Starting phenix.real_space_refine on Sun May 25 05:36:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3n_34470/05_2025/8h3n_34470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3n_34470/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h3n_34470/05_2025/8h3n_34470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3n_34470/05_2025/8h3n_34470.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3n_34470/05_2025/8h3n_34470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3n_34470/05_2025/8h3n_34470.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'TYR:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 7} 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'GLU:plan': 5, '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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'GLU:plan': 5, '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: 16.21, per 1000 atoms: 0.62 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: 6.15 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 4.00 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: 12.47 Time building geometry restraints manager: 7.25 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: 22.420 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 59.890 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.390 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (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 TRP 0.009 0.002 TRP D 103 HIS 0.008 0.001 HIS B 207 PHE 0.020 0.002 PHE C 186 TYR 0.027 0.002 TYR B 265 ARG 0.007 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00683 ( 27) link_NAG-ASN : angle 5.03072 ( 81) hydrogen bonds : bond 0.12934 ( 1055) hydrogen bonds : angle 7.57670 ( 2829) SS BOND : bond 0.00648 ( 41) SS BOND : angle 1.72741 ( 82) covalent geometry : bond 0.00917 (26951) covalent geometry : angle 0.86275 (36684) *********************** 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 : 2.796 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: 0.7881 (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: 0.9038 time to fit residues: 420.8557 Evaluate side-chains 347 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 242 time to evaluate : 2.684 ------------------------------------------------------------------------------- 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 279 optimal weight: 0.9990 chunk 250 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 259 optimal weight: 0.0050 chunk 100 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 300 optimal weight: 20.0000 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 505 HIS A 607 GLN A 675 GLN A1071 GLN A1101 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B1101 HIS C 66 HIS C 121 ASN C 394 ASN C 450 ASN C 755 GLN C1071 GLN C1083 HIS H 79 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.154326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110022 restraints weight = 32871.355| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.89 r_work: 0.3064 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27019 Z= 0.156 Angle : 0.660 17.544 36847 Z= 0.338 Chirality : 0.048 0.594 4246 Planarity : 0.005 0.158 4678 Dihedral : 9.504 73.228 4334 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.84 % Favored : 93.97 % Rotamer: Outliers : 5.62 % Allowed : 20.32 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3269 helix: 1.53 (0.20), residues: 681 sheet: -0.53 (0.18), residues: 760 loop : -1.53 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.009 0.001 HIS B 505 PHE 0.019 0.001 PHE H 100H TYR 0.027 0.001 TYR I 94 ARG 0.004 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 27) link_NAG-ASN : angle 4.17324 ( 81) hydrogen bonds : bond 0.04664 ( 1055) hydrogen bonds : angle 6.21200 ( 2829) SS BOND : bond 0.00492 ( 41) SS BOND : angle 1.54967 ( 82) covalent geometry : bond 0.00353 (26951) covalent geometry : angle 0.62733 (36684) *********************** 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 429 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 270 time to evaluate : 2.807 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 126 VAL cc_start: 0.7964 (p) cc_final: 0.7732 (t) REVERT: A 186 PHE cc_start: 0.4594 (OUTLIER) cc_final: 0.3793 (t80) REVERT: A 470 THR cc_start: 0.8180 (p) cc_final: 0.7962 (p) REVERT: A 994 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7893 (t70) REVERT: E 4 MET cc_start: 0.3715 (mmp) cc_final: 0.2989 (tmt) REVERT: B 278 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8874 (ttpp) REVERT: B 321 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.5914 (pm20) REVERT: B 429 PHE cc_start: 0.5766 (OUTLIER) cc_final: 0.5392 (p90) REVERT: B 440 LYS cc_start: 0.4999 (tptt) cc_final: 0.4258 (ttpp) REVERT: B 811 LYS cc_start: 0.7080 (ptpt) cc_final: 0.6531 (mmtp) REVERT: C 108 THR cc_start: 0.7468 (p) cc_final: 0.7214 (m) REVERT: C 516 GLU cc_start: 0.7361 (tt0) cc_final: 0.7018 (tt0) REVERT: C 1002 GLN cc_start: 0.8374 (tt0) cc_final: 0.7840 (tm-30) REVERT: H 100 TYR cc_start: 0.5764 (OUTLIER) cc_final: 0.5330 (m-80) outliers start: 159 outliers final: 82 residues processed: 398 average time/residue: 0.9501 time to fit residues: 468.1566 Evaluate side-chains 330 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 242 time to evaluate : 2.707 ------------------------------------------------------------------------------- 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 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 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 167 THR 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 320 VAL Chi-restraints excluded: chain B residue 321 GLN 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 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 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 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 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 81 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 244 optimal weight: 0.0770 chunk 53 optimal weight: 2.9990 chunk 326 optimal weight: 0.5980 chunk 69 optimal weight: 0.0270 chunk 173 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 675 GLN A 935 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN C 394 ASN C 755 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.109179 restraints weight = 32766.902| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.67 r_work: 0.3092 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27019 Z= 0.162 Angle : 0.631 17.640 36847 Z= 0.323 Chirality : 0.048 0.596 4246 Planarity : 0.005 0.123 4678 Dihedral : 8.074 68.509 4262 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.16 % Rotamer: Outliers : 6.08 % Allowed : 19.43 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3269 helix: 1.69 (0.20), residues: 676 sheet: -0.37 (0.18), residues: 754 loop : -1.40 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.006 0.001 HIS B 505 PHE 0.018 0.001 PHE E 62 TYR 0.022 0.002 TYR I 94 ARG 0.005 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 27) link_NAG-ASN : angle 4.01701 ( 81) hydrogen bonds : bond 0.04621 ( 1055) hydrogen bonds : angle 6.01313 ( 2829) SS BOND : bond 0.00335 ( 41) SS BOND : angle 1.48434 ( 82) covalent geometry : bond 0.00370 (26951) covalent geometry : angle 0.59961 (36684) *********************** 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 427 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 255 time to evaluate : 3.300 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: 0.7676 (OUTLIER) cc_final: 0.7383 (t0) REVERT: A 122 ASN cc_start: 0.5628 (OUTLIER) cc_final: 0.4985 (p0) REVERT: A 126 VAL cc_start: 0.7857 (p) cc_final: 0.7636 (t) REVERT: A 358 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8481 (mm) REVERT: A 470 THR cc_start: 0.8193 (p) cc_final: 0.7984 (p) REVERT: A 557 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7792 (mtmt) REVERT: A 755 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7327 (mt0) REVERT: A 994 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7803 (t70) REVERT: A 1084 ASP cc_start: 0.6806 (t0) cc_final: 0.6566 (OUTLIER) REVERT: E 4 MET cc_start: 0.3662 (mmp) cc_final: 0.3350 (tpp) REVERT: B 278 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8822 (ttpp) REVERT: B 280 ASN cc_start: 0.7374 (t0) cc_final: 0.7103 (t0) REVERT: B 321 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.5972 (pm20) REVERT: B 390 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7692 (mt) REVERT: B 429 PHE cc_start: 0.5613 (OUTLIER) cc_final: 0.5260 (p90) REVERT: B 440 LYS cc_start: 0.5088 (tptt) cc_final: 0.4360 (ttpp) REVERT: B 532 ASN cc_start: 0.6686 (t0) cc_final: 0.6271 (m-40) REVERT: B 811 LYS cc_start: 0.7011 (ptpt) cc_final: 0.6589 (mmtp) REVERT: C 108 THR cc_start: 0.7448 (p) cc_final: 0.7135 (m) REVERT: C 134 GLN cc_start: 0.5483 (tt0) cc_final: 0.4917 (pm20) REVERT: C 281 GLU cc_start: 0.7661 (pm20) cc_final: 0.7446 (pm20) REVERT: C 314 GLN cc_start: 0.8772 (mt0) cc_final: 0.8317 (mm-40) REVERT: C 907 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8198 (t0) REVERT: C 1002 GLN cc_start: 0.8272 (tt0) cc_final: 0.7756 (tm-30) REVERT: H 100 TYR cc_start: 0.5757 (OUTLIER) cc_final: 0.5234 (m-80) REVERT: I 47 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6279 (tm) REVERT: I 88 CYS cc_start: 0.3789 (OUTLIER) cc_final: 0.1214 (p) outliers start: 172 outliers final: 94 residues processed: 396 average time/residue: 0.9021 time to fit residues: 443.9436 Evaluate side-chains 345 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 238 time to evaluate : 2.860 ------------------------------------------------------------------------------- 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 122 ASN 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 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 557 LYS 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 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 57 ILE Chi-restraints excluded: chain D residue 100 SER 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 208 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 524 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 537 LYS 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 827 THR Chi-restraints excluded: chain B residue 911 VAL 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 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 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 434 ILE 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 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 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 Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 21 optimal weight: 0.0040 chunk 85 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 202 optimal weight: 2.9990 chunk 279 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 E 6 GLN B 544 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110652 restraints weight = 33208.780| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.98 r_work: 0.3086 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1434 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= 0.126 Angle : 0.585 16.280 36847 Z= 0.299 Chirality : 0.046 0.570 4246 Planarity : 0.005 0.094 4678 Dihedral : 7.213 67.458 4249 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % Rotamer: Outliers : 4.98 % Allowed : 20.46 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3269 helix: 1.88 (0.20), residues: 672 sheet: -0.33 (0.18), residues: 755 loop : -1.29 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.004 0.001 HIS B 505 PHE 0.016 0.001 PHE B 400 TYR 0.023 0.001 TYR C 453 ARG 0.005 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 27) link_NAG-ASN : angle 3.84042 ( 81) hydrogen bonds : bond 0.04076 ( 1055) hydrogen bonds : angle 5.78097 ( 2829) SS BOND : bond 0.00294 ( 41) SS BOND : angle 1.39988 ( 82) covalent geometry : bond 0.00275 (26951) covalent geometry : angle 0.55388 (36684) *********************** 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 393 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 252 time to evaluate : 2.938 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 88 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7444 (t0) REVERT: A 234 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7322 (t0) REVERT: A 358 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8516 (mm) REVERT: A 470 THR cc_start: 0.8189 (p) cc_final: 0.7984 (p) REVERT: A 564 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7488 (tm-30) REVERT: A 755 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7328 (mt0) REVERT: A 994 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7906 (t70) REVERT: B 81 ASN cc_start: 0.7076 (p0) cc_final: 0.6585 (p0) REVERT: B 278 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8863 (ttpp) REVERT: B 280 ASN cc_start: 0.7443 (t0) cc_final: 0.7214 (t0) REVERT: B 321 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.5946 (pm20) REVERT: B 390 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7734 (mt) REVERT: B 429 PHE cc_start: 0.5620 (OUTLIER) cc_final: 0.5270 (p90) REVERT: B 440 LYS cc_start: 0.5156 (tptt) cc_final: 0.4429 (ttpp) REVERT: B 532 ASN cc_start: 0.6730 (t0) cc_final: 0.6300 (m-40) REVERT: B 811 LYS cc_start: 0.6988 (ptpt) cc_final: 0.6542 (mmtp) REVERT: B 836 GLN cc_start: 0.6872 (mt0) cc_final: 0.6633 (mm-40) REVERT: C 281 GLU cc_start: 0.7761 (pm20) cc_final: 0.7523 (pm20) REVERT: C 314 GLN cc_start: 0.8828 (mt0) cc_final: 0.8378 (mm-40) REVERT: C 462 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7702 (mtmt) REVERT: C 516 GLU cc_start: 0.7454 (tt0) cc_final: 0.7251 (tt0) REVERT: C 907 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8170 (t0) REVERT: H 100 TYR cc_start: 0.5822 (OUTLIER) cc_final: 0.5285 (m-80) REVERT: I 47 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6179 (tm) outliers start: 141 outliers final: 75 residues processed: 361 average time/residue: 0.9612 time to fit residues: 429.8571 Evaluate side-chains 323 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 235 time to evaluate : 3.211 ------------------------------------------------------------------------------- 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 210 ILE Chi-restraints excluded: chain A residue 234 ASN 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 564 GLN Chi-restraints excluded: chain A residue 588 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 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 2 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 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 537 LYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 602 THR 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 1038 LYS 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 C residue 41 LYS Chi-restraints excluded: chain C residue 110 LEU 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 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 469 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 704 SER Chi-restraints excluded: chain C residue 758 SER 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 976 VAL 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 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 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 249 optimal weight: 0.1980 chunk 17 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 301 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 B 544 ASN C 460 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 = 0.155124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.110459 restraints weight = 32872.076| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.88 r_work: 0.3074 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27019 Z= 0.147 Angle : 0.609 17.124 36847 Z= 0.311 Chirality : 0.047 0.549 4246 Planarity : 0.005 0.091 4678 Dihedral : 6.971 67.162 4234 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 5.34 % Allowed : 20.42 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3269 helix: 1.85 (0.20), residues: 672 sheet: -0.29 (0.18), residues: 766 loop : -1.27 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS D 35 PHE 0.017 0.001 PHE E 62 TYR 0.025 0.002 TYR C 453 ARG 0.004 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 27) link_NAG-ASN : angle 3.93222 ( 81) hydrogen bonds : bond 0.04347 ( 1055) hydrogen bonds : angle 5.81078 ( 2829) SS BOND : bond 0.00317 ( 41) SS BOND : angle 1.48052 ( 82) covalent geometry : bond 0.00333 (26951) covalent geometry : angle 0.57734 (36684) *********************** 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 392 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 241 time to evaluate : 2.701 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: 0.7668 (OUTLIER) cc_final: 0.7365 (t0) REVERT: A 165 ASN cc_start: 0.5564 (OUTLIER) cc_final: 0.4996 (p0) REVERT: A 234 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7380 (t0) REVERT: A 242 LEU cc_start: 0.6815 (mt) cc_final: 0.6584 (mm) REVERT: A 282 ASN cc_start: 0.7952 (p0) cc_final: 0.7303 (t0) REVERT: A 358 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8549 (mm) REVERT: A 557 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.7785 (mtmt) REVERT: A 564 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: A 755 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7303 (mt0) REVERT: A 994 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7961 (t70) REVERT: A 1073 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8253 (mtmm) REVERT: D 56 ASP cc_start: 0.6801 (m-30) cc_final: 0.6291 (m-30) REVERT: B 81 ASN cc_start: 0.7126 (p0) cc_final: 0.6621 (p0) REVERT: B 110 LEU cc_start: 0.8400 (mt) cc_final: 0.8178 (mm) REVERT: B 278 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8856 (ttpp) REVERT: B 321 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.5967 (pm20) REVERT: B 390 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7704 (mt) REVERT: B 400 PHE cc_start: 0.7790 (p90) cc_final: 0.7488 (p90) REVERT: B 429 PHE cc_start: 0.5677 (OUTLIER) cc_final: 0.5266 (p90) REVERT: B 440 LYS cc_start: 0.5104 (tptt) cc_final: 0.4362 (ttpp) REVERT: B 532 ASN cc_start: 0.6911 (t0) cc_final: 0.6474 (m-40) REVERT: B 745 ASP cc_start: 0.6471 (OUTLIER) cc_final: 0.6257 (p0) REVERT: B 811 LYS cc_start: 0.7016 (ptpt) cc_final: 0.6553 (mmtp) REVERT: C 281 GLU cc_start: 0.7768 (pm20) cc_final: 0.7527 (pm20) REVERT: C 314 GLN cc_start: 0.8792 (mt0) cc_final: 0.8379 (mm-40) REVERT: C 394 ASN cc_start: 0.6024 (OUTLIER) cc_final: 0.5804 (t0) REVERT: C 424 LYS cc_start: 0.8048 (tppp) cc_final: 0.7788 (tppt) REVERT: C 462 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7736 (mtmt) REVERT: C 516 GLU cc_start: 0.7502 (tt0) cc_final: 0.7275 (tt0) REVERT: C 907 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8190 (t0) REVERT: C 1092 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6920 (pp20) REVERT: H 100 TYR cc_start: 0.5873 (OUTLIER) cc_final: 0.4966 (m-80) REVERT: I 47 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6158 (tm) outliers start: 151 outliers final: 92 residues processed: 363 average time/residue: 0.9064 time to fit residues: 407.0030 Evaluate side-chains 344 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 233 time to evaluate : 2.699 ------------------------------------------------------------------------------- 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 131 CYS 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 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 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 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 1073 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 E residue 2 ILE 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 208 THR Chi-restraints excluded: chain B residue 210 ILE 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 393 THR Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 552 LEU 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 929 SER 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 302 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 434 ILE 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 758 SER 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 1092 GLU 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 57 ILE 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 32 optimal weight: 3.9990 chunk 74 optimal weight: 0.0770 chunk 90 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 311 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 268 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 230 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 81 ASN B 544 ASN B 836 GLN C 460 ASN ** 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 = 0.3834 r_free = 0.3834 target = 0.156382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.112623 restraints weight = 32777.938| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.94 r_work: 0.3095 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27019 Z= 0.119 Angle : 0.579 15.968 36847 Z= 0.294 Chirality : 0.046 0.551 4246 Planarity : 0.004 0.084 4678 Dihedral : 6.589 66.633 4228 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.04 % Rotamer: Outliers : 4.35 % Allowed : 21.27 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3269 helix: 1.95 (0.20), residues: 672 sheet: -0.16 (0.18), residues: 761 loop : -1.22 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.004 0.001 HIS D 35 PHE 0.014 0.001 PHE H 100H TYR 0.024 0.001 TYR C 453 ARG 0.003 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 27) link_NAG-ASN : angle 3.96624 ( 81) hydrogen bonds : bond 0.03915 ( 1055) hydrogen bonds : angle 5.64827 ( 2829) SS BOND : bond 0.00291 ( 41) SS BOND : angle 1.31585 ( 82) covalent geometry : bond 0.00262 (26951) covalent geometry : angle 0.54574 (36684) *********************** 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 372 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 249 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7770 (t) REVERT: A 165 ASN cc_start: 0.5489 (OUTLIER) cc_final: 0.4694 (m110) REVERT: A 207 HIS cc_start: 0.7717 (t-90) cc_final: 0.7111 (t-170) REVERT: A 234 ASN cc_start: 0.7907 (p0) cc_final: 0.7423 (t0) REVERT: A 282 ASN cc_start: 0.7842 (p0) cc_final: 0.7236 (t0) REVERT: A 557 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7787 (mtmt) REVERT: A 564 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: A 994 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7949 (t70) REVERT: D 56 ASP cc_start: 0.6781 (m-30) cc_final: 0.6297 (m-30) REVERT: E 4 MET cc_start: 0.3469 (tpp) cc_final: 0.2959 (tpp) REVERT: B 81 ASN cc_start: 0.7140 (p0) cc_final: 0.6589 (p0) REVERT: B 167 THR cc_start: 0.7687 (OUTLIER) cc_final: 0.7466 (p) REVERT: B 278 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8852 (ttpp) REVERT: B 321 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6465 (pt0) REVERT: B 390 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7574 (mt) REVERT: B 400 PHE cc_start: 0.7791 (p90) cc_final: 0.7537 (p90) REVERT: B 429 PHE cc_start: 0.5568 (OUTLIER) cc_final: 0.5207 (p90) REVERT: B 440 LYS cc_start: 0.5047 (tptt) cc_final: 0.4362 (ttpp) REVERT: B 532 ASN cc_start: 0.6950 (t0) cc_final: 0.6532 (m-40) REVERT: B 811 LYS cc_start: 0.6984 (ptpt) cc_final: 0.6553 (mmtp) REVERT: C 41 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8125 (mtmm) REVERT: C 97 LYS cc_start: 0.6732 (tmmt) cc_final: 0.6383 (tmtt) REVERT: C 234 ASN cc_start: 0.6916 (OUTLIER) cc_final: 0.6468 (p0) REVERT: C 281 GLU cc_start: 0.7789 (pm20) cc_final: 0.7572 (pm20) REVERT: C 314 GLN cc_start: 0.8795 (mt0) cc_final: 0.8366 (mm-40) REVERT: C 424 LYS cc_start: 0.8075 (tppp) cc_final: 0.7806 (tppt) REVERT: C 462 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7730 (mtpt) REVERT: C 508 TYR cc_start: 0.7578 (m-80) cc_final: 0.7340 (m-80) REVERT: C 516 GLU cc_start: 0.7485 (tt0) cc_final: 0.7270 (tt0) REVERT: C 529 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6519 (tmtm) REVERT: C 1092 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6937 (pp20) REVERT: H 100 TYR cc_start: 0.5749 (OUTLIER) cc_final: 0.5165 (m-80) REVERT: I 47 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6123 (tm) outliers start: 123 outliers final: 67 residues processed: 350 average time/residue: 0.9614 time to fit residues: 410.6965 Evaluate side-chains 319 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 236 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR 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 323 THR 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 557 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR 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 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 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE 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 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 709 ASN 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 1128 VAL 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 227 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 302 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 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 1092 GLU Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 324 optimal weight: 1.9990 chunk 315 optimal weight: 10.0000 chunk 179 optimal weight: 0.8980 chunk 291 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 A1135 ASN B 544 ASN C 121 ASN C 207 HIS C 460 ASN C1005 GLN ** 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 = 0.3806 r_free = 0.3806 target = 0.154093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.109560 restraints weight = 32917.645| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.85 r_work: 0.3055 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27019 Z= 0.196 Angle : 0.654 17.031 36847 Z= 0.334 Chirality : 0.049 0.587 4246 Planarity : 0.005 0.085 4678 Dihedral : 6.880 69.317 4217 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.84 % Favored : 94.00 % Rotamer: Outliers : 5.09 % Allowed : 20.95 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3269 helix: 1.80 (0.20), residues: 665 sheet: -0.23 (0.18), residues: 770 loop : -1.24 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.005 0.001 HIS D 35 PHE 0.023 0.002 PHE E 62 TYR 0.024 0.002 TYR C 453 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 27) link_NAG-ASN : angle 4.33004 ( 81) hydrogen bonds : bond 0.04842 ( 1055) hydrogen bonds : angle 5.91890 ( 2829) SS BOND : bond 0.00408 ( 41) SS BOND : angle 1.58085 ( 82) covalent geometry : bond 0.00453 (26951) covalent geometry : angle 0.61865 (36684) *********************** 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 389 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 245 time to evaluate : 2.966 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 88 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7404 (t0) REVERT: A 234 ASN cc_start: 0.7953 (p0) cc_final: 0.7395 (t0) REVERT: A 557 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7775 (mtmt) REVERT: A 564 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: A 755 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7409 (mt0) REVERT: A 759 PHE cc_start: 0.7450 (m-80) cc_final: 0.7091 (m-80) REVERT: A 994 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7942 (t70) REVERT: A 1073 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8244 (mtmm) REVERT: D 56 ASP cc_start: 0.6850 (m-30) cc_final: 0.6261 (m-30) REVERT: B 81 ASN cc_start: 0.7246 (p0) cc_final: 0.6731 (p0) REVERT: B 278 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8906 (ttpp) REVERT: B 321 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6025 (pm20) REVERT: B 390 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7675 (mt) REVERT: B 429 PHE cc_start: 0.5779 (OUTLIER) cc_final: 0.5398 (p90) REVERT: B 440 LYS cc_start: 0.5049 (tptt) cc_final: 0.4312 (ttpp) REVERT: B 532 ASN cc_start: 0.6909 (t0) cc_final: 0.6507 (m-40) REVERT: C 97 LYS cc_start: 0.6788 (OUTLIER) cc_final: 0.6393 (tmtt) REVERT: C 234 ASN cc_start: 0.7013 (OUTLIER) cc_final: 0.6477 (p0) REVERT: C 281 GLU cc_start: 0.7803 (pm20) cc_final: 0.7576 (pm20) REVERT: C 314 GLN cc_start: 0.8804 (mt0) cc_final: 0.8378 (mm-40) REVERT: C 424 LYS cc_start: 0.8037 (tppp) cc_final: 0.7788 (tppt) REVERT: C 460 ASN cc_start: 0.7828 (m-40) cc_final: 0.7343 (m-40) REVERT: C 462 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7692 (mtpt) REVERT: C 516 GLU cc_start: 0.7564 (tt0) cc_final: 0.7358 (tt0) REVERT: C 529 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6534 (tmtm) REVERT: C 907 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8260 (t0) REVERT: C 1002 GLN cc_start: 0.8362 (tt0) cc_final: 0.7865 (tm-30) REVERT: H 100 TYR cc_start: 0.5823 (OUTLIER) cc_final: 0.5143 (m-80) REVERT: I 47 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6043 (tm) outliers start: 144 outliers final: 95 residues processed: 358 average time/residue: 0.9585 time to fit residues: 423.9568 Evaluate side-chains 350 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 239 time to evaluate : 2.634 ------------------------------------------------------------------------------- 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 131 CYS 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 236 THR Chi-restraints excluded: chain A residue 323 THR 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 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 632 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN 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 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 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 208 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 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 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 827 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 929 SER 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 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 234 ASN 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 434 ILE 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 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 758 SER 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 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 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 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 209 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 314 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 226 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 319 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 625 HIS A 628 GLN A 675 GLN A 935 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111223 restraints weight = 32820.626| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.85 r_work: 0.3086 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27019 Z= 0.136 Angle : 0.596 16.141 36847 Z= 0.304 Chirality : 0.047 0.575 4246 Planarity : 0.005 0.082 4678 Dihedral : 6.541 68.074 4215 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.20 % Favored : 94.68 % Rotamer: Outliers : 4.42 % Allowed : 21.84 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3269 helix: 1.86 (0.20), residues: 672 sheet: -0.12 (0.18), residues: 762 loop : -1.19 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.006 0.001 HIS D 35 PHE 0.017 0.001 PHE C 392 TYR 0.024 0.001 TYR C 453 ARG 0.004 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 27) link_NAG-ASN : angle 3.92669 ( 81) hydrogen bonds : bond 0.04187 ( 1055) hydrogen bonds : angle 5.72821 ( 2829) SS BOND : bond 0.00315 ( 41) SS BOND : angle 1.20807 ( 82) covalent geometry : bond 0.00307 (26951) covalent geometry : angle 0.56549 (36684) *********************** 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 361 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 236 time to evaluate : 2.909 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: 0.7651 (OUTLIER) cc_final: 0.7367 (t0) REVERT: A 207 HIS cc_start: 0.7705 (t-90) cc_final: 0.7112 (t-170) REVERT: A 234 ASN cc_start: 0.7922 (p0) cc_final: 0.7411 (t0) REVERT: A 282 ASN cc_start: 0.7786 (p0) cc_final: 0.7184 (t0) REVERT: A 557 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7789 (mtmt) REVERT: A 564 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: A 624 ILE cc_start: 0.6075 (OUTLIER) cc_final: 0.5778 (mt) REVERT: A 628 GLN cc_start: 0.5698 (OUTLIER) cc_final: 0.5496 (tt0) REVERT: A 755 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: A 994 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7942 (t70) REVERT: A 1073 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8221 (mtmm) REVERT: D 56 ASP cc_start: 0.6821 (m-30) cc_final: 0.6252 (m-30) REVERT: B 81 ASN cc_start: 0.7232 (p0) cc_final: 0.6727 (p0) REVERT: B 278 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8843 (ttpp) REVERT: B 321 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6018 (pm20) REVERT: B 390 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7622 (mt) REVERT: B 429 PHE cc_start: 0.5635 (OUTLIER) cc_final: 0.5256 (p90) REVERT: B 532 ASN cc_start: 0.6961 (t0) cc_final: 0.6573 (m-40) REVERT: B 811 LYS cc_start: 0.7047 (ptpt) cc_final: 0.6592 (mmtp) REVERT: C 97 LYS cc_start: 0.6701 (OUTLIER) cc_final: 0.6212 (pptt) REVERT: C 234 ASN cc_start: 0.7020 (OUTLIER) cc_final: 0.6498 (p0) REVERT: C 314 GLN cc_start: 0.8782 (mt0) cc_final: 0.8369 (mm-40) REVERT: C 424 LYS cc_start: 0.8060 (tppp) cc_final: 0.7830 (tppt) REVERT: C 460 ASN cc_start: 0.7891 (m-40) cc_final: 0.7448 (m-40) REVERT: C 462 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7751 (mtpt) REVERT: C 516 GLU cc_start: 0.7485 (tt0) cc_final: 0.7281 (tt0) REVERT: C 529 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6532 (tmtm) REVERT: C 907 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8184 (t0) REVERT: C 1092 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6981 (pp20) REVERT: H 100 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.5191 (m-80) REVERT: I 47 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6001 (tm) REVERT: I 88 CYS cc_start: 0.3709 (OUTLIER) cc_final: 0.1108 (p) outliers start: 125 outliers final: 82 residues processed: 335 average time/residue: 0.9755 time to fit residues: 399.9821 Evaluate side-chains 332 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 230 time to evaluate : 2.914 ------------------------------------------------------------------------------- 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 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 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER 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 628 GLN 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 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 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 105 GLU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 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 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 620 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 929 SER 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 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 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 234 ASN Chi-restraints excluded: chain C residue 302 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 581 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 758 SER 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 1030 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1125 ASN 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 75 LYS Chi-restraints excluded: chain H residue 100 TYR 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 20 optimal weight: 0.6980 chunk 302 optimal weight: 0.9990 chunk 263 optimal weight: 0.8980 chunk 237 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 206 optimal weight: 0.5980 chunk 225 optimal weight: 5.9990 chunk 158 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 628 GLN A 675 GLN B 280 ASN B 544 ASN C 81 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.156320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111210 restraints weight = 32859.868| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.92 r_work: 0.3097 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27019 Z= 0.123 Angle : 0.590 15.834 36847 Z= 0.300 Chirality : 0.046 0.566 4246 Planarity : 0.005 0.083 4678 Dihedral : 6.354 67.511 4214 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.14 % Favored : 94.74 % Rotamer: Outliers : 3.89 % Allowed : 22.33 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 3269 helix: 1.88 (0.20), residues: 678 sheet: -0.08 (0.18), residues: 766 loop : -1.15 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.006 0.001 HIS D 35 PHE 0.017 0.001 PHE C 392 TYR 0.024 0.001 TYR C 453 ARG 0.003 0.000 ARG C 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 27) link_NAG-ASN : angle 3.79320 ( 81) hydrogen bonds : bond 0.03998 ( 1055) hydrogen bonds : angle 5.65621 ( 2829) SS BOND : bond 0.00374 ( 41) SS BOND : angle 1.73976 ( 82) covalent geometry : bond 0.00274 (26951) covalent geometry : angle 0.55733 (36684) *********************** 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 341 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 231 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7701 (t-90) cc_final: 0.7127 (t-170) REVERT: A 234 ASN cc_start: 0.7882 (p0) cc_final: 0.7433 (t0) REVERT: A 282 ASN cc_start: 0.7763 (p0) cc_final: 0.7174 (t0) REVERT: A 557 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7779 (mtmt) REVERT: A 564 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: A 994 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7937 (t70) REVERT: A 1073 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8230 (mtmm) REVERT: D 25 SER cc_start: 0.7412 (t) cc_final: 0.7065 (m) REVERT: D 56 ASP cc_start: 0.6801 (m-30) cc_final: 0.6299 (m-30) REVERT: B 81 ASN cc_start: 0.7230 (p0) cc_final: 0.6719 (p0) REVERT: B 167 THR cc_start: 0.7677 (OUTLIER) cc_final: 0.7455 (p) REVERT: B 278 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8841 (ttpp) REVERT: B 321 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6008 (pm20) REVERT: B 390 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7501 (tt) REVERT: B 429 PHE cc_start: 0.5646 (OUTLIER) cc_final: 0.5187 (p90) REVERT: B 811 LYS cc_start: 0.7030 (ptpt) cc_final: 0.6595 (mmtp) REVERT: C 41 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8124 (mtmm) REVERT: C 97 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.6190 (pptt) REVERT: C 234 ASN cc_start: 0.7015 (OUTLIER) cc_final: 0.6509 (p0) REVERT: C 314 GLN cc_start: 0.8771 (mt0) cc_final: 0.8362 (mm-40) REVERT: C 394 ASN cc_start: 0.6538 (t0) cc_final: 0.6294 (t0) REVERT: C 424 LYS cc_start: 0.8073 (tppp) cc_final: 0.7838 (tppt) REVERT: C 460 ASN cc_start: 0.7943 (m-40) cc_final: 0.7530 (m-40) REVERT: C 462 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7730 (mtpt) REVERT: C 529 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6498 (tmtm) REVERT: C 907 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8156 (t0) REVERT: C 1092 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6943 (pp20) REVERT: I 47 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6007 (tm) outliers start: 110 outliers final: 79 residues processed: 320 average time/residue: 0.9871 time to fit residues: 386.8924 Evaluate side-chains 321 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 226 time to evaluate : 2.700 ------------------------------------------------------------------------------- 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 323 THR 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 500 THR 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 632 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 E residue 20 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE 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 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 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 620 VAL 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 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1122 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 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 234 ASN Chi-restraints excluded: chain C residue 302 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 754 LEU Chi-restraints excluded: chain C residue 758 SER 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 1030 SER Chi-restraints excluded: chain C residue 1092 GLU 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 I residue 47 LEU Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 87 TYR 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 0 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 77 optimal weight: 0.0870 chunk 79 optimal weight: 0.8980 chunk 301 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN B 280 ASN B 544 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.154506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110235 restraints weight = 32787.509| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.78 r_work: 0.3063 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27019 Z= 0.173 Angle : 0.638 18.215 36847 Z= 0.325 Chirality : 0.048 0.522 4246 Planarity : 0.005 0.082 4678 Dihedral : 6.545 67.727 4208 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.78 % Favored : 94.10 % Rotamer: Outliers : 3.67 % Allowed : 22.47 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3269 helix: 1.79 (0.20), residues: 673 sheet: -0.10 (0.18), residues: 752 loop : -1.17 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.006 0.001 HIS D 35 PHE 0.019 0.002 PHE E 62 TYR 0.026 0.002 TYR A 170 ARG 0.003 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 27) link_NAG-ASN : angle 4.42822 ( 81) hydrogen bonds : bond 0.04576 ( 1055) hydrogen bonds : angle 5.81434 ( 2829) SS BOND : bond 0.00416 ( 41) SS BOND : angle 1.49024 ( 82) covalent geometry : bond 0.00399 (26951) covalent geometry : angle 0.60023 (36684) ********************** 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 328 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 224 time to evaluate : 3.005 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: 0.7677 (OUTLIER) cc_final: 0.7367 (t0) REVERT: A 234 ASN cc_start: 0.7889 (p0) cc_final: 0.7407 (t0) REVERT: A 557 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.7798 (mtmt) REVERT: A 564 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: A 624 ILE cc_start: 0.6006 (OUTLIER) cc_final: 0.5747 (mt) REVERT: A 994 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7972 (t70) REVERT: A 1073 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8273 (mtmm) REVERT: D 56 ASP cc_start: 0.6885 (m-30) cc_final: 0.6314 (m-30) REVERT: B 81 ASN cc_start: 0.7310 (p0) cc_final: 0.6781 (p0) REVERT: B 278 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8864 (ttpp) REVERT: B 321 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6027 (pm20) REVERT: B 357 ARG cc_start: 0.6710 (tmm-80) cc_final: 0.6098 (tmm-80) REVERT: B 390 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7584 (mt) REVERT: B 429 PHE cc_start: 0.5759 (OUTLIER) cc_final: 0.5321 (p90) REVERT: B 811 LYS cc_start: 0.7079 (ptpt) cc_final: 0.6592 (mmtp) REVERT: C 97 LYS cc_start: 0.6719 (OUTLIER) cc_final: 0.6260 (pptt) REVERT: C 234 ASN cc_start: 0.6956 (OUTLIER) cc_final: 0.6517 (p0) REVERT: C 314 GLN cc_start: 0.8818 (mt0) cc_final: 0.8386 (mm-40) REVERT: C 394 ASN cc_start: 0.6597 (t0) cc_final: 0.6387 (t0) REVERT: C 424 LYS cc_start: 0.8060 (tppp) cc_final: 0.7832 (tppt) REVERT: C 460 ASN cc_start: 0.7957 (m-40) cc_final: 0.7543 (m-40) REVERT: C 462 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7744 (mtpt) REVERT: C 529 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6511 (tmtm) REVERT: C 907 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8280 (t0) REVERT: H 22 CYS cc_start: 0.3089 (OUTLIER) cc_final: 0.2868 (t) REVERT: I 47 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.5971 (tm) outliers start: 104 outliers final: 79 residues processed: 310 average time/residue: 0.9846 time to fit residues: 373.5258 Evaluate side-chains 317 residues out of total 2932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 222 time to evaluate : 2.754 ------------------------------------------------------------------------------- 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 376 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 500 THR 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 632 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 850 ILE 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 20 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 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 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 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 620 VAL 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 1038 LYS Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1122 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 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 234 ASN Chi-restraints excluded: chain C residue 302 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 754 LEU Chi-restraints excluded: chain C residue 758 SER 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 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 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 87 TYR 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 286 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 280 ASN B 544 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.153797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.108862 restraints weight = 32815.409| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.67 r_work: 0.3075 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27019 Z= 0.195 Angle : 0.665 17.940 36847 Z= 0.340 Chirality : 0.049 0.565 4246 Planarity : 0.005 0.083 4678 Dihedral : 6.699 67.940 4205 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.94 % Rotamer: Outliers : 4.03 % Allowed : 22.08 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.76 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3269 helix: 1.73 (0.20), residues: 670 sheet: -0.16 (0.18), residues: 782 loop : -1.20 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 52A HIS 0.008 0.001 HIS D 35 PHE 0.022 0.002 PHE E 62 TYR 0.027 0.002 TYR A 170 ARG 0.004 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 27) link_NAG-ASN : angle 4.50318 ( 81) hydrogen bonds : bond 0.04814 ( 1055) hydrogen bonds : angle 5.92507 ( 2829) SS BOND : bond 0.00432 ( 41) SS BOND : angle 1.67400 ( 82) covalent geometry : bond 0.00454 (26951) covalent geometry : angle 0.62681 (36684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20890.14 seconds wall clock time: 362 minutes 12.18 seconds (21732.18 seconds total)