2.13e+01 angle pdb=" C ASN A 709 " pdb=" N ASN A 710 " pdb=" CA ASN A 710 " ideal model delta sigma weight residual 123.33 116.28 7.05 1.64e+00 3.72e-01 1.85e+01 ... (remaining 48575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 20249 16.34 - 32.69: 915 32.69 - 49.03: 159 49.03 - 65.38: 42 65.38 - 81.72: 6 Dihedral angle restraints: 21371 sinusoidal: 8409 harmonic: 12962 Sorted by residual: dihedral pdb=" CA ALA C 570 " pdb=" C ALA C 570 " pdb=" N ASP C 571 " pdb=" CA ASP C 571 " ideal model delta harmonic sigma weight residual 180.00 164.36 15.64 0 5.00e+00 4.00e-02 9.79e+00 dihedral pdb=" N CYS F 90 " pdb=" CA CYS F 90 " pdb=" CB CYS F 90 " pdb=" SG CYS F 90 " ideal model delta sinusoidal sigma weight residual 180.00 120.57 59.43 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ASP A1041 " pdb=" CA ASP A1041 " pdb=" CB ASP A1041 " pdb=" CG ASP A1041 " ideal model delta sinusoidal sigma weight residual 60.00 119.34 -59.34 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 21368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 5004 0.079 - 0.158: 454 0.158 - 0.238: 5 0.238 - 0.317: 2 0.317 - 0.396: 2 Chirality restraints: 5467 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 5464 not shown) Planarity restraints: 6310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.352 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG A1301 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.086 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " 0.325 2.00e-02 2.50e+03 2.83e-01 9.98e+02 pdb=" C7 NAG A1303 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " 0.056 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " -0.499 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " 0.189 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1306 " -0.324 2.00e-02 2.50e+03 2.82e-01 9.96e+02 pdb=" C7 NAG B1306 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG B1306 " -0.058 2.00e-02 2.50e+03 pdb=" N2 NAG B1306 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG B1306 " -0.188 2.00e-02 2.50e+03 ... (remaining 6307 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 941 2.69 - 3.24: 33795 3.24 - 3.79: 53437 3.79 - 4.35: 69937 4.35 - 4.90: 115385 Nonbonded interactions: 273495 Sorted by model distance: nonbonded pdb=" O4 NAG B1304 " pdb=" O6 NAG B1304 " model vdw 2.137 3.040 nonbonded pdb=" OG SER D 91 " pdb=" OE1 GLN D 227 " model vdw 2.209 3.040 nonbonded pdb=" OG SER F 91 " pdb=" OE1 GLN F 227 " model vdw 2.212 3.040 nonbonded pdb=" OG SER H 91 " pdb=" OE1 GLN H 227 " model vdw 2.219 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.223 3.040 ... (remaining 273490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 243 or resid 262 through 1147 or resid 1301 thr \ ough 1305)) selection = (chain 'B' and (resid 26 through 243 or resid 262 through 1147 or resid 1301 thr \ ough 1305)) selection = (chain 'C' and (resid 26 through 1147 or resid 1301 through 1305)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.770 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: 1.310 Check model and map are aligned: 0.260 Set scattering table: 0.350 Process input model: 80.190 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.180 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 35770 Z= 0.191 Angle : 0.553 9.444 48736 Z= 0.314 Chirality : 0.042 0.396 5467 Planarity : 0.010 0.303 6292 Dihedral : 9.471 81.723 12950 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.03 % Favored : 91.81 % Rotamer: Outliers : 5.98 % Allowed : 8.00 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.25 (0.10), residues: 4433 helix: -0.96 (0.19), residues: 632 sheet: -2.54 (0.16), residues: 829 loop : -3.58 (0.09), residues: 2972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 98 HIS 0.004 0.000 HIS B1101 PHE 0.006 0.001 PHE C 318 TYR 0.011 0.001 TYR A1067 ARG 0.008 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.01006 ( 18) link_NAG-ASN : angle 2.96380 ( 54) hydrogen bonds : bond 0.17232 ( 899) hydrogen bonds : angle 6.42232 ( 2379) SS BOND : bond 0.00161 ( 51) SS BOND : angle 0.57090 ( 102) covalent geometry : bond 0.00294 (35701) covalent geometry : angle 0.54400 (48580) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 781 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7736 (mtp85) REVERT: A 48 LEU cc_start: 0.8575 (mp) cc_final: 0.8334 (mt) REVERT: A 52 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7521 (tp40) REVERT: A 274 THR cc_start: 0.8426 (m) cc_final: 0.7921 (m) REVERT: A 290 ASP cc_start: 0.7167 (t70) cc_final: 0.6032 (p0) REVERT: A 318 PHE cc_start: 0.7467 (t80) cc_final: 0.7211 (t80) REVERT: A 720 ILE cc_start: 0.8763 (mp) cc_final: 0.8552 (mm) REVERT: A 776 LYS cc_start: 0.7958 (tmmt) cc_final: 0.7612 (tttm) REVERT: A 777 ASN cc_start: 0.7827 (m-40) cc_final: 0.7490 (m-40) REVERT: A 895 GLN cc_start: 0.7584 (pt0) cc_final: 0.7154 (mt0) REVERT: A 913 GLN cc_start: 0.7292 (pt0) cc_final: 0.6987 (pt0) REVERT: A 921 LYS cc_start: 0.7573 (mmmt) cc_final: 0.7181 (mppt) REVERT: A 925 ASN cc_start: 0.7773 (m-40) cc_final: 0.7141 (m-40) REVERT: A 976 VAL cc_start: 0.8668 (t) cc_final: 0.8403 (p) REVERT: A 993 ILE cc_start: 0.8238 (tp) cc_final: 0.7891 (tt) REVERT: A 1000 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7367 (mmt90) REVERT: A 1002 GLN cc_start: 0.7275 (tp-100) cc_final: 0.6942 (tp-100) REVERT: A 1019 ARG cc_start: 0.6665 (ttm110) cc_final: 0.6219 (ttm110) REVERT: A 1031 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6912 (mt-10) REVERT: A 1038 LYS cc_start: 0.7601 (mtmp) cc_final: 0.7352 (mtmm) REVERT: B 41 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7134 (mttt) REVERT: B 46 SER cc_start: 0.8082 (m) cc_final: 0.7504 (p) REVERT: B 119 ILE cc_start: 0.7511 (mt) cc_final: 0.7230 (tt) REVERT: B 126 VAL cc_start: 0.8106 (t) cc_final: 0.7814 (m) REVERT: B 194 ASN cc_start: 0.8447 (t0) cc_final: 0.8200 (t0) REVERT: B 199 PHE cc_start: 0.7616 (t80) cc_final: 0.7389 (t80) REVERT: B 200 LYS cc_start: 0.7971 (mttt) cc_final: 0.7551 (mttm) REVERT: B 201 ILE cc_start: 0.8202 (mt) cc_final: 0.7836 (mt) REVERT: B 205 HIS cc_start: 0.7139 (t-170) cc_final: 0.6864 (t-170) REVERT: B 276 LEU cc_start: 0.8428 (tp) cc_final: 0.8079 (tt) REVERT: B 278 LYS cc_start: 0.8185 (ttmp) cc_final: 0.7774 (tttm) REVERT: B 298 GLU cc_start: 0.7044 (tt0) cc_final: 0.6824 (tt0) REVERT: B 306 PHE cc_start: 0.7282 (m-10) cc_final: 0.6993 (m-10) REVERT: B 315 THR cc_start: 0.7773 (p) cc_final: 0.7545 (p) REVERT: B 425 LEU cc_start: 0.8693 (mp) cc_final: 0.8201 (pp) REVERT: B 542 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7651 (t0) REVERT: B 584 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7828 (pt) REVERT: B 587 ILE cc_start: 0.8059 (mt) cc_final: 0.7797 (mm) REVERT: B 616 ASN cc_start: 0.5695 (t0) cc_final: 0.5198 (t0) REVERT: B 619 GLU cc_start: 0.5957 (tt0) cc_final: 0.5713 (tt0) REVERT: B 663 ASP cc_start: 0.6883 (t70) cc_final: 0.6660 (t0) REVERT: B 698 SER cc_start: 0.8022 (t) cc_final: 0.7397 (p) REVERT: B 740 MET cc_start: 0.5868 (ttp) cc_final: 0.5640 (ttp) REVERT: B 773 GLU cc_start: 0.6311 (tm-30) cc_final: 0.4978 (tm-30) REVERT: B 774 GLN cc_start: 0.7206 (mm-40) cc_final: 0.5466 (mm-40) REVERT: B 790 LYS cc_start: 0.7732 (mppt) cc_final: 0.7363 (mtmm) REVERT: B 804 GLN cc_start: 0.7728 (mt0) cc_final: 0.7320 (mt0) REVERT: B 895 GLN cc_start: 0.7277 (pt0) cc_final: 0.7057 (mt0) REVERT: B 933 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7019 (mtpp) REVERT: B 974 SER cc_start: 0.6196 (p) cc_final: 0.5544 (m) REVERT: B 1000 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7471 (mtt180) REVERT: B 1010 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.6891 (mp-120) REVERT: B 1019 ARG cc_start: 0.6696 (ttm110) cc_final: 0.6407 (tmm-80) REVERT: B 1074 ASN cc_start: 0.8014 (m-40) cc_final: 0.7803 (m110) REVERT: B 1081 ILE cc_start: 0.8291 (pt) cc_final: 0.7923 (mm) REVERT: B 1118 ASP cc_start: 0.6423 (t70) cc_final: 0.6209 (t0) REVERT: C 33 THR cc_start: 0.7681 (OUTLIER) cc_final: 0.7445 (p) REVERT: C 65 PHE cc_start: 0.6923 (m-10) cc_final: 0.6498 (m-10) REVERT: C 106 PHE cc_start: 0.6687 (m-80) cc_final: 0.6188 (m-80) REVERT: C 126 VAL cc_start: 0.7097 (OUTLIER) cc_final: 0.6777 (t) REVERT: C 190 PHE cc_start: 0.6103 (m-80) cc_final: 0.5775 (m-80) REVERT: C 326 ILE cc_start: 0.8164 (mp) cc_final: 0.7809 (tt) REVERT: C 362 VAL cc_start: 0.7104 (OUTLIER) cc_final: 0.6542 (p) REVERT: C 542 ASN cc_start: 0.7489 (t0) cc_final: 0.7188 (t0) REVERT: C 551 VAL cc_start: 0.8078 (t) cc_final: 0.7844 (t) REVERT: C 644 GLN cc_start: 0.8313 (tp40) cc_final: 0.7439 (tp40) REVERT: C 659 SER cc_start: 0.8692 (t) cc_final: 0.8491 (p) REVERT: C 707 TYR cc_start: 0.7631 (t80) cc_final: 0.7360 (t80) REVERT: C 765 ARG cc_start: 0.7016 (ttp-110) cc_final: 0.6716 (ttp-110) REVERT: C 780 GLU cc_start: 0.7036 (pt0) cc_final: 0.6433 (pt0) REVERT: C 790 LYS cc_start: 0.7791 (mtmm) cc_final: 0.7557 (mtmm) REVERT: C 808 ASP cc_start: 0.7283 (t70) cc_final: 0.6966 (t70) REVERT: C 819 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6847 (mt-10) REVERT: C 820 ASP cc_start: 0.7554 (m-30) cc_final: 0.7301 (m-30) REVERT: C 901 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7433 (tm-30) REVERT: C 914 ASN cc_start: 0.7347 (p0) cc_final: 0.6993 (p0) REVERT: C 960 ASN cc_start: 0.6554 (m110) cc_final: 0.6138 (m110) REVERT: C 973 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6690 (pp) REVERT: C 993 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7624 (mm) REVERT: C 994 ASP cc_start: 0.7583 (m-30) cc_final: 0.6682 (p0) REVERT: C 998 THR cc_start: 0.7873 (m) cc_final: 0.7502 (p) REVERT: C 1129 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7904 (p) REVERT: E 67 LYS cc_start: 0.0561 (OUTLIER) cc_final: 0.0290 (tmmm) REVERT: F 144 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.5842 (tm) REVERT: G 210 LEU cc_start: 0.0009 (OUTLIER) cc_final: -0.0475 (tm) REVERT: H 83 GLU cc_start: 0.3006 (OUTLIER) cc_final: 0.2567 (pp20) REVERT: I 67 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6757 (tmmm) outliers start: 228 outliers final: 96 residues processed: 977 average time/residue: 0.5185 time to fit residues: 828.7602 Evaluate side-chains 724 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 611 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 376 optimal weight: 8.9990 chunk 338 optimal weight: 9.9990 chunk 187 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 228 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 chunk 349 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 212 optimal weight: 6.9990 chunk 260 optimal weight: 0.1980 chunk 405 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 52 GLN A 121 ASN A 173 GLN A 354 ASN A 370 ASN A 388 ASN A 409 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 487 ASN A 563 GLN A 690 GLN A 853 GLN A 901 GLN A1002 GLN A1011 GLN A1048 HIS B 173 GLN B 181 GLN B 186 ASN B 239 GLN B 245 HIS B 354 ASN B 388 ASN B 409 GLN B 422 ASN B 448 ASN B 477 ASN B 487 ASN B 540 ASN B 563 GLN B 784 GLN B 853 GLN B 901 GLN B 914 ASN B 949 GLN B1002 GLN B1010 GLN B1011 GLN B1048 HIS B1119 ASN C 30 ASN C 164 ASN C 183 ASN C 205 HIS C 218 GLN C 354 ASN C 370 ASN C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 477 ASN C 487 ASN C 540 ASN C 580 GLN C 755 GLN C 774 GLN C 784 GLN C 853 GLN C 895 GLN C 913 GLN C 914 ASN C 955 ASN C1011 GLN C1048 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 39 GLN D 40 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 165 GLN D 202 ASN E 52 ASN E 80 GLN E 97 ASN E 127 GLN E 137 GLN E 159 HIS E 201 ASN E 206 GLN F 33 ASN F 39 GLN F 40 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN F 165 GLN F 202 ASN F 207 GLN G 35 ASN G 52 ASN G 80 GLN G 97 ASN G 137 GLN G 159 HIS G 201 ASN G 206 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 39 GLN H 40 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 GLN H 202 ASN I 32 ASN I 52 ASN I 80 GLN I 97 ASN I 127 GLN I 137 GLN I 159 HIS I 201 ASN I 206 GLN Total number of N/Q/H flips: 107 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.224849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.178843 restraints weight = 63624.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.176923 restraints weight = 53449.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.177855 restraints weight = 41901.289| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35770 Z= 0.133 Angle : 0.588 10.872 48736 Z= 0.293 Chirality : 0.044 0.255 5467 Planarity : 0.005 0.054 6292 Dihedral : 7.236 80.336 5506 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 5.85 % Allowed : 13.30 % Favored : 80.85 % 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: -3.59 (0.11), residues: 4433 helix: -0.00 (0.21), residues: 674 sheet: -2.11 (0.16), residues: 830 loop : -3.28 (0.09), residues: 2929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 64 HIS 0.005 0.001 HIS C 66 PHE 0.028 0.001 PHE C 643 TYR 0.021 0.001 TYR B1067 ARG 0.006 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 18) link_NAG-ASN : angle 2.93733 ( 54) hydrogen bonds : bond 0.03681 ( 899) hydrogen bonds : angle 4.84406 ( 2379) SS BOND : bond 0.00240 ( 51) SS BOND : angle 1.67255 ( 102) covalent geometry : bond 0.00293 (35701) covalent geometry : angle 0.57557 (48580) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 649 time to evaluate : 3.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8484 (mm) cc_final: 0.7978 (mt) REVERT: A 318 PHE cc_start: 0.7636 (t80) cc_final: 0.7352 (t80) REVERT: A 537 LYS cc_start: 0.7259 (tmtt) cc_final: 0.6651 (tmtt) REVERT: A 581 THR cc_start: 0.7060 (OUTLIER) cc_final: 0.6589 (t) REVERT: A 586 ASP cc_start: 0.7608 (t0) cc_final: 0.7265 (t0) REVERT: A 649 CYS cc_start: 0.5258 (t) cc_final: 0.4836 (t) REVERT: A 675 GLN cc_start: 0.6581 (pp30) cc_final: 0.6183 (tm-30) REVERT: A 720 ILE cc_start: 0.8662 (mp) cc_final: 0.8397 (mm) REVERT: A 733 LYS cc_start: 0.8250 (mtmt) cc_final: 0.8025 (mtpt) REVERT: A 761 THR cc_start: 0.7611 (OUTLIER) cc_final: 0.7299 (p) REVERT: A 776 LYS cc_start: 0.8194 (tmmt) cc_final: 0.7803 (tttm) REVERT: A 777 ASN cc_start: 0.8177 (m-40) cc_final: 0.7620 (m-40) REVERT: A 813 SER cc_start: 0.8053 (m) cc_final: 0.7847 (p) REVERT: A 821 LEU cc_start: 0.8596 (tp) cc_final: 0.8361 (tp) REVERT: A 823 PHE cc_start: 0.7351 (m-80) cc_final: 0.7133 (m-10) REVERT: A 869 MET cc_start: 0.8423 (mtp) cc_final: 0.8140 (mtp) REVERT: A 895 GLN cc_start: 0.7638 (pt0) cc_final: 0.7188 (mt0) REVERT: A 913 GLN cc_start: 0.7782 (pt0) cc_final: 0.7438 (pt0) REVERT: A 914 ASN cc_start: 0.7360 (p0) cc_final: 0.7140 (p0) REVERT: A 921 LYS cc_start: 0.7721 (mmmt) cc_final: 0.7073 (mppt) REVERT: A 925 ASN cc_start: 0.7760 (m-40) cc_final: 0.7408 (m-40) REVERT: A 933 LYS cc_start: 0.8089 (mtmm) cc_final: 0.7816 (mtmm) REVERT: A 957 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7395 (tt0) REVERT: A 976 VAL cc_start: 0.8454 (t) cc_final: 0.8084 (p) REVERT: A 1002 GLN cc_start: 0.7356 (tp40) cc_final: 0.6668 (tp40) REVERT: A 1038 LYS cc_start: 0.7742 (mtmp) cc_final: 0.7514 (mtmm) REVERT: A 1073 LYS cc_start: 0.8503 (ttmt) cc_final: 0.8079 (mtpp) REVERT: A 1103 PHE cc_start: 0.8152 (m-80) cc_final: 0.7454 (m-10) REVERT: B 40 ASP cc_start: 0.7808 (p0) cc_final: 0.7489 (p0) REVERT: B 41 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7075 (mttt) REVERT: B 46 SER cc_start: 0.8232 (m) cc_final: 0.7667 (p) REVERT: B 52 GLN cc_start: 0.7617 (tm-30) cc_final: 0.6918 (tm-30) REVERT: B 62 VAL cc_start: 0.8032 (m) cc_final: 0.7778 (p) REVERT: B 65 PHE cc_start: 0.6814 (m-80) cc_final: 0.6521 (m-10) REVERT: B 95 ILE cc_start: 0.6465 (tp) cc_final: 0.6131 (mm) REVERT: B 126 VAL cc_start: 0.8118 (t) cc_final: 0.7789 (m) REVERT: B 200 LYS cc_start: 0.8043 (mttt) cc_final: 0.7625 (mttm) REVERT: B 201 ILE cc_start: 0.8290 (mt) cc_final: 0.7981 (mt) REVERT: B 276 LEU cc_start: 0.8491 (tp) cc_final: 0.8189 (tt) REVERT: B 278 LYS cc_start: 0.8198 (ttmp) cc_final: 0.7873 (tttm) REVERT: B 293 LEU cc_start: 0.8092 (tp) cc_final: 0.7848 (tp) REVERT: B 306 PHE cc_start: 0.7551 (m-10) cc_final: 0.7254 (m-10) REVERT: B 308 VAL cc_start: 0.8819 (t) cc_final: 0.8540 (m) REVERT: B 328 ARG cc_start: 0.5866 (mtp85) cc_final: 0.5645 (mmm-85) REVERT: B 542 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7371 (t0) REVERT: B 562 PHE cc_start: 0.8150 (p90) cc_final: 0.7944 (p90) REVERT: B 584 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7797 (tt) REVERT: B 587 ILE cc_start: 0.8265 (mt) cc_final: 0.8043 (mm) REVERT: B 606 ASN cc_start: 0.8316 (m-40) cc_final: 0.8064 (m-40) REVERT: B 616 ASN cc_start: 0.6097 (t0) cc_final: 0.5548 (t0) REVERT: B 663 ASP cc_start: 0.6944 (t70) cc_final: 0.6104 (t0) REVERT: B 698 SER cc_start: 0.8122 (t) cc_final: 0.7449 (p) REVERT: B 703 ASN cc_start: 0.6643 (t0) cc_final: 0.6096 (t0) REVERT: B 710 ASN cc_start: 0.7827 (p0) cc_final: 0.7602 (p0) REVERT: B 726 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7724 (mm) REVERT: B 740 MET cc_start: 0.6218 (ttp) cc_final: 0.6006 (ttp) REVERT: B 742 ILE cc_start: 0.8667 (mm) cc_final: 0.8322 (tp) REVERT: B 774 GLN cc_start: 0.7447 (mm-40) cc_final: 0.6967 (mm-40) REVERT: B 790 LYS cc_start: 0.7899 (mppt) cc_final: 0.7622 (mtmm) REVERT: B 808 ASP cc_start: 0.7704 (t0) cc_final: 0.7176 (p0) REVERT: B 895 GLN cc_start: 0.7458 (pt0) cc_final: 0.7149 (mt0) REVERT: B 931 ILE cc_start: 0.7400 (mm) cc_final: 0.6686 (mt) REVERT: B 933 LYS cc_start: 0.8052 (mtmt) cc_final: 0.7205 (mtpp) REVERT: B 964 LYS cc_start: 0.8089 (ttpp) cc_final: 0.7756 (ttmm) REVERT: B 974 SER cc_start: 0.6224 (p) cc_final: 0.5744 (m) REVERT: B 977 LEU cc_start: 0.7688 (mp) cc_final: 0.7310 (mt) REVERT: B 990 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6336 (mt-10) REVERT: B 1081 ILE cc_start: 0.8424 (pt) cc_final: 0.7974 (mm) REVERT: C 33 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7547 (p) REVERT: C 48 LEU cc_start: 0.7620 (mt) cc_final: 0.7362 (mm) REVERT: C 92 PHE cc_start: 0.7501 (t80) cc_final: 0.7178 (t80) REVERT: C 192 PHE cc_start: 0.7706 (m-80) cc_final: 0.6959 (m-80) REVERT: C 204 LYS cc_start: 0.7816 (tptp) cc_final: 0.7282 (tptp) REVERT: C 304 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7694 (mmmt) REVERT: C 326 ILE cc_start: 0.8107 (mp) cc_final: 0.7520 (tt) REVERT: C 362 VAL cc_start: 0.6892 (OUTLIER) cc_final: 0.6684 (t) REVERT: C 537 LYS cc_start: 0.8303 (tttt) cc_final: 0.7940 (ptmt) REVERT: C 551 VAL cc_start: 0.8180 (t) cc_final: 0.7920 (t) REVERT: C 615 VAL cc_start: 0.8110 (p) cc_final: 0.7836 (m) REVERT: C 644 GLN cc_start: 0.7938 (tp40) cc_final: 0.7489 (tp40) REVERT: C 725 GLU cc_start: 0.7088 (pt0) cc_final: 0.6847 (pt0) REVERT: C 765 ARG cc_start: 0.7201 (ttp-110) cc_final: 0.6927 (ttp-110) REVERT: C 780 GLU cc_start: 0.7206 (pt0) cc_final: 0.6805 (pt0) REVERT: C 790 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7749 (mtmm) REVERT: C 808 ASP cc_start: 0.7334 (t70) cc_final: 0.6972 (t0) REVERT: C 819 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6849 (mt-10) REVERT: C 901 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: C 914 ASN cc_start: 0.7580 (p0) cc_final: 0.7105 (p0) REVERT: C 945 LEU cc_start: 0.7850 (mm) cc_final: 0.7637 (mt) REVERT: C 973 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6645 (pp) REVERT: C 993 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7621 (mm) REVERT: C 994 ASP cc_start: 0.7367 (m-30) cc_final: 0.6640 (p0) REVERT: C 1028 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7909 (ttmt) REVERT: C 1103 PHE cc_start: 0.7542 (m-10) cc_final: 0.7318 (m-10) REVERT: C 1107 ARG cc_start: 0.7477 (tpp80) cc_final: 0.7163 (ttm-80) REVERT: C 1129 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7944 (p) REVERT: C 1136 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.8101 (p) REVERT: E 67 LYS cc_start: 0.0493 (OUTLIER) cc_final: 0.0269 (tmmm) REVERT: G 158 MET cc_start: 0.5357 (mmm) cc_final: 0.4992 (mmm) REVERT: G 207 MET cc_start: 0.2831 (mpp) cc_final: 0.0829 (ptp) REVERT: H 83 GLU cc_start: 0.2617 (OUTLIER) cc_final: 0.2396 (pp20) REVERT: I 67 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6699 (tmmm) outliers start: 223 outliers final: 134 residues processed: 826 average time/residue: 0.4657 time to fit residues: 626.7811 Evaluate side-chains 752 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 600 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 405 optimal weight: 0.0070 chunk 123 optimal weight: 2.9990 chunk 162 optimal weight: 0.3980 chunk 330 optimal weight: 9.9990 chunk 331 optimal weight: 6.9990 chunk 363 optimal weight: 8.9990 chunk 372 optimal weight: 0.3980 chunk 198 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 302 optimal weight: 0.9990 chunk 439 optimal weight: 40.0000 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 205 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 81 ASN C 422 ASN C 913 GLN C 955 ASN C1002 GLN C1048 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.224245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.177871 restraints weight = 64065.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.176165 restraints weight = 48064.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.177274 restraints weight = 37067.210| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 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 : 0.002 0.053 35770 Z= 0.110 Angle : 0.579 10.989 48736 Z= 0.287 Chirality : 0.044 0.298 5467 Planarity : 0.004 0.048 6292 Dihedral : 6.990 80.909 5474 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 5.93 % Allowed : 14.74 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.18 (0.12), residues: 4433 helix: 0.48 (0.21), residues: 682 sheet: -1.79 (0.16), residues: 912 loop : -3.09 (0.10), residues: 2839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 104 HIS 0.017 0.001 HIS B1048 PHE 0.038 0.001 PHE B 981 TYR 0.025 0.001 TYR A 655 ARG 0.005 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 18) link_NAG-ASN : angle 2.80762 ( 54) hydrogen bonds : bond 0.03295 ( 899) hydrogen bonds : angle 4.67259 ( 2379) SS BOND : bond 0.00563 ( 51) SS BOND : angle 1.84893 ( 102) covalent geometry : bond 0.00244 (35701) covalent geometry : angle 0.56563 (48580) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 610 time to evaluate : 3.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8224 (tp40) cc_final: 0.7634 (tp-100) REVERT: A 54 LEU cc_start: 0.8569 (mm) cc_final: 0.8137 (mt) REVERT: A 118 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7893 (tp) REVERT: A 537 LYS cc_start: 0.7195 (tmtt) cc_final: 0.6491 (tmtt) REVERT: A 644 GLN cc_start: 0.7477 (tp40) cc_final: 0.6963 (tp40) REVERT: A 675 GLN cc_start: 0.6679 (pp30) cc_final: 0.6349 (tm-30) REVERT: A 720 ILE cc_start: 0.8727 (mp) cc_final: 0.8517 (mm) REVERT: A 736 VAL cc_start: 0.8425 (p) cc_final: 0.8210 (t) REVERT: A 776 LYS cc_start: 0.8242 (tmmt) cc_final: 0.7903 (tttp) REVERT: A 777 ASN cc_start: 0.8157 (m-40) cc_final: 0.7636 (m-40) REVERT: A 813 SER cc_start: 0.8266 (m) cc_final: 0.7962 (p) REVERT: A 820 ASP cc_start: 0.6855 (m-30) cc_final: 0.6593 (m-30) REVERT: A 823 PHE cc_start: 0.7407 (m-80) cc_final: 0.7183 (m-10) REVERT: A 825 LYS cc_start: 0.7714 (mmmm) cc_final: 0.7448 (ttmt) REVERT: A 869 MET cc_start: 0.8486 (mtp) cc_final: 0.8245 (mtp) REVERT: A 895 GLN cc_start: 0.7609 (pt0) cc_final: 0.7227 (pt0) REVERT: A 913 GLN cc_start: 0.7740 (pt0) cc_final: 0.7468 (pt0) REVERT: A 921 LYS cc_start: 0.7743 (mmmt) cc_final: 0.7283 (mppt) REVERT: A 925 ASN cc_start: 0.7736 (m-40) cc_final: 0.7456 (m-40) REVERT: A 933 LYS cc_start: 0.8047 (mtmm) cc_final: 0.7714 (mtmm) REVERT: A 957 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: A 976 VAL cc_start: 0.8452 (t) cc_final: 0.7952 (p) REVERT: A 1038 LYS cc_start: 0.7669 (mtmp) cc_final: 0.7391 (mtmm) REVERT: A 1072 GLU cc_start: 0.8077 (pm20) cc_final: 0.7860 (pm20) REVERT: A 1073 LYS cc_start: 0.8465 (ttmt) cc_final: 0.8044 (mtpp) REVERT: B 40 ASP cc_start: 0.7804 (p0) cc_final: 0.7521 (p0) REVERT: B 46 SER cc_start: 0.8244 (m) cc_final: 0.7689 (p) REVERT: B 52 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7284 (tm-30) REVERT: B 62 VAL cc_start: 0.8058 (m) cc_final: 0.7820 (p) REVERT: B 65 PHE cc_start: 0.6728 (m-80) cc_final: 0.6514 (m-10) REVERT: B 95 ILE cc_start: 0.6498 (tp) cc_final: 0.6177 (mm) REVERT: B 200 LYS cc_start: 0.8111 (mttt) cc_final: 0.7655 (mttm) REVERT: B 228 ASP cc_start: 0.6587 (t70) cc_final: 0.6297 (t70) REVERT: B 276 LEU cc_start: 0.8486 (tp) cc_final: 0.8136 (tt) REVERT: B 278 LYS cc_start: 0.8153 (ttmp) cc_final: 0.7843 (tttm) REVERT: B 281 GLU cc_start: 0.7140 (pp20) cc_final: 0.6933 (pp20) REVERT: B 306 PHE cc_start: 0.7534 (m-10) cc_final: 0.7226 (m-10) REVERT: B 308 VAL cc_start: 0.8882 (t) cc_final: 0.8650 (p) REVERT: B 542 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7369 (t0) REVERT: B 606 ASN cc_start: 0.8273 (m-40) cc_final: 0.8051 (m-40) REVERT: B 616 ASN cc_start: 0.5989 (t0) cc_final: 0.5344 (t0) REVERT: B 698 SER cc_start: 0.8186 (t) cc_final: 0.7556 (p) REVERT: B 703 ASN cc_start: 0.6685 (t0) cc_final: 0.6181 (t0) REVERT: B 774 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7027 (mm-40) REVERT: B 790 LYS cc_start: 0.7905 (mppt) cc_final: 0.7613 (mtmm) REVERT: B 808 ASP cc_start: 0.7744 (t0) cc_final: 0.7167 (p0) REVERT: B 819 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7149 (mt-10) REVERT: B 881 THR cc_start: 0.8624 (m) cc_final: 0.8360 (t) REVERT: B 895 GLN cc_start: 0.7404 (pt0) cc_final: 0.7041 (mt0) REVERT: B 906 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7414 (m-10) REVERT: B 921 LYS cc_start: 0.7821 (mmmt) cc_final: 0.7486 (mmmm) REVERT: B 933 LYS cc_start: 0.7981 (mtmt) cc_final: 0.6974 (mtpp) REVERT: B 964 LYS cc_start: 0.8047 (ttpp) cc_final: 0.7722 (ttmm) REVERT: B 974 SER cc_start: 0.6204 (p) cc_final: 0.5703 (m) REVERT: B 977 LEU cc_start: 0.7701 (mp) cc_final: 0.7440 (tp) REVERT: B 981 PHE cc_start: 0.6760 (m-80) cc_final: 0.5962 (m-80) REVERT: B 990 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6266 (mt-10) REVERT: B 1004 LEU cc_start: 0.8388 (tp) cc_final: 0.8099 (tp) REVERT: B 1018 ILE cc_start: 0.8267 (mt) cc_final: 0.7954 (mm) REVERT: B 1081 ILE cc_start: 0.8353 (pt) cc_final: 0.8113 (pt) REVERT: B 1091 ARG cc_start: 0.7098 (ttm170) cc_final: 0.6811 (ttm-80) REVERT: C 104 TRP cc_start: 0.6324 (m-10) cc_final: 0.5889 (m-10) REVERT: C 177 MET cc_start: -0.0283 (tmt) cc_final: -0.0701 (tmt) REVERT: C 189 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7358 (mt-10) REVERT: C 204 LYS cc_start: 0.7935 (tptp) cc_final: 0.7398 (tptp) REVERT: C 326 ILE cc_start: 0.8120 (mp) cc_final: 0.7541 (tt) REVERT: C 537 LYS cc_start: 0.8278 (tttt) cc_final: 0.8067 (tttt) REVERT: C 551 VAL cc_start: 0.8122 (t) cc_final: 0.7909 (t) REVERT: C 644 GLN cc_start: 0.7938 (tp40) cc_final: 0.7504 (tp40) REVERT: C 707 TYR cc_start: 0.7869 (t80) cc_final: 0.7563 (t80) REVERT: C 740 MET cc_start: 0.7330 (mmm) cc_final: 0.6900 (mmm) REVERT: C 759 PHE cc_start: 0.6054 (m-80) cc_final: 0.5825 (m-10) REVERT: C 765 ARG cc_start: 0.7097 (ttp-110) cc_final: 0.6737 (ttp-110) REVERT: C 780 GLU cc_start: 0.7125 (pt0) cc_final: 0.6714 (pt0) REVERT: C 790 LYS cc_start: 0.7916 (mtmm) cc_final: 0.7632 (mtmm) REVERT: C 819 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6753 (mt-10) REVERT: C 901 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: C 902 MET cc_start: 0.7779 (tpp) cc_final: 0.7523 (tpp) REVERT: C 914 ASN cc_start: 0.7592 (p0) cc_final: 0.7309 (p0) REVERT: C 945 LEU cc_start: 0.7784 (mm) cc_final: 0.7572 (mt) REVERT: C 973 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6683 (pp) REVERT: C 993 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7654 (mm) REVERT: C 994 ASP cc_start: 0.7156 (m-30) cc_final: 0.6716 (p0) REVERT: C 998 THR cc_start: 0.7893 (m) cc_final: 0.7542 (p) REVERT: C 1017 GLU cc_start: 0.6894 (tm-30) cc_final: 0.6691 (tm-30) REVERT: C 1019 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7285 (tpp-160) REVERT: C 1028 LYS cc_start: 0.8278 (ttmm) cc_final: 0.7914 (ttmt) REVERT: C 1129 VAL cc_start: 0.8117 (OUTLIER) cc_final: 0.7880 (p) REVERT: C 1136 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8076 (p) REVERT: D 155 VAL cc_start: 0.5948 (OUTLIER) cc_final: 0.5614 (t) REVERT: E 67 LYS cc_start: 0.0434 (OUTLIER) cc_final: 0.0179 (tmmm) REVERT: F 144 LEU cc_start: 0.5153 (OUTLIER) cc_final: 0.4788 (tm) REVERT: F 148 CYS cc_start: 0.4210 (OUTLIER) cc_final: 0.3926 (m) REVERT: G 158 MET cc_start: 0.5376 (mmm) cc_final: 0.4959 (mmm) REVERT: H 49 MET cc_start: 0.6156 (mmm) cc_final: 0.5766 (mmm) REVERT: I 67 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6655 (tmmm) outliers start: 226 outliers final: 145 residues processed: 785 average time/residue: 0.4557 time to fit residues: 579.3316 Evaluate side-chains 746 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 585 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1048 HIS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 274 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 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 16 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 379 optimal weight: 6.9990 chunk 304 optimal weight: 2.9990 chunk 326 optimal weight: 30.0000 chunk 423 optimal weight: 0.6980 chunk 426 optimal weight: 20.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 580 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 690 GLN C 913 GLN C 955 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 GLN H 209 ASN I 127 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.219121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.169199 restraints weight = 62782.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.163518 restraints weight = 41464.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.165188 restraints weight = 41330.427| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 35770 Z= 0.201 Angle : 0.626 10.262 48736 Z= 0.317 Chirality : 0.046 0.281 5467 Planarity : 0.005 0.056 6292 Dihedral : 7.125 81.561 5464 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.47 % Favored : 90.50 % Rotamer: Outliers : 5.80 % Allowed : 15.45 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.05 (0.12), residues: 4433 helix: 0.52 (0.21), residues: 667 sheet: -1.58 (0.17), residues: 855 loop : -3.00 (0.10), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 64 HIS 0.021 0.001 HIS A 205 PHE 0.028 0.002 PHE B 981 TYR 0.026 0.001 TYR C 91 ARG 0.009 0.001 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 18) link_NAG-ASN : angle 2.46368 ( 54) hydrogen bonds : bond 0.03886 ( 899) hydrogen bonds : angle 4.77873 ( 2379) SS BOND : bond 0.00487 ( 51) SS BOND : angle 2.06395 ( 102) covalent geometry : bond 0.00440 (35701) covalent geometry : angle 0.61486 (48580) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 601 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6395 (OUTLIER) cc_final: 0.6094 (p0) REVERT: A 52 GLN cc_start: 0.8144 (tp40) cc_final: 0.7614 (tp-100) REVERT: A 64 TRP cc_start: 0.6423 (t60) cc_final: 0.6172 (t60) REVERT: A 130 VAL cc_start: 0.6539 (OUTLIER) cc_final: 0.6295 (t) REVERT: A 565 PHE cc_start: 0.6549 (m-10) cc_final: 0.6315 (m-10) REVERT: A 644 GLN cc_start: 0.7822 (tp40) cc_final: 0.7600 (tp-100) REVERT: A 655 TYR cc_start: 0.7481 (t80) cc_final: 0.7210 (t80) REVERT: A 675 GLN cc_start: 0.6551 (pp30) cc_final: 0.6260 (tm-30) REVERT: A 720 ILE cc_start: 0.8835 (mp) cc_final: 0.8602 (mm) REVERT: A 736 VAL cc_start: 0.8778 (p) cc_final: 0.8568 (t) REVERT: A 776 LYS cc_start: 0.8386 (tmmt) cc_final: 0.7963 (tttp) REVERT: A 777 ASN cc_start: 0.8328 (m-40) cc_final: 0.7683 (m-40) REVERT: A 813 SER cc_start: 0.8373 (m) cc_final: 0.8036 (p) REVERT: A 825 LYS cc_start: 0.7826 (mmmm) cc_final: 0.7487 (ttmt) REVERT: A 869 MET cc_start: 0.8660 (mtp) cc_final: 0.8375 (mtp) REVERT: A 913 GLN cc_start: 0.7921 (pt0) cc_final: 0.7696 (pt0) REVERT: A 922 LEU cc_start: 0.8346 (tp) cc_final: 0.8111 (tt) REVERT: A 925 ASN cc_start: 0.7942 (m-40) cc_final: 0.7584 (m-40) REVERT: A 933 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7808 (mtmm) REVERT: A 965 GLN cc_start: 0.7642 (tt0) cc_final: 0.7376 (tt0) REVERT: A 976 VAL cc_start: 0.8407 (t) cc_final: 0.7959 (p) REVERT: A 1072 GLU cc_start: 0.8138 (pm20) cc_final: 0.7735 (pm20) REVERT: A 1073 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8102 (mtpp) REVERT: A 1091 ARG cc_start: 0.7710 (ttm170) cc_final: 0.7400 (ttm-80) REVERT: B 40 ASP cc_start: 0.8047 (p0) cc_final: 0.7807 (p0) REVERT: B 46 SER cc_start: 0.8447 (m) cc_final: 0.7957 (p) REVERT: B 52 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7453 (tm-30) REVERT: B 62 VAL cc_start: 0.8145 (m) cc_final: 0.7898 (p) REVERT: B 65 PHE cc_start: 0.7523 (m-80) cc_final: 0.6877 (m-10) REVERT: B 170 TYR cc_start: 0.7002 (t80) cc_final: 0.6631 (t80) REVERT: B 200 LYS cc_start: 0.8152 (mttt) cc_final: 0.7632 (mttm) REVERT: B 228 ASP cc_start: 0.6682 (t70) cc_final: 0.6149 (t70) REVERT: B 276 LEU cc_start: 0.8572 (tp) cc_final: 0.8022 (tt) REVERT: B 278 LYS cc_start: 0.8294 (ttmp) cc_final: 0.7955 (tttm) REVERT: B 281 GLU cc_start: 0.7486 (pp20) cc_final: 0.7189 (pp20) REVERT: B 306 PHE cc_start: 0.7972 (m-10) cc_final: 0.7562 (m-10) REVERT: B 465 GLU cc_start: 0.6820 (pt0) cc_final: 0.6417 (pt0) REVERT: B 542 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7431 (t0) REVERT: B 563 GLN cc_start: 0.7464 (mt0) cc_final: 0.6978 (mt0) REVERT: B 569 ILE cc_start: 0.8038 (pt) cc_final: 0.7775 (mp) REVERT: B 577 ARG cc_start: 0.8376 (ttp-110) cc_final: 0.8143 (ttp-110) REVERT: B 765 ARG cc_start: 0.7120 (ttp-170) cc_final: 0.6742 (ttp-170) REVERT: B 774 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6876 (mm-40) REVERT: B 790 LYS cc_start: 0.8001 (mppt) cc_final: 0.7737 (mtmm) REVERT: B 808 ASP cc_start: 0.7827 (t0) cc_final: 0.7138 (p0) REVERT: B 819 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7144 (mt-10) REVERT: B 822 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8577 (mt) REVERT: B 856 LYS cc_start: 0.8378 (tptt) cc_final: 0.8177 (tptt) REVERT: B 895 GLN cc_start: 0.7504 (pt0) cc_final: 0.7036 (pt0) REVERT: B 921 LYS cc_start: 0.7920 (mmmt) cc_final: 0.7686 (mppt) REVERT: B 933 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7225 (mtpp) REVERT: B 957 GLN cc_start: 0.6718 (tm130) cc_final: 0.6101 (tm130) REVERT: B 964 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7832 (ttmm) REVERT: B 974 SER cc_start: 0.6879 (p) cc_final: 0.6437 (m) REVERT: B 977 LEU cc_start: 0.7851 (mp) cc_final: 0.7604 (mm) REVERT: B 990 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: B 1006 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8184 (t) REVERT: B 1018 ILE cc_start: 0.8262 (mt) cc_final: 0.7975 (mm) REVERT: B 1081 ILE cc_start: 0.8421 (pt) cc_final: 0.8195 (pt) REVERT: C 106 PHE cc_start: 0.6637 (m-80) cc_final: 0.6403 (m-80) REVERT: C 129 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7710 (ttmt) REVERT: C 177 MET cc_start: -0.0407 (tmt) cc_final: -0.0760 (tmt) REVERT: C 201 ILE cc_start: 0.8424 (mp) cc_final: 0.7975 (tt) REVERT: C 203 SER cc_start: 0.8333 (t) cc_final: 0.7907 (m) REVERT: C 279 TYR cc_start: 0.8429 (m-80) cc_final: 0.8179 (m-10) REVERT: C 326 ILE cc_start: 0.8171 (mp) cc_final: 0.7586 (tt) REVERT: C 537 LYS cc_start: 0.8455 (tttt) cc_final: 0.8122 (tttp) REVERT: C 602 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7659 (p) REVERT: C 657 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.7833 (t0) REVERT: C 734 THR cc_start: 0.8485 (p) cc_final: 0.8197 (m) REVERT: C 740 MET cc_start: 0.7739 (mmm) cc_final: 0.7367 (mmm) REVERT: C 765 ARG cc_start: 0.7520 (ttp-110) cc_final: 0.7210 (ttm110) REVERT: C 780 GLU cc_start: 0.7349 (pt0) cc_final: 0.7004 (pt0) REVERT: C 790 LYS cc_start: 0.8067 (mtmm) cc_final: 0.7772 (mtmm) REVERT: C 819 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6934 (mt-10) REVERT: C 901 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: C 902 MET cc_start: 0.8138 (tpp) cc_final: 0.7846 (tpt) REVERT: C 914 ASN cc_start: 0.7762 (p0) cc_final: 0.7446 (p0) REVERT: C 945 LEU cc_start: 0.8052 (mm) cc_final: 0.7789 (mt) REVERT: C 953 ASN cc_start: 0.8098 (m-40) cc_final: 0.7896 (m-40) REVERT: C 957 GLN cc_start: 0.7484 (pt0) cc_final: 0.7263 (tm-30) REVERT: C 973 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7245 (pp) REVERT: C 993 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7777 (mm) REVERT: C 994 ASP cc_start: 0.7409 (m-30) cc_final: 0.6853 (p0) REVERT: C 998 THR cc_start: 0.8088 (m) cc_final: 0.7761 (p) REVERT: C 1017 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6565 (tm-30) REVERT: C 1031 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7338 (tp30) REVERT: C 1107 ARG cc_start: 0.7431 (tpp80) cc_final: 0.7141 (ttm-80) REVERT: C 1129 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7927 (p) REVERT: C 1136 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8187 (p) REVERT: D 155 VAL cc_start: 0.5936 (OUTLIER) cc_final: 0.5595 (t) REVERT: E 67 LYS cc_start: 0.0638 (OUTLIER) cc_final: 0.0349 (tmmm) REVERT: F 148 CYS cc_start: 0.5018 (OUTLIER) cc_final: 0.4783 (m) REVERT: F 226 ILE cc_start: -0.3570 (OUTLIER) cc_final: -0.4170 (pt) REVERT: G 158 MET cc_start: 0.5376 (mmm) cc_final: 0.4967 (mmm) REVERT: G 207 MET cc_start: 0.3417 (mpp) cc_final: 0.0908 (ptp) REVERT: H 49 MET cc_start: 0.5900 (mmm) cc_final: 0.5438 (mmm) REVERT: H 234 MET cc_start: 0.4340 (tmm) cc_final: 0.3971 (tmm) REVERT: I 67 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6846 (tmmm) outliers start: 221 outliers final: 156 residues processed: 770 average time/residue: 0.5065 time to fit residues: 638.6918 Evaluate side-chains 751 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 577 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 213 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 273 optimal weight: 1.9990 chunk 363 optimal weight: 8.9990 chunk 264 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 344 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 347 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 556 ASN B 920 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 913 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.219800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.170247 restraints weight = 62752.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163889 restraints weight = 51694.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.166439 restraints weight = 38159.823| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 35770 Z= 0.130 Angle : 0.578 10.541 48736 Z= 0.289 Chirality : 0.045 0.285 5467 Planarity : 0.004 0.052 6292 Dihedral : 6.958 82.693 5453 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 5.80 % Allowed : 16.73 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.82 (0.12), residues: 4433 helix: 0.79 (0.21), residues: 667 sheet: -1.46 (0.16), residues: 912 loop : -2.88 (0.10), residues: 2854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 104 HIS 0.013 0.001 HIS B1048 PHE 0.044 0.001 PHE B 981 TYR 0.025 0.001 TYR A 170 ARG 0.008 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 18) link_NAG-ASN : angle 2.26741 ( 54) hydrogen bonds : bond 0.03334 ( 899) hydrogen bonds : angle 4.62364 ( 2379) SS BOND : bond 0.00503 ( 51) SS BOND : angle 1.73440 ( 102) covalent geometry : bond 0.00291 (35701) covalent geometry : angle 0.56874 (48580) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 572 time to evaluate : 3.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6406 (OUTLIER) cc_final: 0.6154 (p0) REVERT: A 52 GLN cc_start: 0.8013 (tp40) cc_final: 0.7455 (tp-100) REVERT: A 64 TRP cc_start: 0.6338 (t60) cc_final: 0.6091 (t60) REVERT: A 130 VAL cc_start: 0.6299 (OUTLIER) cc_final: 0.5956 (t) REVERT: A 224 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: A 537 LYS cc_start: 0.7376 (tmtt) cc_final: 0.6591 (tmtt) REVERT: A 644 GLN cc_start: 0.7724 (tp40) cc_final: 0.7483 (tp-100) REVERT: A 655 TYR cc_start: 0.7626 (t80) cc_final: 0.7338 (t80) REVERT: A 675 GLN cc_start: 0.6649 (pp30) cc_final: 0.6261 (tm-30) REVERT: A 720 ILE cc_start: 0.8860 (mp) cc_final: 0.8647 (mm) REVERT: A 776 LYS cc_start: 0.8357 (tmmt) cc_final: 0.8020 (tttm) REVERT: A 777 ASN cc_start: 0.8233 (m-40) cc_final: 0.7615 (m-40) REVERT: A 869 MET cc_start: 0.8603 (mtp) cc_final: 0.8402 (mtp) REVERT: A 895 GLN cc_start: 0.7747 (pt0) cc_final: 0.7260 (pt0) REVERT: A 921 LYS cc_start: 0.7781 (mmmt) cc_final: 0.7398 (mtmm) REVERT: A 922 LEU cc_start: 0.8350 (tp) cc_final: 0.8103 (tt) REVERT: A 925 ASN cc_start: 0.7951 (m-40) cc_final: 0.7648 (m-40) REVERT: A 933 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7769 (mtmm) REVERT: A 957 GLN cc_start: 0.7709 (tt0) cc_final: 0.7484 (tt0) REVERT: A 964 LYS cc_start: 0.8482 (ttmm) cc_final: 0.8259 (ttmm) REVERT: A 976 VAL cc_start: 0.8294 (t) cc_final: 0.7822 (p) REVERT: A 1072 GLU cc_start: 0.8141 (pm20) cc_final: 0.7711 (pm20) REVERT: A 1091 ARG cc_start: 0.7628 (ttm170) cc_final: 0.7302 (ttm-80) REVERT: A 1107 ARG cc_start: 0.7483 (mtt90) cc_final: 0.7237 (mtt90) REVERT: B 40 ASP cc_start: 0.8062 (p0) cc_final: 0.7848 (p0) REVERT: B 46 SER cc_start: 0.8395 (m) cc_final: 0.7910 (p) REVERT: B 52 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7517 (tm-30) REVERT: B 56 LEU cc_start: 0.8775 (tp) cc_final: 0.8489 (tt) REVERT: B 65 PHE cc_start: 0.7400 (m-80) cc_final: 0.6823 (m-10) REVERT: B 85 PRO cc_start: 0.7637 (Cg_exo) cc_final: 0.7422 (Cg_endo) REVERT: B 120 VAL cc_start: 0.8264 (m) cc_final: 0.7966 (p) REVERT: B 169 GLU cc_start: 0.6290 (pm20) cc_final: 0.6023 (pm20) REVERT: B 170 TYR cc_start: 0.6966 (t80) cc_final: 0.6656 (t80) REVERT: B 200 LYS cc_start: 0.8142 (mttt) cc_final: 0.7635 (mttm) REVERT: B 228 ASP cc_start: 0.6537 (t70) cc_final: 0.6096 (t70) REVERT: B 276 LEU cc_start: 0.8544 (tp) cc_final: 0.7989 (tt) REVERT: B 278 LYS cc_start: 0.8237 (ttmp) cc_final: 0.7940 (tttm) REVERT: B 281 GLU cc_start: 0.7513 (pp20) cc_final: 0.7176 (pp20) REVERT: B 306 PHE cc_start: 0.7985 (m-10) cc_final: 0.7543 (m-10) REVERT: B 308 VAL cc_start: 0.8983 (t) cc_final: 0.8736 (p) REVERT: B 406 GLU cc_start: 0.4878 (tm-30) cc_final: 0.4164 (tp30) REVERT: B 465 GLU cc_start: 0.6836 (pt0) cc_final: 0.6354 (pt0) REVERT: B 542 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7466 (t0) REVERT: B 563 GLN cc_start: 0.7395 (mt0) cc_final: 0.7048 (mt0) REVERT: B 569 ILE cc_start: 0.7972 (pt) cc_final: 0.7734 (mp) REVERT: B 656 VAL cc_start: 0.8605 (m) cc_final: 0.8391 (p) REVERT: B 698 SER cc_start: 0.8276 (t) cc_final: 0.7481 (p) REVERT: B 765 ARG cc_start: 0.6979 (ttp-170) cc_final: 0.6758 (ttp-170) REVERT: B 774 GLN cc_start: 0.7410 (mm-40) cc_final: 0.6870 (mm-40) REVERT: B 790 LYS cc_start: 0.8319 (mppt) cc_final: 0.7867 (mtmm) REVERT: B 819 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7110 (mt-10) REVERT: B 822 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8617 (mt) REVERT: B 895 GLN cc_start: 0.7514 (pt0) cc_final: 0.7132 (pt0) REVERT: B 921 LYS cc_start: 0.7890 (mmmt) cc_final: 0.7644 (mppt) REVERT: B 957 GLN cc_start: 0.6679 (tm130) cc_final: 0.6039 (tm130) REVERT: B 964 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7863 (ttmm) REVERT: B 974 SER cc_start: 0.7054 (p) cc_final: 0.6679 (m) REVERT: B 990 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: B 1018 ILE cc_start: 0.8089 (mt) cc_final: 0.7880 (mm) REVERT: B 1081 ILE cc_start: 0.8397 (pt) cc_final: 0.8170 (pt) REVERT: C 91 TYR cc_start: 0.7665 (t80) cc_final: 0.7414 (t80) REVERT: C 129 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7709 (tptt) REVERT: C 168 PHE cc_start: 0.4805 (t80) cc_final: 0.4193 (t80) REVERT: C 190 PHE cc_start: 0.6643 (m-80) cc_final: 0.6333 (m-80) REVERT: C 203 SER cc_start: 0.8335 (t) cc_final: 0.7865 (m) REVERT: C 279 TYR cc_start: 0.8451 (m-80) cc_final: 0.8187 (m-10) REVERT: C 326 ILE cc_start: 0.8118 (mp) cc_final: 0.7583 (tt) REVERT: C 328 ARG cc_start: 0.7202 (mtp85) cc_final: 0.6894 (mtp85) REVERT: C 537 LYS cc_start: 0.8462 (tttt) cc_final: 0.8018 (tttp) REVERT: C 602 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7570 (p) REVERT: C 734 THR cc_start: 0.8525 (p) cc_final: 0.8226 (m) REVERT: C 740 MET cc_start: 0.7719 (mmm) cc_final: 0.7374 (mmm) REVERT: C 780 GLU cc_start: 0.7407 (pt0) cc_final: 0.6962 (pt0) REVERT: C 790 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7755 (mtmm) REVERT: C 819 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6845 (mt-10) REVERT: C 823 PHE cc_start: 0.7216 (m-80) cc_final: 0.6989 (t80) REVERT: C 901 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: C 902 MET cc_start: 0.7927 (tpp) cc_final: 0.7611 (tpp) REVERT: C 914 ASN cc_start: 0.7754 (p0) cc_final: 0.7523 (p0) REVERT: C 945 LEU cc_start: 0.7977 (mm) cc_final: 0.7714 (mt) REVERT: C 973 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7290 (pp) REVERT: C 993 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7708 (mm) REVERT: C 994 ASP cc_start: 0.7358 (m-30) cc_final: 0.6856 (p0) REVERT: C 998 THR cc_start: 0.8025 (m) cc_final: 0.7707 (p) REVERT: C 1019 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7289 (tpt170) REVERT: C 1031 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7271 (mm-30) REVERT: C 1038 LYS cc_start: 0.7759 (mmtm) cc_final: 0.7313 (mmmm) REVERT: C 1107 ARG cc_start: 0.7448 (tpp80) cc_final: 0.7248 (mtp85) REVERT: C 1129 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7922 (p) REVERT: C 1136 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8254 (p) REVERT: D 155 VAL cc_start: 0.5969 (OUTLIER) cc_final: 0.5620 (t) REVERT: D 176 VAL cc_start: 0.5997 (OUTLIER) cc_final: 0.5769 (t) REVERT: F 226 ILE cc_start: -0.3604 (OUTLIER) cc_final: -0.4235 (pt) REVERT: G 158 MET cc_start: 0.5275 (mmm) cc_final: 0.4859 (mmm) REVERT: G 207 MET cc_start: 0.3134 (mpp) cc_final: 0.0982 (ptp) REVERT: H 49 MET cc_start: 0.5983 (mmm) cc_final: 0.5591 (mmm) REVERT: H 160 MET cc_start: 0.2847 (mmt) cc_final: -0.0542 (mtp) REVERT: I 67 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6880 (tmmm) outliers start: 221 outliers final: 161 residues processed: 744 average time/residue: 0.4565 time to fit residues: 551.4178 Evaluate side-chains 734 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 556 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1048 HIS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 616 ASN 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 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 221 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 144 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 303 optimal weight: 0.9990 chunk 329 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 419 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 286 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 396 optimal weight: 0.0670 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN B 239 GLN B 703 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.218717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.169141 restraints weight = 62679.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.164730 restraints weight = 40334.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.166473 restraints weight = 34038.030| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35770 Z= 0.125 Angle : 0.585 17.324 48736 Z= 0.289 Chirality : 0.044 0.268 5467 Planarity : 0.004 0.052 6292 Dihedral : 6.916 82.531 5447 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 5.43 % Allowed : 17.34 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.05 % 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: -2.66 (0.12), residues: 4433 helix: 0.96 (0.21), residues: 663 sheet: -1.34 (0.16), residues: 922 loop : -2.78 (0.10), residues: 2848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 64 HIS 0.013 0.001 HIS B1048 PHE 0.041 0.001 PHE B 981 TYR 0.020 0.001 TYR A 170 ARG 0.015 0.000 ARG B 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 18) link_NAG-ASN : angle 2.19874 ( 54) hydrogen bonds : bond 0.03296 ( 899) hydrogen bonds : angle 4.57297 ( 2379) SS BOND : bond 0.00367 ( 51) SS BOND : angle 1.39192 ( 102) covalent geometry : bond 0.00280 (35701) covalent geometry : angle 0.57743 (48580) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 564 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6309 (OUTLIER) cc_final: 0.6034 (p0) REVERT: A 130 VAL cc_start: 0.6442 (OUTLIER) cc_final: 0.6099 (t) REVERT: A 224 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: A 537 LYS cc_start: 0.7481 (tmtt) cc_final: 0.6672 (tmtt) REVERT: A 644 GLN cc_start: 0.7837 (tp40) cc_final: 0.7599 (tp-100) REVERT: A 655 TYR cc_start: 0.7703 (t80) cc_final: 0.7368 (t80) REVERT: A 675 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6122 (tm-30) REVERT: A 720 ILE cc_start: 0.8799 (mp) cc_final: 0.8584 (mm) REVERT: A 776 LYS cc_start: 0.8362 (tmmt) cc_final: 0.8050 (tttm) REVERT: A 777 ASN cc_start: 0.8203 (m-40) cc_final: 0.7585 (m-40) REVERT: A 778 THR cc_start: 0.8312 (m) cc_final: 0.7597 (p) REVERT: A 813 SER cc_start: 0.8117 (m) cc_final: 0.7778 (p) REVERT: A 869 MET cc_start: 0.8620 (mtp) cc_final: 0.8411 (mtp) REVERT: A 895 GLN cc_start: 0.7807 (pt0) cc_final: 0.7338 (pt0) REVERT: A 921 LYS cc_start: 0.7754 (mmmt) cc_final: 0.7454 (mtmm) REVERT: A 922 LEU cc_start: 0.8315 (tp) cc_final: 0.8086 (tt) REVERT: A 925 ASN cc_start: 0.7937 (m-40) cc_final: 0.7675 (m-40) REVERT: A 933 LYS cc_start: 0.8022 (mtmm) cc_final: 0.7728 (mtmm) REVERT: A 936 ASP cc_start: 0.7198 (m-30) cc_final: 0.6989 (m-30) REVERT: A 976 VAL cc_start: 0.8424 (t) cc_final: 0.8022 (p) REVERT: A 1031 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7203 (mt-10) REVERT: A 1072 GLU cc_start: 0.8068 (pm20) cc_final: 0.7646 (pm20) REVERT: A 1091 ARG cc_start: 0.7572 (ttm170) cc_final: 0.7249 (ttm-80) REVERT: A 1103 PHE cc_start: 0.8133 (m-80) cc_final: 0.7867 (m-10) REVERT: B 40 ASP cc_start: 0.8030 (p0) cc_final: 0.7824 (p0) REVERT: B 46 SER cc_start: 0.8395 (m) cc_final: 0.7893 (p) REVERT: B 52 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7213 (tm-30) REVERT: B 56 LEU cc_start: 0.8733 (tp) cc_final: 0.8524 (tt) REVERT: B 65 PHE cc_start: 0.7384 (m-80) cc_final: 0.6791 (m-10) REVERT: B 85 PRO cc_start: 0.7604 (Cg_exo) cc_final: 0.7399 (Cg_endo) REVERT: B 120 VAL cc_start: 0.8259 (m) cc_final: 0.7931 (p) REVERT: B 169 GLU cc_start: 0.6291 (pm20) cc_final: 0.5928 (pm20) REVERT: B 170 TYR cc_start: 0.6975 (t80) cc_final: 0.6660 (t80) REVERT: B 200 LYS cc_start: 0.8227 (mttt) cc_final: 0.7680 (mttm) REVERT: B 228 ASP cc_start: 0.6537 (t70) cc_final: 0.6195 (t70) REVERT: B 276 LEU cc_start: 0.8565 (tp) cc_final: 0.8310 (tp) REVERT: B 278 LYS cc_start: 0.8241 (ttmp) cc_final: 0.7951 (tttm) REVERT: B 281 GLU cc_start: 0.7516 (pp20) cc_final: 0.7190 (pp20) REVERT: B 297 SER cc_start: 0.8200 (m) cc_final: 0.7855 (p) REVERT: B 308 VAL cc_start: 0.8943 (t) cc_final: 0.8714 (p) REVERT: B 465 GLU cc_start: 0.6887 (pt0) cc_final: 0.6545 (pt0) REVERT: B 542 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7408 (t0) REVERT: B 569 ILE cc_start: 0.7976 (pt) cc_final: 0.7722 (mp) REVERT: B 574 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7164 (p0) REVERT: B 774 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6880 (mm-40) REVERT: B 790 LYS cc_start: 0.8346 (mppt) cc_final: 0.8007 (mtmm) REVERT: B 819 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6851 (mt-10) REVERT: B 822 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8620 (mt) REVERT: B 895 GLN cc_start: 0.7488 (pt0) cc_final: 0.7117 (pt0) REVERT: B 921 LYS cc_start: 0.7921 (mmmt) cc_final: 0.7659 (mppt) REVERT: B 957 GLN cc_start: 0.6546 (tm130) cc_final: 0.5997 (tm130) REVERT: B 964 LYS cc_start: 0.8139 (ttpp) cc_final: 0.7829 (ttmm) REVERT: B 974 SER cc_start: 0.7044 (p) cc_final: 0.6701 (m) REVERT: B 990 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: B 1018 ILE cc_start: 0.8156 (mt) cc_final: 0.7921 (mm) REVERT: B 1121 PHE cc_start: 0.8124 (p90) cc_final: 0.7842 (p90) REVERT: C 91 TYR cc_start: 0.7692 (t80) cc_final: 0.7391 (t80) REVERT: C 129 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7775 (tptt) REVERT: C 168 PHE cc_start: 0.4874 (t80) cc_final: 0.4331 (t80) REVERT: C 177 MET cc_start: -0.0327 (tmt) cc_final: -0.0636 (tmt) REVERT: C 201 ILE cc_start: 0.8366 (mp) cc_final: 0.8015 (tt) REVERT: C 203 SER cc_start: 0.8396 (t) cc_final: 0.7984 (m) REVERT: C 279 TYR cc_start: 0.8426 (m-80) cc_final: 0.8199 (m-10) REVERT: C 281 GLU cc_start: 0.8094 (pm20) cc_final: 0.7844 (pm20) REVERT: C 319 ARG cc_start: 0.7341 (ptp90) cc_final: 0.7051 (ptp90) REVERT: C 326 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7636 (tt) REVERT: C 328 ARG cc_start: 0.7146 (mtp85) cc_final: 0.6901 (mtp85) REVERT: C 537 LYS cc_start: 0.8400 (tttt) cc_final: 0.7967 (tttp) REVERT: C 542 ASN cc_start: 0.7555 (t0) cc_final: 0.7259 (t0) REVERT: C 557 LYS cc_start: 0.8624 (mtpp) cc_final: 0.8239 (mtpp) REVERT: C 734 THR cc_start: 0.8364 (p) cc_final: 0.8082 (m) REVERT: C 764 LYS cc_start: 0.7578 (tttm) cc_final: 0.7241 (tmmt) REVERT: C 765 ARG cc_start: 0.7552 (ttm110) cc_final: 0.7309 (ttm110) REVERT: C 780 GLU cc_start: 0.7346 (pt0) cc_final: 0.6927 (pt0) REVERT: C 790 LYS cc_start: 0.7924 (mtmm) cc_final: 0.7629 (mtmm) REVERT: C 819 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6794 (mt-10) REVERT: C 823 PHE cc_start: 0.7219 (m-80) cc_final: 0.6979 (t80) REVERT: C 901 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: C 902 MET cc_start: 0.8091 (tpp) cc_final: 0.7760 (tpp) REVERT: C 914 ASN cc_start: 0.7749 (p0) cc_final: 0.7465 (p0) REVERT: C 973 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7333 (pp) REVERT: C 994 ASP cc_start: 0.7404 (m-30) cc_final: 0.7035 (p0) REVERT: C 998 THR cc_start: 0.8026 (m) cc_final: 0.7703 (p) REVERT: C 1019 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7336 (tpp-160) REVERT: C 1031 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7192 (mm-30) REVERT: C 1038 LYS cc_start: 0.7596 (mmtm) cc_final: 0.7205 (mmmm) REVERT: C 1129 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7833 (p) REVERT: C 1136 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8170 (p) REVERT: D 155 VAL cc_start: 0.6051 (OUTLIER) cc_final: 0.5705 (t) REVERT: D 176 VAL cc_start: 0.6075 (OUTLIER) cc_final: 0.5862 (t) REVERT: F 226 ILE cc_start: -0.3685 (OUTLIER) cc_final: -0.4370 (pt) REVERT: G 158 MET cc_start: 0.5121 (mmm) cc_final: 0.4790 (mmm) REVERT: H 49 MET cc_start: 0.6065 (mmm) cc_final: 0.5667 (mmm) REVERT: H 160 MET cc_start: 0.2975 (mmt) cc_final: -0.0722 (mtp) REVERT: H 234 MET cc_start: 0.4288 (tmm) cc_final: 0.3893 (tmm) REVERT: I 67 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6869 (tmmm) outliers start: 207 outliers final: 165 residues processed: 724 average time/residue: 0.4686 time to fit residues: 552.6062 Evaluate side-chains 736 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 553 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1048 HIS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 221 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 246 optimal weight: 9.9990 chunk 389 optimal weight: 10.0000 chunk 320 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 308 optimal weight: 40.0000 chunk 104 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 336 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 81 ASN B 87 ASN B 271 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 901 GLN C 913 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** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.213233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.163016 restraints weight = 62186.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158205 restraints weight = 44919.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159992 restraints weight = 44244.761| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 35770 Z= 0.320 Angle : 0.735 17.377 48736 Z= 0.374 Chirality : 0.050 0.311 5467 Planarity : 0.005 0.051 6292 Dihedral : 7.468 82.349 5441 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 6.11 % Allowed : 17.13 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.88 (0.12), residues: 4433 helix: 0.45 (0.20), residues: 673 sheet: -1.54 (0.16), residues: 936 loop : -2.83 (0.10), residues: 2824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.003 TRP A 64 HIS 0.013 0.002 HIS B1048 PHE 0.046 0.002 PHE B 981 TYR 0.034 0.002 TYR B 904 ARG 0.017 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 18) link_NAG-ASN : angle 2.67584 ( 54) hydrogen bonds : bond 0.04742 ( 899) hydrogen bonds : angle 5.13648 ( 2379) SS BOND : bond 0.00493 ( 51) SS BOND : angle 1.91699 ( 102) covalent geometry : bond 0.00695 (35701) covalent geometry : angle 0.72508 (48580) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 604 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6733 (OUTLIER) cc_final: 0.6368 (p0) REVERT: A 64 TRP cc_start: 0.6295 (t60) cc_final: 0.6022 (t60) REVERT: A 533 LEU cc_start: 0.8449 (tp) cc_final: 0.8229 (tp) REVERT: A 537 LYS cc_start: 0.7710 (tmtt) cc_final: 0.6932 (tmtt) REVERT: A 643 PHE cc_start: 0.6253 (t80) cc_final: 0.5810 (t80) REVERT: A 644 GLN cc_start: 0.7996 (tp40) cc_final: 0.7688 (tp-100) REVERT: A 645 THR cc_start: 0.8096 (p) cc_final: 0.7515 (p) REVERT: A 675 GLN cc_start: 0.6616 (pp30) cc_final: 0.6250 (tm-30) REVERT: A 702 GLU cc_start: 0.7285 (mp0) cc_final: 0.7036 (mp0) REVERT: A 761 THR cc_start: 0.8241 (p) cc_final: 0.7979 (t) REVERT: A 776 LYS cc_start: 0.8389 (tmmt) cc_final: 0.8079 (tttm) REVERT: A 777 ASN cc_start: 0.8390 (m-40) cc_final: 0.7782 (m-40) REVERT: A 803 SER cc_start: 0.8308 (m) cc_final: 0.8018 (p) REVERT: A 869 MET cc_start: 0.8715 (mtp) cc_final: 0.8463 (mtp) REVERT: A 922 LEU cc_start: 0.8380 (tp) cc_final: 0.8132 (tt) REVERT: A 925 ASN cc_start: 0.8112 (m-40) cc_final: 0.7767 (m-40) REVERT: A 933 LYS cc_start: 0.8086 (mtmm) cc_final: 0.7829 (mtmm) REVERT: A 945 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8077 (mp) REVERT: A 957 GLN cc_start: 0.7587 (tt0) cc_final: 0.7315 (tt0) REVERT: A 968 SER cc_start: 0.8350 (p) cc_final: 0.7430 (p) REVERT: A 969 LYS cc_start: 0.8047 (mtmm) cc_final: 0.7616 (mtmm) REVERT: A 970 PHE cc_start: 0.7600 (m-10) cc_final: 0.7093 (m-10) REVERT: A 976 VAL cc_start: 0.8497 (t) cc_final: 0.8066 (p) REVERT: A 1031 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7349 (mt-10) REVERT: A 1040 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7880 (m) REVERT: A 1068 VAL cc_start: 0.7971 (t) cc_final: 0.7761 (m) REVERT: A 1072 GLU cc_start: 0.8152 (pm20) cc_final: 0.7772 (pm20) REVERT: A 1073 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8053 (mtpp) REVERT: A 1091 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7483 (ttm-80) REVERT: B 43 PHE cc_start: 0.8258 (t80) cc_final: 0.8015 (t80) REVERT: B 44 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7922 (mtt180) REVERT: B 46 SER cc_start: 0.8453 (m) cc_final: 0.8024 (p) REVERT: B 52 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7393 (tm-30) REVERT: B 56 LEU cc_start: 0.8783 (tp) cc_final: 0.8522 (tt) REVERT: B 65 PHE cc_start: 0.7645 (m-80) cc_final: 0.7071 (m-10) REVERT: B 81 ASN cc_start: 0.7368 (OUTLIER) cc_final: 0.7073 (p0) REVERT: B 169 GLU cc_start: 0.6690 (pm20) cc_final: 0.6348 (pm20) REVERT: B 170 TYR cc_start: 0.7189 (t80) cc_final: 0.6773 (t80) REVERT: B 200 LYS cc_start: 0.8233 (mttt) cc_final: 0.7715 (mttm) REVERT: B 228 ASP cc_start: 0.6676 (t70) cc_final: 0.6405 (t70) REVERT: B 278 LYS cc_start: 0.8351 (ttmp) cc_final: 0.8014 (tttm) REVERT: B 281 GLU cc_start: 0.7622 (pp20) cc_final: 0.7345 (pp20) REVERT: B 308 VAL cc_start: 0.9023 (t) cc_final: 0.8618 (m) REVERT: B 335 LEU cc_start: 0.4656 (OUTLIER) cc_final: 0.4349 (mm) REVERT: B 563 GLN cc_start: 0.7535 (mt0) cc_final: 0.7237 (mt0) REVERT: B 569 ILE cc_start: 0.8301 (pt) cc_final: 0.7972 (mm) REVERT: B 720 ILE cc_start: 0.8330 (pt) cc_final: 0.8007 (mt) REVERT: B 774 GLN cc_start: 0.7337 (mm-40) cc_final: 0.6961 (mm-40) REVERT: B 790 LYS cc_start: 0.8422 (mppt) cc_final: 0.8057 (mtmm) REVERT: B 858 LEU cc_start: 0.8171 (mt) cc_final: 0.7832 (mt) REVERT: B 933 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7239 (mtpp) REVERT: B 957 GLN cc_start: 0.6852 (tm130) cc_final: 0.6439 (tm130) REVERT: B 964 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7906 (ttmm) REVERT: B 970 PHE cc_start: 0.8130 (m-80) cc_final: 0.7833 (m-10) REVERT: B 974 SER cc_start: 0.7555 (p) cc_final: 0.7289 (m) REVERT: B 990 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: B 1006 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8209 (t) REVERT: B 1018 ILE cc_start: 0.8145 (mt) cc_final: 0.7911 (mm) REVERT: B 1084 ASP cc_start: 0.7272 (p0) cc_final: 0.7046 (p0) REVERT: C 81 ASN cc_start: 0.8040 (m-40) cc_final: 0.7808 (m-40) REVERT: C 129 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7778 (tptt) REVERT: C 203 SER cc_start: 0.8196 (t) cc_final: 0.7972 (m) REVERT: C 237 ARG cc_start: 0.7940 (mtp-110) cc_final: 0.7382 (mtm-85) REVERT: C 279 TYR cc_start: 0.8511 (m-80) cc_final: 0.8254 (m-10) REVERT: C 290 ASP cc_start: 0.7047 (t70) cc_final: 0.6844 (t0) REVERT: C 293 LEU cc_start: 0.8599 (tp) cc_final: 0.8255 (tp) REVERT: C 324 GLU cc_start: 0.7512 (pm20) cc_final: 0.7184 (pm20) REVERT: C 326 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7732 (tt) REVERT: C 537 LYS cc_start: 0.8425 (tttt) cc_final: 0.7629 (tttp) REVERT: C 542 ASN cc_start: 0.7731 (t0) cc_final: 0.7402 (t0) REVERT: C 657 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.7823 (t0) REVERT: C 707 TYR cc_start: 0.7963 (t80) cc_final: 0.7601 (t80) REVERT: C 763 LEU cc_start: 0.8512 (mt) cc_final: 0.8245 (mm) REVERT: C 764 LYS cc_start: 0.7992 (tttm) cc_final: 0.7731 (tttm) REVERT: C 780 GLU cc_start: 0.7450 (pt0) cc_final: 0.7175 (pt0) REVERT: C 790 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7676 (mtmm) REVERT: C 819 GLU cc_start: 0.7228 (mt-10) cc_final: 0.7027 (mt-10) REVERT: C 820 ASP cc_start: 0.7696 (t0) cc_final: 0.7447 (t0) REVERT: C 902 MET cc_start: 0.8188 (tpp) cc_final: 0.7894 (tpp) REVERT: C 904 TYR cc_start: 0.7856 (m-10) cc_final: 0.7486 (m-10) REVERT: C 914 ASN cc_start: 0.7859 (p0) cc_final: 0.7562 (p0) REVERT: C 925 ASN cc_start: 0.8419 (m-40) cc_final: 0.8193 (m-40) REVERT: C 973 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7643 (pp) REVERT: C 994 ASP cc_start: 0.7697 (m-30) cc_final: 0.7433 (p0) REVERT: C 996 LEU cc_start: 0.8543 (tt) cc_final: 0.8274 (tp) REVERT: C 1019 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7353 (tpp-160) REVERT: C 1038 LYS cc_start: 0.8011 (mmtm) cc_final: 0.7569 (mmmm) REVERT: C 1129 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.8045 (p) REVERT: C 1137 VAL cc_start: 0.8718 (t) cc_final: 0.8435 (m) REVERT: D 176 VAL cc_start: 0.6078 (OUTLIER) cc_final: 0.5824 (t) REVERT: F 111 LEU cc_start: 0.3045 (OUTLIER) cc_final: 0.2491 (tm) REVERT: F 153 PHE cc_start: -0.0621 (OUTLIER) cc_final: -0.2316 (m-80) REVERT: G 158 MET cc_start: 0.4939 (mmm) cc_final: 0.4611 (mmm) REVERT: G 207 MET cc_start: 0.3897 (mpp) cc_final: 0.1283 (ptp) REVERT: H 49 MET cc_start: 0.5989 (mmm) cc_final: 0.5533 (mmm) REVERT: I 67 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7235 (tmmm) outliers start: 233 outliers final: 173 residues processed: 777 average time/residue: 0.4687 time to fit residues: 590.8291 Evaluate side-chains 775 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 586 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 221 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 146 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 274 optimal weight: 0.0270 chunk 420 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 327 optimal weight: 8.9990 chunk 158 optimal weight: 0.6980 chunk 173 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 895 GLN B 218 GLN B 360 ASN B 913 GLN B 920 GLN B1101 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 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** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.217309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.161440 restraints weight = 61761.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.159766 restraints weight = 42752.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162898 restraints weight = 25277.400| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35770 Z= 0.125 Angle : 0.631 17.618 48736 Z= 0.313 Chirality : 0.045 0.294 5467 Planarity : 0.004 0.056 6292 Dihedral : 6.999 83.321 5428 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 4.85 % Allowed : 18.88 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.61 (0.12), residues: 4433 helix: 0.82 (0.21), residues: 671 sheet: -1.26 (0.16), residues: 938 loop : -2.73 (0.11), residues: 2824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP A 64 HIS 0.013 0.001 HIS B1048 PHE 0.039 0.001 PHE B 981 TYR 0.042 0.001 TYR B 904 ARG 0.012 0.001 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 18) link_NAG-ASN : angle 2.24349 ( 54) hydrogen bonds : bond 0.03444 ( 899) hydrogen bonds : angle 4.77046 ( 2379) SS BOND : bond 0.00312 ( 51) SS BOND : angle 1.53244 ( 102) covalent geometry : bond 0.00282 (35701) covalent geometry : angle 0.62325 (48580) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 572 time to evaluate : 3.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6464 (OUTLIER) cc_final: 0.6169 (p0) REVERT: A 64 TRP cc_start: 0.6172 (t60) cc_final: 0.5745 (t60) REVERT: A 537 LYS cc_start: 0.7604 (tmtt) cc_final: 0.6794 (tmtt) REVERT: A 644 GLN cc_start: 0.7806 (tp40) cc_final: 0.7577 (tp-100) REVERT: A 645 THR cc_start: 0.7910 (p) cc_final: 0.7549 (p) REVERT: A 675 GLN cc_start: 0.6583 (OUTLIER) cc_final: 0.6164 (tm-30) REVERT: A 720 ILE cc_start: 0.8873 (mp) cc_final: 0.8612 (mm) REVERT: A 761 THR cc_start: 0.8021 (p) cc_final: 0.7716 (t) REVERT: A 776 LYS cc_start: 0.8203 (tmmt) cc_final: 0.7966 (tttm) REVERT: A 777 ASN cc_start: 0.8253 (m-40) cc_final: 0.7699 (m-40) REVERT: A 803 SER cc_start: 0.7995 (m) cc_final: 0.7721 (p) REVERT: A 921 LYS cc_start: 0.7776 (mmmt) cc_final: 0.7476 (mtmm) REVERT: A 922 LEU cc_start: 0.8335 (tp) cc_final: 0.8096 (tt) REVERT: A 925 ASN cc_start: 0.7996 (m-40) cc_final: 0.7762 (m-40) REVERT: A 933 LYS cc_start: 0.8016 (mtmm) cc_final: 0.7737 (mtmm) REVERT: A 957 GLN cc_start: 0.7568 (tt0) cc_final: 0.7306 (tt0) REVERT: A 968 SER cc_start: 0.8124 (p) cc_final: 0.7132 (p) REVERT: A 970 PHE cc_start: 0.7362 (m-10) cc_final: 0.6909 (m-10) REVERT: A 976 VAL cc_start: 0.8498 (t) cc_final: 0.8086 (p) REVERT: A 1091 ARG cc_start: 0.7556 (ttm170) cc_final: 0.7270 (ttm-80) REVERT: B 43 PHE cc_start: 0.8127 (t80) cc_final: 0.7846 (t80) REVERT: B 44 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7821 (mtt180) REVERT: B 46 SER cc_start: 0.8346 (m) cc_final: 0.7919 (p) REVERT: B 52 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7530 (tm-30) REVERT: B 65 PHE cc_start: 0.7546 (m-80) cc_final: 0.7068 (m-10) REVERT: B 169 GLU cc_start: 0.6357 (pm20) cc_final: 0.6052 (pm20) REVERT: B 170 TYR cc_start: 0.7070 (t80) cc_final: 0.6660 (t80) REVERT: B 200 LYS cc_start: 0.8293 (mttt) cc_final: 0.7714 (mttm) REVERT: B 278 LYS cc_start: 0.8229 (ttmp) cc_final: 0.7980 (tttm) REVERT: B 281 GLU cc_start: 0.7602 (pp20) cc_final: 0.7299 (pp20) REVERT: B 297 SER cc_start: 0.8226 (m) cc_final: 0.7859 (p) REVERT: B 308 VAL cc_start: 0.8946 (t) cc_final: 0.8568 (m) REVERT: B 563 GLN cc_start: 0.7453 (mt0) cc_final: 0.7174 (mt0) REVERT: B 569 ILE cc_start: 0.8069 (pt) cc_final: 0.7779 (mp) REVERT: B 708 SER cc_start: 0.8597 (t) cc_final: 0.8117 (m) REVERT: B 774 GLN cc_start: 0.7533 (mm-40) cc_final: 0.7141 (mm-40) REVERT: B 790 LYS cc_start: 0.8344 (mppt) cc_final: 0.7961 (mtmm) REVERT: B 858 LEU cc_start: 0.8102 (mt) cc_final: 0.7744 (mt) REVERT: B 895 GLN cc_start: 0.7425 (pt0) cc_final: 0.7005 (pt0) REVERT: B 921 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7456 (mmmm) REVERT: B 957 GLN cc_start: 0.6720 (tm130) cc_final: 0.6314 (tm130) REVERT: B 964 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7874 (ttmm) REVERT: B 974 SER cc_start: 0.7415 (p) cc_final: 0.7070 (m) REVERT: B 977 LEU cc_start: 0.8034 (mm) cc_final: 0.7761 (mt) REVERT: B 990 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: B 1018 ILE cc_start: 0.8191 (mt) cc_final: 0.7984 (mm) REVERT: B 1084 ASP cc_start: 0.7046 (p0) cc_final: 0.6838 (p0) REVERT: C 81 ASN cc_start: 0.7884 (m-40) cc_final: 0.7642 (m-40) REVERT: C 129 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7619 (tptt) REVERT: C 203 SER cc_start: 0.8115 (t) cc_final: 0.7901 (m) REVERT: C 204 LYS cc_start: 0.8305 (tptp) cc_final: 0.7804 (tptp) REVERT: C 237 ARG cc_start: 0.7933 (mtp-110) cc_final: 0.7422 (mtm-85) REVERT: C 279 TYR cc_start: 0.8426 (m-80) cc_final: 0.8192 (m-10) REVERT: C 281 GLU cc_start: 0.8612 (pm20) cc_final: 0.8271 (pm20) REVERT: C 321 GLN cc_start: 0.8087 (pm20) cc_final: 0.7856 (pm20) REVERT: C 326 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7821 (tt) REVERT: C 542 ASN cc_start: 0.7640 (t0) cc_final: 0.7358 (t0) REVERT: C 707 TYR cc_start: 0.7949 (t80) cc_final: 0.7630 (t80) REVERT: C 764 LYS cc_start: 0.7610 (tttm) cc_final: 0.7410 (tmtt) REVERT: C 780 GLU cc_start: 0.7335 (pt0) cc_final: 0.6981 (pt0) REVERT: C 790 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7619 (mtmm) REVERT: C 819 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6796 (mt-10) REVERT: C 820 ASP cc_start: 0.7509 (t0) cc_final: 0.7239 (t0) REVERT: C 823 PHE cc_start: 0.7174 (m-80) cc_final: 0.6921 (t80) REVERT: C 886 TRP cc_start: 0.8728 (p90) cc_final: 0.6663 (p90) REVERT: C 925 ASN cc_start: 0.8316 (m-40) cc_final: 0.8078 (m-40) REVERT: C 957 GLN cc_start: 0.7161 (tm-30) cc_final: 0.6907 (tm-30) REVERT: C 973 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7710 (pp) REVERT: C 994 ASP cc_start: 0.7660 (m-30) cc_final: 0.7444 (p0) REVERT: C 1019 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7317 (tpt170) REVERT: C 1038 LYS cc_start: 0.7602 (mmtm) cc_final: 0.7259 (mmmm) REVERT: C 1129 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.7995 (p) REVERT: D 176 VAL cc_start: 0.6049 (OUTLIER) cc_final: 0.5802 (t) REVERT: F 111 LEU cc_start: 0.3161 (OUTLIER) cc_final: 0.2620 (tm) REVERT: F 153 PHE cc_start: -0.0697 (OUTLIER) cc_final: -0.2312 (m-80) REVERT: G 158 MET cc_start: 0.5161 (mmm) cc_final: 0.4761 (mmm) REVERT: G 207 MET cc_start: 0.3311 (mpp) cc_final: 0.1184 (ptp) REVERT: G 234 TYR cc_start: 0.5975 (t80) cc_final: 0.5690 (t80) REVERT: H 49 MET cc_start: 0.5998 (mmm) cc_final: 0.5429 (mmm) REVERT: H 160 MET cc_start: 0.2814 (mmt) cc_final: -0.0360 (mtp) REVERT: H 208 MET cc_start: 0.4380 (mmm) cc_final: 0.2439 (tpt) REVERT: H 234 MET cc_start: 0.4019 (tmm) cc_final: 0.3660 (tmm) REVERT: I 67 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7183 (tmmm) outliers start: 185 outliers final: 145 residues processed: 716 average time/residue: 0.4592 time to fit residues: 537.9561 Evaluate side-chains 713 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 557 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1048 HIS Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 221 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 102 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 chunk 178 optimal weight: 0.4980 chunk 236 optimal weight: 0.8980 chunk 358 optimal weight: 8.9990 chunk 289 optimal weight: 3.9990 chunk 295 optimal weight: 0.7980 chunk 386 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 402 optimal weight: 40.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 603 ASN A 641 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 271 GLN B 920 GLN B1083 HIS ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 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** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.216523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.160990 restraints weight = 61808.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.159188 restraints weight = 39473.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161309 restraints weight = 24934.518| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35770 Z= 0.175 Angle : 0.653 17.854 48736 Z= 0.325 Chirality : 0.046 0.291 5467 Planarity : 0.004 0.055 6292 Dihedral : 6.995 82.302 5426 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 4.77 % Allowed : 19.15 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.61 (0.12), residues: 4433 helix: 0.82 (0.21), residues: 670 sheet: -1.29 (0.17), residues: 923 loop : -2.71 (0.11), residues: 2840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 64 HIS 0.015 0.001 HIS B1101 PHE 0.044 0.002 PHE B 981 TYR 0.045 0.001 TYR B 904 ARG 0.011 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 18) link_NAG-ASN : angle 2.33272 ( 54) hydrogen bonds : bond 0.03720 ( 899) hydrogen bonds : angle 4.81676 ( 2379) SS BOND : bond 0.00396 ( 51) SS BOND : angle 1.72849 ( 102) covalent geometry : bond 0.00389 (35701) covalent geometry : angle 0.64443 (48580) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 579 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.6414 (p0) REVERT: A 64 TRP cc_start: 0.6163 (t60) cc_final: 0.5813 (t60) REVERT: A 274 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.7549 (p) REVERT: A 537 LYS cc_start: 0.7684 (tmtt) cc_final: 0.6806 (tmtt) REVERT: A 645 THR cc_start: 0.7957 (p) cc_final: 0.7704 (p) REVERT: A 675 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.6030 (tm-30) REVERT: A 720 ILE cc_start: 0.8905 (mp) cc_final: 0.8651 (mm) REVERT: A 761 THR cc_start: 0.8186 (p) cc_final: 0.7899 (t) REVERT: A 776 LYS cc_start: 0.8290 (tmmt) cc_final: 0.7982 (tttm) REVERT: A 777 ASN cc_start: 0.8307 (m-40) cc_final: 0.7712 (m-40) REVERT: A 803 SER cc_start: 0.8187 (m) cc_final: 0.7905 (p) REVERT: A 922 LEU cc_start: 0.8338 (tp) cc_final: 0.8079 (tt) REVERT: A 925 ASN cc_start: 0.8059 (m-40) cc_final: 0.7729 (m-40) REVERT: A 933 LYS cc_start: 0.8083 (mtmm) cc_final: 0.7807 (mtmm) REVERT: A 968 SER cc_start: 0.8037 (p) cc_final: 0.7113 (p) REVERT: A 970 PHE cc_start: 0.7237 (m-10) cc_final: 0.6785 (m-10) REVERT: A 976 VAL cc_start: 0.8406 (t) cc_final: 0.7954 (p) REVERT: A 1031 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7143 (mt-10) REVERT: A 1072 GLU cc_start: 0.8093 (pm20) cc_final: 0.7743 (pm20) REVERT: A 1073 LYS cc_start: 0.8454 (ttmt) cc_final: 0.7965 (mtpp) REVERT: A 1091 ARG cc_start: 0.7639 (ttm170) cc_final: 0.7387 (ttm-80) REVERT: A 1103 PHE cc_start: 0.8102 (m-80) cc_final: 0.7888 (m-10) REVERT: B 43 PHE cc_start: 0.8148 (t80) cc_final: 0.7900 (t80) REVERT: B 44 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7622 (mtt180) REVERT: B 46 SER cc_start: 0.8449 (m) cc_final: 0.8049 (p) REVERT: B 52 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7407 (tm-30) REVERT: B 65 PHE cc_start: 0.7569 (m-80) cc_final: 0.7191 (m-10) REVERT: B 80 ASP cc_start: 0.5312 (p0) cc_final: 0.4951 (p0) REVERT: B 81 ASN cc_start: 0.7374 (p0) cc_final: 0.6813 (p0) REVERT: B 121 ASN cc_start: 0.6353 (t0) cc_final: 0.6146 (t0) REVERT: B 169 GLU cc_start: 0.6449 (pm20) cc_final: 0.6145 (pm20) REVERT: B 170 TYR cc_start: 0.7161 (t80) cc_final: 0.6725 (t80) REVERT: B 200 LYS cc_start: 0.8272 (mttt) cc_final: 0.7680 (mttm) REVERT: B 224 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6707 (mm-30) REVERT: B 278 LYS cc_start: 0.8304 (ttmp) cc_final: 0.8046 (tttm) REVERT: B 281 GLU cc_start: 0.7650 (pp20) cc_final: 0.7341 (pp20) REVERT: B 297 SER cc_start: 0.8255 (m) cc_final: 0.7921 (p) REVERT: B 308 VAL cc_start: 0.8961 (t) cc_final: 0.8558 (m) REVERT: B 328 ARG cc_start: 0.7247 (mmm-85) cc_final: 0.6835 (mmm-85) REVERT: B 335 LEU cc_start: 0.4648 (OUTLIER) cc_final: 0.4377 (mm) REVERT: B 537 LYS cc_start: 0.7803 (tttt) cc_final: 0.7600 (tttp) REVERT: B 569 ILE cc_start: 0.8147 (pt) cc_final: 0.7903 (mp) REVERT: B 708 SER cc_start: 0.8620 (t) cc_final: 0.8150 (m) REVERT: B 774 GLN cc_start: 0.7571 (mm-40) cc_final: 0.7109 (mm-40) REVERT: B 790 LYS cc_start: 0.8391 (mppt) cc_final: 0.7691 (mtmm) REVERT: B 858 LEU cc_start: 0.8175 (mt) cc_final: 0.7873 (mt) REVERT: B 895 GLN cc_start: 0.7464 (pt0) cc_final: 0.7053 (pt0) REVERT: B 921 LYS cc_start: 0.8004 (mmmt) cc_final: 0.7610 (mmmt) REVERT: B 957 GLN cc_start: 0.6810 (tm130) cc_final: 0.6378 (tm130) REVERT: B 964 LYS cc_start: 0.8254 (ttpp) cc_final: 0.7927 (ttmm) REVERT: B 974 SER cc_start: 0.7454 (p) cc_final: 0.7139 (m) REVERT: B 1006 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8193 (t) REVERT: B 1084 ASP cc_start: 0.7318 (p0) cc_final: 0.7006 (p0) REVERT: C 81 ASN cc_start: 0.7846 (m-40) cc_final: 0.7620 (m-40) REVERT: C 129 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7635 (tptt) REVERT: C 203 SER cc_start: 0.8228 (t) cc_final: 0.7827 (m) REVERT: C 204 LYS cc_start: 0.8296 (tptp) cc_final: 0.7885 (tptp) REVERT: C 237 ARG cc_start: 0.8000 (mtp-110) cc_final: 0.7380 (mtm-85) REVERT: C 279 TYR cc_start: 0.8450 (m-80) cc_final: 0.8202 (m-10) REVERT: C 290 ASP cc_start: 0.7127 (t70) cc_final: 0.6878 (t0) REVERT: C 321 GLN cc_start: 0.8164 (pm20) cc_final: 0.7857 (pm20) REVERT: C 326 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.7893 (tt) REVERT: C 537 LYS cc_start: 0.8570 (tttt) cc_final: 0.7878 (tttt) REVERT: C 542 ASN cc_start: 0.7741 (t0) cc_final: 0.7431 (t0) REVERT: C 707 TYR cc_start: 0.7988 (t80) cc_final: 0.7674 (t80) REVERT: C 740 MET cc_start: 0.7630 (mmm) cc_final: 0.7148 (tpp) REVERT: C 764 LYS cc_start: 0.7838 (tttm) cc_final: 0.7633 (tttm) REVERT: C 780 GLU cc_start: 0.7453 (pt0) cc_final: 0.6989 (pt0) REVERT: C 790 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7669 (mtmm) REVERT: C 819 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6882 (mt-10) REVERT: C 820 ASP cc_start: 0.7631 (t0) cc_final: 0.7392 (t0) REVERT: C 823 PHE cc_start: 0.7284 (m-80) cc_final: 0.7021 (t80) REVERT: C 886 TRP cc_start: 0.8740 (p90) cc_final: 0.7414 (p90) REVERT: C 925 ASN cc_start: 0.8308 (m-40) cc_final: 0.8075 (m-40) REVERT: C 957 GLN cc_start: 0.7137 (tm-30) cc_final: 0.6913 (tm-30) REVERT: C 973 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7803 (pp) REVERT: C 994 ASP cc_start: 0.7714 (m-30) cc_final: 0.7494 (p0) REVERT: C 1019 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7146 (tpt170) REVERT: C 1038 LYS cc_start: 0.7679 (mmtm) cc_final: 0.7352 (mmmm) REVERT: C 1083 HIS cc_start: 0.7482 (t70) cc_final: 0.7203 (t-90) REVERT: C 1129 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.8046 (p) REVERT: D 176 VAL cc_start: 0.6051 (OUTLIER) cc_final: 0.5795 (t) REVERT: F 111 LEU cc_start: 0.3127 (OUTLIER) cc_final: 0.2580 (tm) REVERT: F 153 PHE cc_start: -0.0561 (OUTLIER) cc_final: -0.2227 (m-80) REVERT: G 158 MET cc_start: 0.5040 (mmm) cc_final: 0.4640 (mmm) REVERT: G 207 MET cc_start: 0.3675 (mpp) cc_final: 0.1382 (ptp) REVERT: G 234 TYR cc_start: 0.6040 (t80) cc_final: 0.5759 (t80) REVERT: H 49 MET cc_start: 0.6036 (mmm) cc_final: 0.5612 (mmm) REVERT: H 160 MET cc_start: 0.2814 (mmt) cc_final: -0.0335 (mtp) REVERT: H 208 MET cc_start: 0.4080 (mmm) cc_final: 0.3829 (mmm) REVERT: H 234 MET cc_start: 0.4009 (tmm) cc_final: 0.3599 (tmm) REVERT: I 67 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7218 (tmmm) outliers start: 182 outliers final: 154 residues processed: 716 average time/residue: 0.4927 time to fit residues: 575.0187 Evaluate side-chains 729 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 562 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 221 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 417 optimal weight: 7.9990 chunk 196 optimal weight: 0.6980 chunk 385 optimal weight: 20.0000 chunk 80 optimal weight: 0.0870 chunk 184 optimal weight: 2.9990 chunk 353 optimal weight: 10.0000 chunk 309 optimal weight: 0.3980 chunk 265 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 335 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 920 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 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** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.216911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.162845 restraints weight = 61466.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.159589 restraints weight = 42280.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.161452 restraints weight = 26750.565| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35770 Z= 0.152 Angle : 0.640 17.392 48736 Z= 0.318 Chirality : 0.046 0.288 5467 Planarity : 0.004 0.055 6292 Dihedral : 6.891 82.120 5424 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 4.59 % Allowed : 19.38 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.53 (0.12), residues: 4433 helix: 0.91 (0.21), residues: 659 sheet: -1.22 (0.17), residues: 909 loop : -2.64 (0.11), residues: 2865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 64 HIS 0.012 0.001 HIS B1048 PHE 0.043 0.002 PHE B 981 TYR 0.035 0.001 TYR B 904 ARG 0.013 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 18) link_NAG-ASN : angle 2.18090 ( 54) hydrogen bonds : bond 0.03517 ( 899) hydrogen bonds : angle 4.81818 ( 2379) SS BOND : bond 0.00396 ( 51) SS BOND : angle 1.61846 ( 102) covalent geometry : bond 0.00342 (35701) covalent geometry : angle 0.63262 (48580) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8866 Ramachandran restraints generated. 4433 Oldfield, 0 Emsley, 4433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 582 time to evaluate : 4.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6365 (p0) REVERT: A 64 TRP cc_start: 0.6115 (t60) cc_final: 0.5782 (t60) REVERT: A 274 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.7560 (p) REVERT: A 537 LYS cc_start: 0.7697 (tmtt) cc_final: 0.6781 (tmtt) REVERT: A 655 TYR cc_start: 0.7158 (t80) cc_final: 0.6881 (t80) REVERT: A 675 GLN cc_start: 0.6481 (OUTLIER) cc_final: 0.5810 (tm-30) REVERT: A 720 ILE cc_start: 0.8925 (mp) cc_final: 0.8653 (mm) REVERT: A 761 THR cc_start: 0.8128 (p) cc_final: 0.7841 (t) REVERT: A 776 LYS cc_start: 0.8294 (tmmt) cc_final: 0.8024 (tttm) REVERT: A 777 ASN cc_start: 0.8257 (m-40) cc_final: 0.7709 (m-40) REVERT: A 803 SER cc_start: 0.8124 (m) cc_final: 0.7865 (p) REVERT: A 825 LYS cc_start: 0.7924 (mmmm) cc_final: 0.7543 (ttmt) REVERT: A 856 LYS cc_start: 0.7541 (mmtm) cc_final: 0.7270 (mmtm) REVERT: A 922 LEU cc_start: 0.8353 (tp) cc_final: 0.8105 (tt) REVERT: A 925 ASN cc_start: 0.8058 (m-40) cc_final: 0.7744 (m-40) REVERT: A 933 LYS cc_start: 0.8067 (mtmm) cc_final: 0.7777 (mtmm) REVERT: A 957 GLN cc_start: 0.7614 (tt0) cc_final: 0.7282 (tt0) REVERT: A 968 SER cc_start: 0.8105 (p) cc_final: 0.7168 (p) REVERT: A 970 PHE cc_start: 0.7294 (m-10) cc_final: 0.6876 (m-10) REVERT: A 976 VAL cc_start: 0.8460 (t) cc_final: 0.8050 (p) REVERT: A 1031 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7085 (mt-10) REVERT: A 1072 GLU cc_start: 0.8055 (pm20) cc_final: 0.7693 (pm20) REVERT: A 1073 LYS cc_start: 0.8452 (ttmt) cc_final: 0.7876 (mtpp) REVERT: A 1091 ARG cc_start: 0.7643 (ttm170) cc_final: 0.7343 (ttm-80) REVERT: A 1103 PHE cc_start: 0.8089 (m-80) cc_final: 0.7854 (m-10) REVERT: B 43 PHE cc_start: 0.8161 (t80) cc_final: 0.7944 (t80) REVERT: B 46 SER cc_start: 0.8473 (m) cc_final: 0.8038 (p) REVERT: B 52 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7362 (tm-30) REVERT: B 65 PHE cc_start: 0.7651 (m-80) cc_final: 0.7188 (m-10) REVERT: B 81 ASN cc_start: 0.7458 (p0) cc_final: 0.6942 (p0) REVERT: B 121 ASN cc_start: 0.6450 (t0) cc_final: 0.6219 (t0) REVERT: B 169 GLU cc_start: 0.6401 (pm20) cc_final: 0.6156 (pm20) REVERT: B 170 TYR cc_start: 0.7167 (t80) cc_final: 0.6741 (t80) REVERT: B 200 LYS cc_start: 0.8246 (mttt) cc_final: 0.7669 (mttm) REVERT: B 278 LYS cc_start: 0.8305 (ttmp) cc_final: 0.8015 (tttm) REVERT: B 281 GLU cc_start: 0.7648 (pp20) cc_final: 0.7332 (pp20) REVERT: B 297 SER cc_start: 0.8189 (m) cc_final: 0.7879 (p) REVERT: B 308 VAL cc_start: 0.8950 (t) cc_final: 0.8572 (m) REVERT: B 328 ARG cc_start: 0.7179 (mmm-85) cc_final: 0.6791 (mmm-85) REVERT: B 335 LEU cc_start: 0.4828 (OUTLIER) cc_final: 0.4563 (mm) REVERT: B 569 ILE cc_start: 0.8130 (pt) cc_final: 0.7863 (mp) REVERT: B 737 ASP cc_start: 0.7307 (t0) cc_final: 0.6494 (t0) REVERT: B 774 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7024 (mm-40) REVERT: B 790 LYS cc_start: 0.8405 (mppt) cc_final: 0.8083 (mtpt) REVERT: B 856 LYS cc_start: 0.8603 (mmtm) cc_final: 0.8373 (tppt) REVERT: B 858 LEU cc_start: 0.8182 (mt) cc_final: 0.7861 (mt) REVERT: B 895 GLN cc_start: 0.7421 (pt0) cc_final: 0.7018 (pt0) REVERT: B 921 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7543 (mmmt) REVERT: B 957 GLN cc_start: 0.6773 (tm130) cc_final: 0.6346 (tm130) REVERT: B 964 LYS cc_start: 0.8236 (ttpp) cc_final: 0.7934 (ttmm) REVERT: B 974 SER cc_start: 0.7407 (p) cc_final: 0.7079 (m) REVERT: B 1084 ASP cc_start: 0.7241 (p0) cc_final: 0.6905 (p0) REVERT: C 81 ASN cc_start: 0.8012 (m-40) cc_final: 0.7788 (m-40) REVERT: C 129 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7738 (tptt) REVERT: C 190 PHE cc_start: 0.6796 (m-80) cc_final: 0.6526 (m-80) REVERT: C 203 SER cc_start: 0.8416 (t) cc_final: 0.7994 (m) REVERT: C 204 LYS cc_start: 0.8296 (tptp) cc_final: 0.7838 (tptp) REVERT: C 237 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7317 (mtm-85) REVERT: C 279 TYR cc_start: 0.8378 (m-80) cc_final: 0.8157 (m-10) REVERT: C 290 ASP cc_start: 0.7153 (t70) cc_final: 0.6863 (t0) REVERT: C 321 GLN cc_start: 0.8086 (pm20) cc_final: 0.7782 (pm20) REVERT: C 326 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7920 (tt) REVERT: C 537 LYS cc_start: 0.8509 (tttt) cc_final: 0.7779 (tttt) REVERT: C 542 ASN cc_start: 0.7722 (t0) cc_final: 0.7424 (t0) REVERT: C 707 TYR cc_start: 0.7941 (t80) cc_final: 0.7627 (t80) REVERT: C 742 ILE cc_start: 0.8615 (mm) cc_final: 0.8227 (tp) REVERT: C 764 LYS cc_start: 0.7739 (tttm) cc_final: 0.7527 (tmtt) REVERT: C 773 GLU cc_start: 0.6757 (tm-30) cc_final: 0.6394 (tm-30) REVERT: C 780 GLU cc_start: 0.7404 (pt0) cc_final: 0.7063 (pt0) REVERT: C 790 LYS cc_start: 0.7926 (mtmm) cc_final: 0.7627 (mtmm) REVERT: C 819 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6801 (mt-10) REVERT: C 820 ASP cc_start: 0.7537 (t0) cc_final: 0.7292 (t0) REVERT: C 823 PHE cc_start: 0.7197 (m-80) cc_final: 0.6952 (t80) REVERT: C 886 TRP cc_start: 0.8716 (p90) cc_final: 0.6679 (p90) REVERT: C 957 GLN cc_start: 0.7107 (tm-30) cc_final: 0.6821 (tm-30) REVERT: C 1019 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7391 (tpt170) REVERT: C 1038 LYS cc_start: 0.7645 (mmtm) cc_final: 0.7335 (mmmm) REVERT: C 1083 HIS cc_start: 0.7477 (t70) cc_final: 0.7210 (t-90) REVERT: C 1129 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7993 (p) REVERT: D 176 VAL cc_start: 0.6043 (OUTLIER) cc_final: 0.5782 (t) REVERT: F 111 LEU cc_start: 0.3052 (OUTLIER) cc_final: 0.2487 (tm) REVERT: F 153 PHE cc_start: -0.0512 (OUTLIER) cc_final: -0.2142 (m-80) REVERT: G 158 MET cc_start: 0.5033 (mmm) cc_final: 0.4648 (mmm) REVERT: G 207 MET cc_start: 0.3630 (mpp) cc_final: 0.1466 (ptp) REVERT: G 234 TYR cc_start: 0.5992 (t80) cc_final: 0.5756 (t80) REVERT: H 49 MET cc_start: 0.6044 (mmm) cc_final: 0.5437 (mmm) REVERT: H 160 MET cc_start: 0.2956 (mmt) cc_final: -0.0227 (mtp) REVERT: H 208 MET cc_start: 0.3806 (mmm) cc_final: 0.2154 (tpp) REVERT: I 67 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7202 (tmmm) outliers start: 175 outliers final: 153 residues processed: 712 average time/residue: 0.5002 time to fit residues: 579.9508 Evaluate side-chains 734 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 570 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 221 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 193 PHE Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 327 optimal weight: 30.0000 chunk 81 optimal weight: 0.8980 chunk 389 optimal weight: 3.9990 chunk 298 optimal weight: 0.3980 chunk 147 optimal weight: 0.8980 chunk 424 optimal weight: 20.0000 chunk 362 optimal weight: 10.0000 chunk 171 optimal weight: 0.2980 chunk 195 optimal weight: 0.5980 chunk 417 optimal weight: 8.9990 chunk 193 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 603 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 271 GLN B 920 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 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** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.215793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.160932 restraints weight = 61878.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.157775 restraints weight = 48357.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.159822 restraints weight = 27825.762| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.222 35770 Z= 0.185 Angle : 0.747 59.127 48736 Z= 0.394 Chirality : 0.045 0.351 5467 Planarity : 0.004 0.055 6292 Dihedral : 6.867 82.122 5420 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 4.51 % Allowed : 19.43 % Favored : 76.06 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.52 (0.12), residues: 4433 helix: 0.91 (0.21), residues: 659 sheet: -1.21 (0.17), residues: 913 loop : -2.64 (0.11), residues: 2861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 64 HIS 0.011 0.001 HIS B1048 PHE 0.041 0.002 PHE B 981 TYR 0.034 0.001 TYR C 904 ARG 0.012 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 18) link_NAG-ASN : angle 2.18085 ( 54) hydrogen bonds : bond 0.03602 ( 899) hydrogen bonds : angle 4.82091 ( 2379) SS BOND : bond 0.01821 ( 51) SS BOND : angle 3.50723 ( 102) covalent geometry : bond 0.00418 (35701) covalent geometry : angle 0.72745 (48580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13761.28 seconds wall clock time: 238 minutes 46.56 seconds (14326.56 seconds total)