Starting phenix.real_space_refine on Mon Aug 25 08:03:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3n_34470/08_2025/8h3n_34470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3n_34470/08_2025/8h3n_34470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h3n_34470/08_2025/8h3n_34470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3n_34470/08_2025/8h3n_34470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h3n_34470/08_2025/8h3n_34470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3n_34470/08_2025/8h3n_34470.map" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 115 5.16 5 C 16876 2.51 5 N 4346 2.21 5 O 5001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26338 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7883 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 54, 'TRANS': 962} Chain breaks: 7 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 751 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7608 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 52, 'TRANS': 932} Chain breaks: 9 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 7572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7572 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 51, 'TRANS': 925} Chain breaks: 10 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "H" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 660 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 661 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.38, per 1000 atoms: 0.20 Number of scatterers: 26338 At special positions: 0 Unit cell: (131.6, 118.816, 187.248, 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 115 16.00 O 5001 8.00 N 4346 7.00 C 16876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 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=2.04 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 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 H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " 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 234 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A1134 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 343 " " NAG A1310 " - " ASN A 717 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B1134 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 717 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C1134 " " NAG C1304 " - " ASN C1098 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C 717 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6264 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 50 sheets defined 24.7% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 155 through 158 removed outlier: 3.544A pdb=" N ARG A 158 " --> pdb=" O SER A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 158' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.706A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.392A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.576A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.670A pdb=" N LYS A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.506A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.248A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.503A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.805A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.549A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.823A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.467A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.599A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.943A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.180A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 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 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.314A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.613A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.782A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.664A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.602A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.519A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.186A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.620A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.513A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.550A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.653A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 52 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.051A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.766A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.513A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.149A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.531A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.092A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.552A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.343A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.606A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.606A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.398A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.782A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.264A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AB9, first strand: chain 'D' and resid 34 through 37 removed outlier: 6.768A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 94 through 95 removed outlier: 3.792A pdb=" N TYR D 102 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AC3, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.608A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.928A pdb=" N THR E 53 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR E 49 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN E 37 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 47 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR E 87 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.680A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.516A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.557A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC9, first strand: chain 'B' and resid 324 through 328 removed outlier: 5.449A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.642A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.458A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.273A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.600A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.479A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.861A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.887A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.543A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.430A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 328 removed outlier: 5.268A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.207A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.382A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.536A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.496A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.679A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.806A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 33 through 34 Processing sheet with id=AF5, first strand: chain 'I' and resid 62 through 65 removed outlier: 4.009A pdb=" N SER I 63 " --> pdb=" O THR I 74 " (cutoff:3.500A) 1067 hydrogen bonds defined for protein. 2829 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.61 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.31: 4218 1.31 - 1.61: 22589 1.61 - 1.92: 143 1.92 - 2.23: 0 2.23 - 2.53: 1 Bond restraints: 26951 Sorted by residual: bond pdb=" CB PRO E 8 " pdb=" CG PRO E 8 " ideal model delta sigma weight residual 1.492 2.532 -1.040 5.00e-02 4.00e+02 4.33e+02 bond pdb=" CG PRO E 8 " pdb=" CD PRO E 8 " ideal model delta sigma weight residual 1.503 0.998 0.505 3.40e-02 8.65e+02 2.20e+02 bond pdb=" CG PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 1.503 1.139 0.364 3.40e-02 8.65e+02 1.14e+02 bond pdb=" N PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 1.473 1.554 -0.081 1.40e-02 5.10e+03 3.38e+01 bond pdb=" N PRO B 209 " pdb=" CA PRO B 209 " ideal model delta sigma weight residual 1.470 1.434 0.036 1.01e-02 9.80e+03 1.30e+01 ... (remaining 26946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.45: 36680 16.45 - 32.89: 3 32.89 - 49.34: 0 49.34 - 65.78: 0 65.78 - 82.23: 1 Bond angle restraints: 36684 Sorted by residual: angle pdb=" CB PRO E 8 " pdb=" CG PRO E 8 " pdb=" CD PRO E 8 " ideal model delta sigma weight residual 106.10 23.87 82.23 3.20e+00 9.77e-02 6.60e+02 angle pdb=" CA PRO E 8 " pdb=" N PRO E 8 " pdb=" CD PRO E 8 " ideal model delta sigma weight residual 112.00 90.02 21.98 1.40e+00 5.10e-01 2.47e+02 angle pdb=" CA PRO B 209 " pdb=" N PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 112.00 95.09 16.91 1.40e+00 5.10e-01 1.46e+02 angle pdb=" N PRO B 209 " pdb=" CD PRO B 209 " pdb=" CG PRO B 209 " ideal model delta sigma weight residual 103.20 85.72 17.48 1.50e+00 4.44e-01 1.36e+02 angle pdb=" CA PRO E 95 " pdb=" N PRO E 95 " pdb=" CD PRO E 95 " ideal model delta sigma weight residual 111.50 96.33 15.17 1.40e+00 5.10e-01 1.17e+02 ... (remaining 36679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.07: 14513 21.07 - 42.13: 1371 42.13 - 63.20: 362 63.20 - 84.26: 60 84.26 - 105.33: 23 Dihedral angle restraints: 16329 sinusoidal: 6596 harmonic: 9733 Sorted by residual: dihedral pdb=" CA SER E 7 " pdb=" C SER E 7 " pdb=" N PRO E 8 " pdb=" CA PRO E 8 " ideal model delta harmonic sigma weight residual 180.00 111.99 68.01 0 5.00e+00 4.00e-02 1.85e+02 dihedral pdb=" CA TYR I 94 " pdb=" C TYR I 94 " pdb=" N PRO I 95 " pdb=" CA PRO I 95 " ideal model delta harmonic sigma weight residual -180.00 -112.14 -67.86 0 5.00e+00 4.00e-02 1.84e+02 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 172.50 -79.50 1 1.00e+01 1.00e-02 7.85e+01 ... (remaining 16326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 4230 0.156 - 0.312: 13 0.312 - 0.467: 0 0.467 - 0.623: 2 0.623 - 0.779: 1 Chirality restraints: 4246 Sorted by residual: chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.36e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.05e+00 ... (remaining 4243 not shown) Planarity restraints: 4705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 7 " -0.128 5.00e-02 4.00e+02 1.73e-01 4.80e+01 pdb=" N PRO E 8 " 0.298 5.00e-02 4.00e+02 pdb=" CA PRO E 8 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO E 8 " -0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 94 " -0.096 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO E 95 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 138 " 0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO A 139 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " 0.047 5.00e-02 4.00e+02 ... (remaining 4702 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 133 2.51 - 3.11: 19800 3.11 - 3.70: 40149 3.70 - 4.30: 60949 4.30 - 4.90: 99735 Nonbonded interactions: 220766 Sorted by model distance: nonbonded pdb=" O PRO B 631 " pdb=" OG1 THR B 632 " model vdw 1.912 3.040 nonbonded pdb=" O3 NAG B1308 " pdb=" O7 NAG B1308 " model vdw 1.981 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.017 3.040 nonbonded pdb=" O GLY B 283 " pdb=" OG1 THR B 284 " model vdw 2.017 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.032 3.040 ... (remaining 220761 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 27 through 140 or resid 164 through 173 or resid 187 throu \ gh 241 or (resid 242 and (name N or name CA or name C or name O or name CB or na \ me CG )) or resid 264 through 368 or resid 377 through 456 or resid 491 through \ 563 or (resid 564 and (name N or name CA or name C or name O or name CB )) or re \ sid 565 through 567 or (resid 568 and (name N or name CA or name C or name O or \ name CB )) or resid 569 through 570 or (resid 571 through 572 and (name N or nam \ e CA or name C or name O or name CB )) or resid 573 through 620 or resid 629 thr \ ough 1138 or resid 1302 through 1309)) selection = (chain 'B' and (resid 27 through 140 or resid 164 through 197 or (resid 198 and \ (name N or name CA or name C or name O or name CB )) or resid 199 through 368 or \ resid 377 through 620 or resid 629 through 828 or resid 848 through 1138 or res \ id 1302 through 1309)) selection = (chain 'C' and (resid 27 through 173 or resid 187 through 241 or (resid 242 and \ (name N or name CA or name C or name O or name CB or name CG )) or resid 264 thr \ ough 456 or resid 491 through 1138 or resid 1301 through 1308)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.930 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.009 1.040 27019 Z= 0.301 Angle : 0.896 82.227 36847 Z= 0.463 Chirality : 0.050 0.779 4246 Planarity : 0.006 0.173 4678 Dihedral : 17.751 105.330 9942 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.16 % Favored : 92.60 % Rotamer: Outliers : 4.45 % Allowed : 23.50 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.14), residues: 3269 helix: 0.95 (0.20), residues: 687 sheet: -0.65 (0.18), residues: 750 loop : -1.80 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.027 0.002 TYR B 265 PHE 0.020 0.002 PHE C 186 TRP 0.009 0.002 TRP D 103 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00917 (26951) covalent geometry : angle 0.86275 (36684) SS BOND : bond 0.00648 ( 41) SS BOND : angle 1.72741 ( 82) hydrogen bonds : bond 0.12934 ( 1055) hydrogen bonds : angle 7.57670 ( 2829) link_NAG-ASN : bond 0.00683 ( 27) link_NAG-ASN : angle 5.03072 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 261 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.7883 (p) REVERT: E 79 GLN cc_start: 0.5984 (mt0) cc_final: 0.5753 (mt0) REVERT: B 440 LYS cc_start: 0.5493 (tptt) cc_final: 0.4855 (ttpp) REVERT: C 108 THR cc_start: 0.7482 (p) cc_final: 0.7242 (m) REVERT: C 406 GLU cc_start: 0.6911 (mp0) cc_final: 0.6676 (mp0) REVERT: C 1002 GLN cc_start: 0.8038 (tt0) cc_final: 0.7720 (tm-30) REVERT: H 100 TYR cc_start: 0.5632 (OUTLIER) cc_final: 0.5316 (m-80) REVERT: I 88 CYS cc_start: 0.3816 (OUTLIER) cc_final: 0.1636 (p) outliers start: 126 outliers final: 102 residues processed: 377 average time/residue: 0.4480 time to fit residues: 208.2523 Evaluate side-chains 346 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 241 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 88 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 125 ASN A 414 GLN A 505 HIS A 675 GLN A1101 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 544 ASN B1101 HIS C 66 HIS C 121 ASN C 394 ASN C 450 ASN C 755 GLN C1071 GLN C1083 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.155179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.111236 restraints weight = 32927.783| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.85 r_work: 0.3086 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27019 Z= 0.138 Angle : 0.644 17.454 36847 Z= 0.328 Chirality : 0.047 0.589 4246 Planarity : 0.005 0.157 4678 Dihedral : 9.309 70.472 4334 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.54 % Favored : 94.28 % Rotamer: Outliers : 5.37 % Allowed : 20.35 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.14), residues: 3269 helix: 1.59 (0.20), residues: 682 sheet: -0.53 (0.18), residues: 761 loop : -1.48 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.027 0.001 TYR I 94 PHE 0.018 0.001 PHE H 100H TRP 0.014 0.001 TRP H 47 HIS 0.009 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00304 (26951) covalent geometry : angle 0.61150 (36684) SS BOND : bond 0.00517 ( 41) SS BOND : angle 1.48639 ( 82) hydrogen bonds : bond 0.04370 ( 1055) hydrogen bonds : angle 6.13195 ( 2829) link_NAG-ASN : bond 0.00572 ( 27) link_NAG-ASN : angle 4.14036 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 272 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7987 (p) cc_final: 0.7733 (t) REVERT: A 169 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7556 (mt-10) REVERT: A 186 PHE cc_start: 0.4613 (OUTLIER) cc_final: 0.4217 (t80) REVERT: A 210 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6951 (mm) REVERT: A 470 THR cc_start: 0.8169 (p) cc_final: 0.7949 (p) REVERT: A 994 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7857 (t70) REVERT: E 4 MET cc_start: 0.3728 (mmp) cc_final: 0.3021 (tmt) REVERT: B 278 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8848 (ttpp) REVERT: B 353 TRP cc_start: 0.6578 (p-90) cc_final: 0.6238 (p-90) REVERT: B 429 PHE cc_start: 0.5688 (OUTLIER) cc_final: 0.5337 (p90) REVERT: B 440 LYS cc_start: 0.4954 (tptt) cc_final: 0.4229 (ttpp) REVERT: B 811 LYS cc_start: 0.6992 (ptpt) cc_final: 0.6516 (mmtp) REVERT: C 108 THR cc_start: 0.7467 (p) cc_final: 0.7234 (m) REVERT: C 516 GLU cc_start: 0.7329 (tt0) cc_final: 0.7011 (tt0) REVERT: H 100 TYR cc_start: 0.5752 (OUTLIER) cc_final: 0.5288 (m-80) REVERT: I 47 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6337 (tm) outliers start: 152 outliers final: 77 residues processed: 397 average time/residue: 0.4306 time to fit residues: 211.6892 Evaluate side-chains 329 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 245 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 225 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 318 optimal weight: 0.0050 chunk 97 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 323 optimal weight: 0.5980 chunk 137 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 935 GLN A1071 GLN E 6 GLN B 544 ASN C 394 ASN C 755 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.154684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.110980 restraints weight = 33188.958| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.81 r_work: 0.3074 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27019 Z= 0.150 Angle : 0.616 17.451 36847 Z= 0.315 Chirality : 0.047 0.563 4246 Planarity : 0.005 0.124 4678 Dihedral : 7.867 67.744 4256 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.57 % Favored : 94.28 % Rotamer: Outliers : 5.44 % Allowed : 19.82 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.14), residues: 3269 helix: 1.73 (0.20), residues: 678 sheet: -0.42 (0.18), residues: 770 loop : -1.37 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.023 0.001 TYR I 94 PHE 0.018 0.001 PHE H 100H TRP 0.013 0.001 TRP H 47 HIS 0.006 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00337 (26951) covalent geometry : angle 0.58490 (36684) SS BOND : bond 0.00300 ( 41) SS BOND : angle 1.51233 ( 82) hydrogen bonds : bond 0.04475 ( 1055) hydrogen bonds : angle 5.95509 ( 2829) link_NAG-ASN : bond 0.00613 ( 27) link_NAG-ASN : angle 3.95215 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 251 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7452 (t0) REVERT: A 126 VAL cc_start: 0.7956 (p) cc_final: 0.7728 (t) REVERT: A 169 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7522 (mt-10) REVERT: A 470 THR cc_start: 0.8182 (p) cc_final: 0.7978 (p) REVERT: A 755 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7394 (mt0) REVERT: A 759 PHE cc_start: 0.7351 (m-80) cc_final: 0.6958 (m-80) REVERT: A 994 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7871 (t70) REVERT: A 1084 ASP cc_start: 0.6904 (t0) cc_final: 0.6581 (OUTLIER) REVERT: A 1086 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7277 (mtmt) REVERT: D 56 ASP cc_start: 0.6771 (m-30) cc_final: 0.6140 (m-30) REVERT: E 4 MET cc_start: 0.3797 (mmp) cc_final: 0.3544 (tpp) REVERT: B 278 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8863 (ttpp) REVERT: B 280 ASN cc_start: 0.7431 (t0) cc_final: 0.7182 (t0) REVERT: B 321 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6012 (pm20) REVERT: B 353 TRP cc_start: 0.6497 (p-90) cc_final: 0.6212 (p-90) REVERT: B 390 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7704 (mt) REVERT: B 429 PHE cc_start: 0.5738 (OUTLIER) cc_final: 0.5348 (p90) REVERT: B 440 LYS cc_start: 0.5100 (tptt) cc_final: 0.4352 (ttpp) REVERT: B 745 ASP cc_start: 0.6492 (OUTLIER) cc_final: 0.6277 (p0) REVERT: B 811 LYS cc_start: 0.7000 (ptpt) cc_final: 0.6566 (mmtp) REVERT: B 935 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7553 (tp40) REVERT: C 108 THR cc_start: 0.7477 (p) cc_final: 0.7048 (m) REVERT: C 516 GLU cc_start: 0.7424 (tt0) cc_final: 0.7138 (tt0) REVERT: C 907 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8158 (t0) REVERT: C 1002 GLN cc_start: 0.8337 (tt0) cc_final: 0.7844 (tm-30) REVERT: H 100 TYR cc_start: 0.5757 (OUTLIER) cc_final: 0.5247 (m-80) REVERT: I 47 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6323 (tm) outliers start: 154 outliers final: 85 residues processed: 379 average time/residue: 0.4180 time to fit residues: 196.3275 Evaluate side-chains 338 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 241 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 81 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 4 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 chunk 180 optimal weight: 0.4980 chunk 224 optimal weight: 0.9990 chunk 193 optimal weight: 0.0070 chunk 248 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 279 optimal weight: 0.9980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS A 628 GLN A 675 GLN A 935 GLN B 544 ASN C 460 ASN C 755 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.155730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111654 restraints weight = 32920.307| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.92 r_work: 0.3081 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27019 Z= 0.122 Angle : 0.583 16.479 36847 Z= 0.297 Chirality : 0.046 0.573 4246 Planarity : 0.005 0.094 4678 Dihedral : 7.155 67.124 4243 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.11 % Favored : 94.74 % Rotamer: Outliers : 5.09 % Allowed : 20.39 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.15), residues: 3269 helix: 1.85 (0.20), residues: 678 sheet: -0.31 (0.18), residues: 756 loop : -1.25 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.023 0.001 TYR C 453 PHE 0.016 0.001 PHE B 400 TRP 0.013 0.001 TRP H 47 HIS 0.005 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00265 (26951) covalent geometry : angle 0.55175 (36684) SS BOND : bond 0.00261 ( 41) SS BOND : angle 1.35350 ( 82) hydrogen bonds : bond 0.04014 ( 1055) hydrogen bonds : angle 5.75732 ( 2829) link_NAG-ASN : bond 0.00549 ( 27) link_NAG-ASN : angle 3.82518 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 256 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASN cc_start: 0.5554 (OUTLIER) cc_final: 0.4790 (m110) REVERT: A 169 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 234 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7371 (t0) REVERT: A 242 LEU cc_start: 0.6908 (mt) cc_final: 0.6621 (mm) REVERT: A 282 ASN cc_start: 0.7902 (p0) cc_final: 0.7237 (t0) REVERT: A 358 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8520 (mm) REVERT: A 470 THR cc_start: 0.8188 (p) cc_final: 0.7982 (p) REVERT: A 557 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.7769 (mtmt) REVERT: A 564 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: A 755 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7349 (mt0) REVERT: A 994 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7902 (t70) REVERT: A 1084 ASP cc_start: 0.6950 (t0) cc_final: 0.6703 (t0) REVERT: B 81 ASN cc_start: 0.7059 (p0) cc_final: 0.6587 (p0) REVERT: B 278 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8879 (ttpp) REVERT: B 280 ASN cc_start: 0.7417 (t0) cc_final: 0.7210 (t0) REVERT: B 321 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.5960 (pm20) REVERT: B 353 TRP cc_start: 0.6584 (p-90) cc_final: 0.6207 (p-90) REVERT: B 390 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7724 (mt) REVERT: B 429 PHE cc_start: 0.5649 (OUTLIER) cc_final: 0.5240 (p90) REVERT: B 440 LYS cc_start: 0.5138 (tptt) cc_final: 0.4422 (ttpp) REVERT: B 532 ASN cc_start: 0.6728 (t0) cc_final: 0.6448 (m-40) REVERT: B 745 ASP cc_start: 0.6451 (OUTLIER) cc_final: 0.6242 (p0) REVERT: B 811 LYS cc_start: 0.6999 (ptpt) cc_final: 0.6555 (mmtp) REVERT: B 836 GLN cc_start: 0.6887 (mt0) cc_final: 0.6657 (mm-40) REVERT: C 41 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8091 (mtmm) REVERT: C 424 LYS cc_start: 0.8046 (tppp) cc_final: 0.7782 (tppt) REVERT: C 462 LYS cc_start: 0.8096 (mtpp) cc_final: 0.7696 (mtpt) REVERT: C 516 GLU cc_start: 0.7412 (tt0) cc_final: 0.7146 (tt0) REVERT: C 1092 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6989 (pp20) REVERT: H 100 TYR cc_start: 0.5821 (OUTLIER) cc_final: 0.5323 (m-80) REVERT: I 47 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6239 (tm) outliers start: 144 outliers final: 73 residues processed: 373 average time/residue: 0.4199 time to fit residues: 192.9316 Evaluate side-chains 328 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 239 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 174 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 161 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 625 HIS A 675 GLN A1135 ASN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN C 460 ASN C 755 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.109235 restraints weight = 32674.910| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.95 r_work: 0.3037 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 27019 Z= 0.228 Angle : 0.681 18.384 36847 Z= 0.349 Chirality : 0.050 0.555 4246 Planarity : 0.005 0.093 4678 Dihedral : 7.390 68.038 4230 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.30 % Favored : 93.55 % Rotamer: Outliers : 5.48 % Allowed : 20.53 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.76 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.14), residues: 3269 helix: 1.58 (0.20), residues: 677 sheet: -0.30 (0.18), residues: 776 loop : -1.32 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.023 0.002 TYR B 265 PHE 0.026 0.002 PHE E 62 TRP 0.012 0.002 TRP D 47 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00531 (26951) covalent geometry : angle 0.64588 (36684) SS BOND : bond 0.00489 ( 41) SS BOND : angle 1.83778 ( 82) hydrogen bonds : bond 0.05151 ( 1055) hydrogen bonds : angle 6.06543 ( 2829) link_NAG-ASN : bond 0.00501 ( 27) link_NAG-ASN : angle 4.29498 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 247 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7482 (t0) REVERT: A 165 ASN cc_start: 0.5509 (OUTLIER) cc_final: 0.4924 (p0) REVERT: A 358 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8498 (mm) REVERT: A 557 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.7791 (mtmt) REVERT: A 564 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: A 755 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7386 (mt0) REVERT: A 994 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7941 (t70) REVERT: D 56 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6297 (m-30) REVERT: B 81 ASN cc_start: 0.7143 (p0) cc_final: 0.6612 (p0) REVERT: B 278 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8895 (ttpp) REVERT: B 321 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6003 (pm20) REVERT: B 353 TRP cc_start: 0.6442 (p-90) cc_final: 0.6092 (p-90) REVERT: B 357 ARG cc_start: 0.6598 (tmm-80) cc_final: 0.6100 (tmm-80) REVERT: B 390 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7687 (mt) REVERT: B 400 PHE cc_start: 0.7874 (p90) cc_final: 0.7571 (p90) REVERT: B 440 LYS cc_start: 0.5207 (tptt) cc_final: 0.4398 (ttpp) REVERT: B 532 ASN cc_start: 0.6840 (t0) cc_final: 0.6552 (m-40) REVERT: B 745 ASP cc_start: 0.6769 (OUTLIER) cc_final: 0.6567 (p0) REVERT: C 234 ASN cc_start: 0.6810 (OUTLIER) cc_final: 0.6593 (p0) REVERT: C 314 GLN cc_start: 0.8839 (mt0) cc_final: 0.8396 (mm-40) REVERT: C 462 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7759 (mtmt) REVERT: C 907 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8300 (t0) REVERT: C 1002 GLN cc_start: 0.8375 (tt0) cc_final: 0.7863 (tm-30) REVERT: H 100 TYR cc_start: 0.5889 (OUTLIER) cc_final: 0.5185 (m-80) REVERT: I 47 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6159 (tm) outliers start: 155 outliers final: 96 residues processed: 368 average time/residue: 0.4950 time to fit residues: 223.8048 Evaluate side-chains 348 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 236 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 84 optimal weight: 2.9990 chunk 248 optimal weight: 0.0020 chunk 243 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS A 675 GLN A 935 GLN B 544 ASN B 836 GLN C 121 ASN C 460 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.154709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.109731 restraints weight = 32915.970| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.69 r_work: 0.3100 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27019 Z= 0.148 Angle : 0.619 16.759 36847 Z= 0.315 Chirality : 0.047 0.578 4246 Planarity : 0.005 0.085 4678 Dihedral : 7.008 66.857 4227 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.05 % Favored : 94.77 % Rotamer: Outliers : 5.02 % Allowed : 20.88 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.14), residues: 3269 helix: 1.82 (0.20), residues: 667 sheet: -0.28 (0.18), residues: 777 loop : -1.27 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.024 0.001 TYR C 453 PHE 0.016 0.001 PHE B 643 TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00332 (26951) covalent geometry : angle 0.58375 (36684) SS BOND : bond 0.00341 ( 41) SS BOND : angle 1.29954 ( 82) hydrogen bonds : bond 0.04338 ( 1055) hydrogen bonds : angle 5.85064 ( 2829) link_NAG-ASN : bond 0.00558 ( 27) link_NAG-ASN : angle 4.25046 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 241 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7395 (t0) REVERT: A 234 ASN cc_start: 0.7964 (p0) cc_final: 0.7007 (m-40) REVERT: A 358 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8523 (mm) REVERT: A 557 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7740 (mtmt) REVERT: A 564 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: A 755 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7367 (mt0) REVERT: A 994 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7853 (t70) REVERT: A 1073 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8226 (mtmm) REVERT: D 56 ASP cc_start: 0.6844 (m-30) cc_final: 0.6283 (m-30) REVERT: B 81 ASN cc_start: 0.7088 (p0) cc_final: 0.6539 (p0) REVERT: B 110 LEU cc_start: 0.8415 (mt) cc_final: 0.8203 (mm) REVERT: B 278 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8817 (ttpp) REVERT: B 321 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.5973 (pm20) REVERT: B 353 TRP cc_start: 0.6500 (p-90) cc_final: 0.6189 (p-90) REVERT: B 390 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7720 (mt) REVERT: B 429 PHE cc_start: 0.5662 (OUTLIER) cc_final: 0.5269 (p90) REVERT: B 440 LYS cc_start: 0.5252 (tptt) cc_final: 0.4441 (ttpp) REVERT: B 532 ASN cc_start: 0.6914 (t0) cc_final: 0.6513 (m-40) REVERT: B 745 ASP cc_start: 0.6773 (OUTLIER) cc_final: 0.6564 (p0) REVERT: B 811 LYS cc_start: 0.7073 (ptpt) cc_final: 0.6593 (mmtp) REVERT: C 233 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7920 (pt) REVERT: C 314 GLN cc_start: 0.8753 (mt0) cc_final: 0.8337 (mm-40) REVERT: C 406 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6672 (mt-10) REVERT: C 424 LYS cc_start: 0.8040 (tppp) cc_final: 0.7788 (tppt) REVERT: C 462 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7693 (mtpt) REVERT: C 516 GLU cc_start: 0.7370 (tt0) cc_final: 0.7132 (tt0) REVERT: C 529 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6501 (tmtm) REVERT: H 100 TYR cc_start: 0.5797 (OUTLIER) cc_final: 0.5255 (m-80) REVERT: I 47 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6187 (tm) REVERT: I 88 CYS cc_start: 0.3782 (OUTLIER) cc_final: 0.1174 (p) outliers start: 142 outliers final: 88 residues processed: 356 average time/residue: 0.5059 time to fit residues: 220.6354 Evaluate side-chains 335 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 230 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 257 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 287 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 165 ASN A 625 HIS A 628 GLN A 675 GLN A 935 GLN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100FASN B 544 ASN C 460 ASN C 755 GLN ** I 90 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 = 0.3781 r_free = 0.3781 target = 0.152161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.106880 restraints weight = 32715.358| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.70 r_work: 0.3057 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 27019 Z= 0.283 Angle : 0.730 18.099 36847 Z= 0.376 Chirality : 0.053 0.627 4246 Planarity : 0.006 0.087 4678 Dihedral : 7.589 68.169 4222 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.61 % Favored : 93.21 % Rotamer: Outliers : 5.62 % Allowed : 20.64 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.76 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.14), residues: 3269 helix: 1.37 (0.20), residues: 677 sheet: -0.33 (0.18), residues: 784 loop : -1.38 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 357 TYR 0.025 0.002 TYR C 453 PHE 0.031 0.002 PHE E 62 TRP 0.012 0.002 TRP D 47 HIS 0.008 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00668 (26951) covalent geometry : angle 0.69238 (36684) SS BOND : bond 0.00581 ( 41) SS BOND : angle 1.86168 ( 82) hydrogen bonds : bond 0.05471 ( 1055) hydrogen bonds : angle 6.19540 ( 2829) link_NAG-ASN : bond 0.00511 ( 27) link_NAG-ASN : angle 4.64902 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 232 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7214 (t0) REVERT: A 358 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8476 (mm) REVERT: A 557 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.7765 (mtmt) REVERT: A 564 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: A 755 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7405 (mt0) REVERT: A 994 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7868 (t70) REVERT: A 1073 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8204 (mtmm) REVERT: D 56 ASP cc_start: 0.6882 (m-30) cc_final: 0.6292 (m-30) REVERT: B 81 ASN cc_start: 0.7120 (p0) cc_final: 0.6568 (p0) REVERT: B 278 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8877 (ttpp) REVERT: B 321 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6092 (pm20) REVERT: B 333 THR cc_start: 0.5797 (OUTLIER) cc_final: 0.5548 (m) REVERT: B 353 TRP cc_start: 0.6500 (p-90) cc_final: 0.6236 (p-90) REVERT: B 357 ARG cc_start: 0.6707 (tmm-80) cc_final: 0.6116 (tmm-80) REVERT: B 390 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7709 (mt) REVERT: B 532 ASN cc_start: 0.6909 (t0) cc_final: 0.6598 (m-40) REVERT: B 592 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.6525 (p90) REVERT: B 990 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7377 (mm-30) REVERT: C 314 GLN cc_start: 0.8772 (mt0) cc_final: 0.8354 (mm-40) REVERT: C 462 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7738 (mtpt) REVERT: C 516 GLU cc_start: 0.7545 (tt0) cc_final: 0.7285 (tt0) REVERT: C 529 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6558 (tmtm) REVERT: C 907 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8252 (t0) REVERT: H 100 TYR cc_start: 0.5877 (OUTLIER) cc_final: 0.5373 (m-80) REVERT: I 47 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6175 (tm) REVERT: I 88 CYS cc_start: 0.3698 (OUTLIER) cc_final: 0.1151 (p) outliers start: 159 outliers final: 105 residues processed: 360 average time/residue: 0.5084 time to fit residues: 224.6264 Evaluate side-chains 349 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 226 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 163 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 207 HIS A 675 GLN D 100FASN B 280 ASN B 544 ASN C 755 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.154898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.110188 restraints weight = 32720.648| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.95 r_work: 0.3059 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27019 Z= 0.171 Angle : 0.647 16.891 36847 Z= 0.331 Chirality : 0.048 0.620 4246 Planarity : 0.005 0.084 4678 Dihedral : 7.189 67.560 4222 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.51 % Favored : 94.31 % Rotamer: Outliers : 5.12 % Allowed : 21.27 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.76 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.14), residues: 3269 helix: 1.50 (0.20), residues: 684 sheet: -0.23 (0.18), residues: 763 loop : -1.32 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 509 TYR 0.025 0.002 TYR C 453 PHE 0.017 0.002 PHE H 100H TRP 0.011 0.002 TRP H 47 HIS 0.009 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00393 (26951) covalent geometry : angle 0.60950 (36684) SS BOND : bond 0.00424 ( 41) SS BOND : angle 1.95992 ( 82) hydrogen bonds : bond 0.04611 ( 1055) hydrogen bonds : angle 5.97877 ( 2829) link_NAG-ASN : bond 0.00502 ( 27) link_NAG-ASN : angle 4.25816 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 230 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7204 (t0) REVERT: A 358 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8499 (mm) REVERT: A 557 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.7771 (mtmt) REVERT: A 564 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: A 755 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7426 (mt0) REVERT: A 994 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7849 (t70) REVERT: A 1073 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8244 (mtmm) REVERT: D 56 ASP cc_start: 0.6924 (m-30) cc_final: 0.6347 (m-30) REVERT: B 81 ASN cc_start: 0.7213 (p0) cc_final: 0.6655 (p0) REVERT: B 110 LEU cc_start: 0.8458 (mt) cc_final: 0.8244 (mm) REVERT: B 278 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8840 (ttpp) REVERT: B 321 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6031 (pm20) REVERT: B 333 THR cc_start: 0.5611 (OUTLIER) cc_final: 0.5355 (m) REVERT: B 353 TRP cc_start: 0.6475 (p-90) cc_final: 0.6188 (p-90) REVERT: B 357 ARG cc_start: 0.6738 (tmm-80) cc_final: 0.5949 (tmm-80) REVERT: B 390 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7689 (mt) REVERT: B 532 ASN cc_start: 0.6984 (t0) cc_final: 0.6653 (m-40) REVERT: B 675 GLN cc_start: 0.7314 (tp40) cc_final: 0.6945 (tp-100) REVERT: B 745 ASP cc_start: 0.6951 (OUTLIER) cc_final: 0.6736 (p0) REVERT: B 1101 HIS cc_start: 0.7269 (m90) cc_final: 0.6874 (m90) REVERT: C 97 LYS cc_start: 0.6705 (OUTLIER) cc_final: 0.6244 (tmtt) REVERT: C 169 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: C 314 GLN cc_start: 0.8786 (mt0) cc_final: 0.8353 (mm-40) REVERT: C 424 LYS cc_start: 0.8066 (tppp) cc_final: 0.7823 (tppt) REVERT: C 460 ASN cc_start: 0.7844 (m-40) cc_final: 0.7341 (m-40) REVERT: C 462 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7748 (mtpt) REVERT: C 516 GLU cc_start: 0.7493 (tt0) cc_final: 0.7259 (tt0) REVERT: C 529 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6583 (tmtm) REVERT: C 907 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8255 (t0) REVERT: C 1002 GLN cc_start: 0.8311 (tt0) cc_final: 0.7788 (tm-30) REVERT: H 36 TRP cc_start: 0.4655 (OUTLIER) cc_final: 0.4300 (m100) REVERT: H 100 TYR cc_start: 0.5834 (OUTLIER) cc_final: 0.5316 (m-80) REVERT: I 47 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6137 (tm) REVERT: I 88 CYS cc_start: 0.3739 (OUTLIER) cc_final: 0.1112 (p) outliers start: 145 outliers final: 95 residues processed: 347 average time/residue: 0.5129 time to fit residues: 218.1172 Evaluate side-chains 335 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 220 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 121 optimal weight: 0.5980 chunk 291 optimal weight: 0.5980 chunk 306 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 59 optimal weight: 0.0070 chunk 329 optimal weight: 10.0000 chunk 280 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 675 GLN D 100FASN B 81 ASN B 280 ASN B 544 ASN B 836 GLN C 394 ASN C1005 GLN ** I 90 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 = 0.3821 r_free = 0.3821 target = 0.155536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111791 restraints weight = 33004.793| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.90 r_work: 0.3091 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27019 Z= 0.120 Angle : 0.597 16.148 36847 Z= 0.304 Chirality : 0.046 0.599 4246 Planarity : 0.005 0.083 4678 Dihedral : 6.719 66.261 4222 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.26 % Favored : 94.59 % Rotamer: Outliers : 3.82 % Allowed : 22.58 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.76 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.14), residues: 3269 helix: 1.89 (0.20), residues: 667 sheet: -0.10 (0.18), residues: 747 loop : -1.25 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 577 TYR 0.024 0.001 TYR C 453 PHE 0.015 0.001 PHE H 100H TRP 0.013 0.001 TRP H 47 HIS 0.006 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00263 (26951) covalent geometry : angle 0.56357 (36684) SS BOND : bond 0.00343 ( 41) SS BOND : angle 1.62795 ( 82) hydrogen bonds : bond 0.03955 ( 1055) hydrogen bonds : angle 5.73405 ( 2829) link_NAG-ASN : bond 0.00538 ( 27) link_NAG-ASN : angle 3.92902 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 231 time to evaluate : 1.183 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: A 234 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7277 (t0) REVERT: A 358 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8545 (mm) REVERT: A 557 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7756 (mtmt) REVERT: A 564 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: A 994 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7896 (t70) REVERT: A 1073 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8241 (mtmm) REVERT: D 56 ASP cc_start: 0.6859 (m-30) cc_final: 0.6306 (m-30) REVERT: B 81 ASN cc_start: 0.7166 (p0) cc_final: 0.6614 (p0) REVERT: B 167 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7430 (p) REVERT: B 278 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8835 (ttpp) REVERT: B 321 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.5981 (pm20) REVERT: B 333 THR cc_start: 0.5553 (OUTLIER) cc_final: 0.5314 (m) REVERT: B 353 TRP cc_start: 0.6434 (p-90) cc_final: 0.5468 (p-90) REVERT: B 390 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7572 (mt) REVERT: B 429 PHE cc_start: 0.5618 (OUTLIER) cc_final: 0.5120 (p90) REVERT: B 532 ASN cc_start: 0.7010 (t0) cc_final: 0.6633 (m-40) REVERT: B 675 GLN cc_start: 0.7259 (tp40) cc_final: 0.6900 (tp-100) REVERT: B 745 ASP cc_start: 0.6748 (OUTLIER) cc_final: 0.6499 (p0) REVERT: B 811 LYS cc_start: 0.7045 (ptpt) cc_final: 0.6568 (mmtp) REVERT: C 97 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6179 (pptt) REVERT: C 314 GLN cc_start: 0.8781 (mt0) cc_final: 0.8342 (mm-40) REVERT: C 424 LYS cc_start: 0.8072 (tppp) cc_final: 0.7828 (tppt) REVERT: C 460 ASN cc_start: 0.7889 (m-40) cc_final: 0.7457 (m-40) REVERT: C 462 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7699 (mtpt) REVERT: C 516 GLU cc_start: 0.7488 (tt0) cc_final: 0.7279 (tt0) REVERT: C 529 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6546 (tmtm) REVERT: C 907 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8183 (t0) REVERT: C 1092 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6985 (pp20) REVERT: H 36 TRP cc_start: 0.4577 (OUTLIER) cc_final: 0.4282 (m100) REVERT: H 100 TYR cc_start: 0.5822 (OUTLIER) cc_final: 0.5185 (m-80) REVERT: I 47 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6100 (tm) outliers start: 108 outliers final: 71 residues processed: 314 average time/residue: 0.5213 time to fit residues: 199.6740 Evaluate side-chains 313 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 222 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 293 optimal weight: 3.9990 chunk 54 optimal weight: 0.0070 chunk 249 optimal weight: 0.5980 chunk 222 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 278 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 675 GLN B 280 ASN B 544 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.154986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.110026 restraints weight = 32876.319| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.70 r_work: 0.3106 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27019 Z= 0.140 Angle : 0.616 16.508 36847 Z= 0.314 Chirality : 0.047 0.607 4246 Planarity : 0.005 0.083 4678 Dihedral : 6.659 65.999 4219 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.35 % Favored : 94.49 % Rotamer: Outliers : 3.60 % Allowed : 22.90 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.76 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.14), residues: 3269 helix: 1.84 (0.20), residues: 673 sheet: -0.09 (0.18), residues: 754 loop : -1.21 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.025 0.001 TYR A 170 PHE 0.015 0.001 PHE E 62 TRP 0.013 0.001 TRP H 47 HIS 0.008 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00316 (26951) covalent geometry : angle 0.58042 (36684) SS BOND : bond 0.00331 ( 41) SS BOND : angle 1.33304 ( 82) hydrogen bonds : bond 0.04230 ( 1055) hydrogen bonds : angle 5.74960 ( 2829) link_NAG-ASN : bond 0.00510 ( 27) link_NAG-ASN : angle 4.25149 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 231 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7285 (tt0) REVERT: A 234 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7296 (t0) REVERT: A 358 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8536 (mm) REVERT: A 557 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7737 (mtmt) REVERT: A 564 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: A 994 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7841 (t70) REVERT: A 1073 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8244 (mtmm) REVERT: D 56 ASP cc_start: 0.6818 (m-30) cc_final: 0.6268 (m-30) REVERT: B 81 ASN cc_start: 0.7229 (p0) cc_final: 0.6706 (p0) REVERT: B 278 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8814 (ttpp) REVERT: B 321 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6005 (pm20) REVERT: B 333 THR cc_start: 0.5622 (OUTLIER) cc_final: 0.5347 (m) REVERT: B 353 TRP cc_start: 0.6492 (p-90) cc_final: 0.5446 (p-90) REVERT: B 357 ARG cc_start: 0.6700 (tmm-80) cc_final: 0.6177 (tmm-80) REVERT: B 390 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7573 (mt) REVERT: B 429 PHE cc_start: 0.5671 (OUTLIER) cc_final: 0.5194 (p90) REVERT: B 532 ASN cc_start: 0.6974 (t0) cc_final: 0.6596 (m-40) REVERT: B 675 GLN cc_start: 0.7242 (tp40) cc_final: 0.6854 (tp-100) REVERT: B 811 LYS cc_start: 0.7041 (ptpt) cc_final: 0.6608 (mmtp) REVERT: C 97 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6199 (pptt) REVERT: C 314 GLN cc_start: 0.8720 (mt0) cc_final: 0.8313 (mm-40) REVERT: C 424 LYS cc_start: 0.8054 (tppp) cc_final: 0.7815 (tppt) REVERT: C 460 ASN cc_start: 0.7916 (m-40) cc_final: 0.7483 (m-40) REVERT: C 462 LYS cc_start: 0.8097 (mtpp) cc_final: 0.7744 (mtpt) REVERT: C 516 GLU cc_start: 0.7408 (tt0) cc_final: 0.7176 (tt0) REVERT: C 529 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6488 (tmtm) REVERT: C 907 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8124 (t0) REVERT: C 1092 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6969 (pp20) REVERT: H 34 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5304 (mmt) REVERT: H 36 TRP cc_start: 0.4656 (OUTLIER) cc_final: 0.4334 (m100) REVERT: H 100 TYR cc_start: 0.5811 (OUTLIER) cc_final: 0.5264 (m-80) REVERT: I 47 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6061 (tm) outliers start: 102 outliers final: 69 residues processed: 310 average time/residue: 0.5216 time to fit residues: 195.3882 Evaluate side-chains 312 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 224 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 195 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 0.0370 chunk 24 optimal weight: 0.0980 chunk 231 optimal weight: 0.6980 chunk 248 optimal weight: 0.0670 chunk 253 optimal weight: 3.9990 chunk 188 optimal weight: 0.0370 chunk 309 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 overall best weight: 0.1874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 675 GLN A 955 ASN D 100FASN B 280 ASN B 544 ASN B 955 ASN C 121 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 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 = 0.3855 r_free = 0.3855 target = 0.158293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113985 restraints weight = 32818.586| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.70 r_work: 0.3160 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27019 Z= 0.102 Angle : 0.574 14.904 36847 Z= 0.290 Chirality : 0.045 0.554 4246 Planarity : 0.004 0.081 4678 Dihedral : 6.032 64.062 4215 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.47 % Favored : 95.38 % Rotamer: Outliers : 2.37 % Allowed : 24.13 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.15), residues: 3269 helix: 1.98 (0.20), residues: 680 sheet: 0.07 (0.18), residues: 760 loop : -1.09 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 577 TYR 0.024 0.001 TYR C 453 PHE 0.013 0.001 PHE C 456 TRP 0.014 0.001 TRP H 47 HIS 0.005 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00215 (26951) covalent geometry : angle 0.54503 (36684) SS BOND : bond 0.00221 ( 41) SS BOND : angle 0.99749 ( 82) hydrogen bonds : bond 0.03396 ( 1055) hydrogen bonds : angle 5.41644 ( 2829) link_NAG-ASN : bond 0.00573 ( 27) link_NAG-ASN : angle 3.78879 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10912.80 seconds wall clock time: 186 minutes 31.64 seconds (11191.64 seconds total)