Starting phenix.real_space_refine on Fri Mar 6 11:55:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a94_11684/03_2026/7a94_11684.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a94_11684/03_2026/7a94_11684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7a94_11684/03_2026/7a94_11684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a94_11684/03_2026/7a94_11684.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a94_11684/03_2026/7a94_11684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a94_11684/03_2026/7a94_11684.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 143 5.16 5 C 19433 2.51 5 N 5046 2.21 5 O 5840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 258 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30463 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8456 Classifications: {'peptide': 1080} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1025} Chain breaks: 5 Chain: "B" Number of atoms: 8445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8445 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 54, 'TRANS': 1024} Chain breaks: 5 Chain: "C" Number of atoms: 8438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8438 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 54, 'TRANS': 1023} Chain breaks: 5 Chain: "D" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.85, per 1000 atoms: 0.22 Number of scatterers: 30463 At special positions: 0 Unit cell: (147.686, 160.622, 247.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 143 16.00 O 5840 8.00 N 5046 7.00 C 19433 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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 616 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 717 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B1134 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7172 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 56 sheets defined 32.2% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.955A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.173A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' 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 619 through 624 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 747 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: 4.212A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 4.127A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.737A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.880A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 4.612A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.560A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.269A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.692A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 992 through 1033 removed outlier: 3.711A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.760A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.597A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.381A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.051A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.515A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.432A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.298A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.582A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.520A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 removed outlier: 4.470A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.673A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.352A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.712A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B1009 " --> pdb=" O GLN B1005 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG B1014 " --> pdb=" O GLN B1010 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 Processing helix chain 'C' and resid 147 through 150 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.532A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.649A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 624 Proline residue: C 621 - end of helix removed outlier: 4.099A pdb=" N ILE C 624 " --> pdb=" O PRO C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.550A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.645A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.204A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.702A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 4.277A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.713A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.113A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.568A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C1004 " --> pdb=" O ARG C1000 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN C1023 " --> pdb=" O ARG C1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.886A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 81 removed outlier: 3.530A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.696A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix removed outlier: 4.064A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.648A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 225 through 249 removed outlier: 3.592A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 304 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.909A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.564A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 414 removed outlier: 3.786A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.670A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.133A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 4.403A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.628A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.667A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.904A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 600 removed outlier: 4.367A pdb=" N LYS D 600 " --> pdb=" O LYS D 596 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 9.206A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.104A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.857A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.274A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.951A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.193A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.539A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.527A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.133A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.133A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.943A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.170A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.752A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.636A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.613A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.921A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC6, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.726A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.174A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.144A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 13.241A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 13.756A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.521A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 11.976A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD1, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AD2, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.383A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.315A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.714A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.240A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.786A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.420A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.513A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.724A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.950A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.775A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.568A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 357 removed outlier: 6.732A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 357 removed outlier: 5.082A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.113A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.724A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.752A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.598A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AG1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.397A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'D' and resid 347 through 352 removed outlier: 5.395A pdb=" N ALA D 348 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU D 359 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP D 350 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG D 357 " --> pdb=" O ASP D 350 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY D 352 " --> pdb=" O ASP D 355 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3378 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: 7.09 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9782 1.34 - 1.47: 7854 1.47 - 1.59: 13360 1.59 - 1.72: 0 1.72 - 1.84: 194 Bond restraints: 31190 Sorted by residual: bond pdb=" N VAL C 615 " pdb=" CA VAL C 615 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.08e-02 8.57e+03 1.30e+01 bond pdb=" N ASN A 343 " pdb=" CA ASN A 343 " ideal model delta sigma weight residual 1.458 1.489 -0.031 9.00e-03 1.23e+04 1.20e+01 bond pdb=" N HIS D 345 " pdb=" CA HIS D 345 " ideal model delta sigma weight residual 1.455 1.487 -0.032 9.60e-03 1.09e+04 1.14e+01 bond pdb=" N VAL B1133 " pdb=" CA VAL B1133 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N VAL C1133 " pdb=" CA VAL C1133 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.65e+00 ... (remaining 31185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 40673 1.99 - 3.97: 1574 3.97 - 5.96: 172 5.96 - 7.94: 14 7.94 - 9.93: 6 Bond angle restraints: 42439 Sorted by residual: angle pdb=" CA HIS D 345 " pdb=" C HIS D 345 " pdb=" N PRO D 346 " ideal model delta sigma weight residual 117.95 121.94 -3.99 7.70e-01 1.69e+00 2.69e+01 angle pdb=" C ASN A 282 " pdb=" CA ASN A 282 " pdb=" CB ASN A 282 " ideal model delta sigma weight residual 111.13 117.45 -6.32 1.61e+00 3.86e-01 1.54e+01 angle pdb=" N PRO B 589 " pdb=" CA PRO B 589 " pdb=" C PRO B 589 " ideal model delta sigma weight residual 112.47 104.39 8.08 2.06e+00 2.36e-01 1.54e+01 angle pdb=" CA HIS D 345 " pdb=" C HIS D 345 " pdb=" O HIS D 345 " ideal model delta sigma weight residual 120.34 116.77 3.57 9.20e-01 1.18e+00 1.51e+01 angle pdb=" C GLN C 613 " pdb=" N ASP C 614 " pdb=" CA ASP C 614 " ideal model delta sigma weight residual 123.03 117.90 5.13 1.34e+00 5.57e-01 1.46e+01 ... (remaining 42434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17445 17.92 - 35.84: 1095 35.84 - 53.76: 206 53.76 - 71.68: 66 71.68 - 89.60: 37 Dihedral angle restraints: 18849 sinusoidal: 7700 harmonic: 11149 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -141.74 55.74 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CA GLU A 96 " pdb=" C GLU A 96 " pdb=" N LYS A 97 " pdb=" CA LYS A 97 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA PRO A 589 " pdb=" C PRO A 589 " pdb=" N CYS A 590 " pdb=" CA CYS A 590 " ideal model delta harmonic sigma weight residual -180.00 -151.03 -28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 18846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4319 0.089 - 0.179: 464 0.179 - 0.268: 19 0.268 - 0.358: 5 0.358 - 0.447: 3 Chirality restraints: 4810 Sorted by residual: chirality pdb=" CA CYS B 590 " pdb=" N CYS B 590 " pdb=" C CYS B 590 " pdb=" CB CYS B 590 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CA ASN A 282 " pdb=" N ASN A 282 " pdb=" C ASN A 282 " pdb=" CB ASN A 282 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 4807 not shown) Planarity restraints: 5491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.335 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG B1302 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.177 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " -0.322 2.00e-02 2.50e+03 2.79e-01 9.76e+02 pdb=" C7 NAG A1303 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1302 " 0.283 2.00e-02 2.50e+03 2.44e-01 7.42e+02 pdb=" C7 NAG A1302 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG A1302 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG A1302 " -0.427 2.00e-02 2.50e+03 pdb=" O7 NAG A1302 " 0.049 2.00e-02 2.50e+03 ... (remaining 5488 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 422 2.65 - 3.21: 29968 3.21 - 3.77: 45794 3.77 - 4.34: 63884 4.34 - 4.90: 103237 Nonbonded interactions: 243305 Sorted by model distance: nonbonded pdb=" O TRP A 353 " pdb=" NH1 ARG A 466 " model vdw 2.085 3.120 nonbonded pdb=" OD1 ASN D 90 " pdb=" OG1 THR D 92 " model vdw 2.091 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.126 3.040 nonbonded pdb=" OD1 ASP D 382 " pdb=" OH TYR D 385 " model vdw 2.153 3.040 nonbonded pdb=" OD1 ASN A 777 " pdb=" NH1 ARG A1019 " model vdw 2.214 3.120 ... (remaining 243300 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 14 through 826 or resid 855 through 1306)) selection = (chain 'B' and (resid 14 through 624 or resid 633 through 826 or resid 855 throu \ gh 1306)) selection = (chain 'C' and (resid 14 through 624 or resid 633 through 1306)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.660 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 0.007 0.378 31260 Z= 0.325 Angle : 0.890 17.587 42598 Z= 0.506 Chirality : 0.055 0.447 4810 Planarity : 0.011 0.285 5468 Dihedral : 13.402 89.597 11542 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.87 % Allowed : 4.57 % Favored : 94.57 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.12), residues: 3785 helix: -1.71 (0.14), residues: 988 sheet: 0.49 (0.18), residues: 725 loop : -1.58 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.096 0.011 ARG D 161 TYR 0.035 0.005 TYR D 207 PHE 0.045 0.003 PHE A 486 TRP 0.035 0.002 TRP A 886 HIS 0.011 0.002 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00677 (31190) covalent geometry : angle 0.86924 (42439) SS BOND : bond 0.00449 ( 45) SS BOND : angle 1.52106 ( 90) hydrogen bonds : bond 0.22346 ( 1226) hydrogen bonds : angle 9.01738 ( 3378) metal coordination : bond 0.26767 ( 2) link_NAG-ASN : bond 0.01042 ( 23) link_NAG-ASN : angle 4.61890 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.8374 (mt) cc_final: 0.7915 (mt) REVERT: A 215 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8313 (t70) REVERT: A 231 ILE cc_start: 0.7678 (mm) cc_final: 0.7454 (mm) REVERT: A 387 LEU cc_start: 0.9283 (mt) cc_final: 0.9082 (mt) REVERT: A 508 TYR cc_start: 0.8873 (m-80) cc_final: 0.8218 (m-80) REVERT: A 740 MET cc_start: 0.8848 (ttm) cc_final: 0.8551 (ttt) REVERT: A 1017 GLU cc_start: 0.8405 (pp20) cc_final: 0.8086 (tm-30) REVERT: B 79 PHE cc_start: 0.8054 (t80) cc_final: 0.7722 (t80) REVERT: B 133 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: B 633 TRP cc_start: 0.8378 (OUTLIER) cc_final: 0.8137 (m-90) REVERT: B 869 MET cc_start: 0.9058 (mtt) cc_final: 0.8856 (mtm) REVERT: B 1050 MET cc_start: 0.8687 (ptp) cc_final: 0.8431 (ptp) REVERT: C 273 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7458 (tpp80) REVERT: C 489 TYR cc_start: 0.8439 (m-80) cc_final: 0.8075 (m-80) REVERT: C 505 TYR cc_start: 0.9588 (m-80) cc_final: 0.9081 (t80) REVERT: D 62 MET cc_start: 0.8777 (ttp) cc_final: 0.8495 (ptt) REVERT: D 270 MET cc_start: 0.3121 (ptm) cc_final: 0.2440 (tmm) REVERT: D 408 MET cc_start: 0.9204 (mpp) cc_final: 0.8501 (tpt) REVERT: D 455 MET cc_start: 0.7416 (tpt) cc_final: 0.5703 (tpt) REVERT: D 480 MET cc_start: 0.7059 (mmp) cc_final: 0.6405 (ptt) REVERT: D 516 TYR cc_start: 0.9274 (t80) cc_final: 0.8965 (t80) outliers start: 29 outliers final: 6 residues processed: 192 average time/residue: 0.1652 time to fit residues: 55.0107 Evaluate side-chains 106 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain D residue 385 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.0270 chunk 298 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 474 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 474 GLN B 501 ASN B 764 ASN B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 125 ASN C 146 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 544 ASN C 641 ASN D 330 ASN D 432 ASN D 442 GLN D 522 GLN D 599 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.088042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.054651 restraints weight = 143353.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.056001 restraints weight = 91490.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.056559 restraints weight = 58325.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.056585 restraints weight = 54165.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.056679 restraints weight = 48504.535| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 31260 Z= 0.137 Angle : 0.656 9.827 42598 Z= 0.344 Chirality : 0.046 0.248 4810 Planarity : 0.004 0.048 5468 Dihedral : 6.465 59.004 4609 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.13 % Allowed : 6.80 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 3785 helix: 0.04 (0.16), residues: 988 sheet: 0.40 (0.18), residues: 752 loop : -1.09 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 158 TYR 0.017 0.001 TYR A1067 PHE 0.026 0.002 PHE B 133 TRP 0.019 0.001 TRP C 633 HIS 0.007 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00290 (31190) covalent geometry : angle 0.64766 (42439) SS BOND : bond 0.00403 ( 45) SS BOND : angle 1.17638 ( 90) hydrogen bonds : bond 0.05753 ( 1226) hydrogen bonds : angle 6.15759 ( 3378) metal coordination : bond 0.00820 ( 2) link_NAG-ASN : bond 0.00295 ( 23) link_NAG-ASN : angle 2.36945 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 1.144 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 106 PHE cc_start: 0.8772 (m-80) cc_final: 0.8413 (m-80) REVERT: A 215 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8531 (t0) REVERT: A 231 ILE cc_start: 0.7512 (mm) cc_final: 0.7286 (mm) REVERT: A 740 MET cc_start: 0.8925 (ttm) cc_final: 0.8725 (ttt) REVERT: A 1017 GLU cc_start: 0.8417 (pp20) cc_final: 0.8193 (tm-30) REVERT: B 79 PHE cc_start: 0.8025 (t80) cc_final: 0.7476 (t80) REVERT: B 133 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: B 365 TYR cc_start: 0.6993 (p90) cc_final: 0.6789 (p90) REVERT: B 633 TRP cc_start: 0.8326 (OUTLIER) cc_final: 0.7886 (m-90) REVERT: B 1050 MET cc_start: 0.8389 (ptp) cc_final: 0.8036 (ptp) REVERT: C 118 LEU cc_start: 0.9585 (tp) cc_final: 0.9278 (mt) REVERT: C 135 PHE cc_start: 0.8238 (m-80) cc_final: 0.7850 (m-80) REVERT: C 338 PHE cc_start: 0.7752 (m-80) cc_final: 0.7523 (m-80) REVERT: C 392 PHE cc_start: 0.9282 (m-80) cc_final: 0.8878 (m-10) REVERT: C 489 TYR cc_start: 0.8312 (m-80) cc_final: 0.8031 (m-80) REVERT: C 505 TYR cc_start: 0.9633 (m-80) cc_final: 0.9075 (t80) REVERT: C 819 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8453 (mt-10) REVERT: D 249 MET cc_start: 0.7007 (mmm) cc_final: 0.6792 (tpt) REVERT: D 270 MET cc_start: 0.3845 (ptm) cc_final: 0.3510 (tmm) REVERT: D 323 MET cc_start: 0.6895 (ttp) cc_final: 0.6508 (tmm) REVERT: D 408 MET cc_start: 0.9418 (mpp) cc_final: 0.8904 (tpt) REVERT: D 455 MET cc_start: 0.7556 (tpt) cc_final: 0.6498 (tpt) REVERT: D 480 MET cc_start: 0.8021 (mmp) cc_final: 0.7335 (ptt) outliers start: 38 outliers final: 19 residues processed: 145 average time/residue: 0.1617 time to fit residues: 41.3116 Evaluate side-chains 121 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 385 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 180 optimal weight: 0.6980 chunk 374 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 278 optimal weight: 2.9990 chunk 223 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN D 524 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.086974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.054884 restraints weight = 144554.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054246 restraints weight = 100060.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.054307 restraints weight = 88285.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.054726 restraints weight = 68547.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.054822 restraints weight = 60246.752| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31260 Z= 0.172 Angle : 0.616 12.293 42598 Z= 0.320 Chirality : 0.044 0.203 4810 Planarity : 0.004 0.045 5468 Dihedral : 5.878 56.960 4605 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.34 % Allowed : 8.06 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.13), residues: 3785 helix: 0.52 (0.17), residues: 992 sheet: 0.44 (0.18), residues: 758 loop : -1.10 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 246 TYR 0.033 0.001 TYR C 365 PHE 0.017 0.001 PHE B 133 TRP 0.017 0.001 TRP C 633 HIS 0.007 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00393 (31190) covalent geometry : angle 0.60916 (42439) SS BOND : bond 0.00555 ( 45) SS BOND : angle 1.12009 ( 90) hydrogen bonds : bond 0.05097 ( 1226) hydrogen bonds : angle 5.77290 ( 3378) metal coordination : bond 0.00087 ( 2) link_NAG-ASN : bond 0.00265 ( 23) link_NAG-ASN : angle 2.07293 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8691 (m-80) cc_final: 0.8350 (m-80) REVERT: A 1017 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8181 (tm-30) REVERT: B 633 TRP cc_start: 0.8312 (OUTLIER) cc_final: 0.7863 (m-90) REVERT: B 1050 MET cc_start: 0.8475 (ptp) cc_final: 0.8232 (ptp) REVERT: C 118 LEU cc_start: 0.9588 (tp) cc_final: 0.9388 (mm) REVERT: C 135 PHE cc_start: 0.8328 (m-80) cc_final: 0.8010 (m-80) REVERT: C 238 PHE cc_start: 0.8399 (p90) cc_final: 0.8013 (p90) REVERT: C 338 PHE cc_start: 0.7873 (m-80) cc_final: 0.7656 (m-10) REVERT: C 386 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8375 (mtmm) REVERT: C 489 TYR cc_start: 0.8372 (m-80) cc_final: 0.8090 (m-80) REVERT: C 505 TYR cc_start: 0.9647 (m-80) cc_final: 0.9110 (t80) REVERT: C 819 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8484 (mt-10) REVERT: D 62 MET cc_start: 0.8798 (ptt) cc_final: 0.8553 (ptm) REVERT: D 123 MET cc_start: 0.7667 (ppp) cc_final: 0.7428 (ppp) REVERT: D 270 MET cc_start: 0.4288 (ptm) cc_final: 0.3653 (tpp) REVERT: D 455 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.6720 (tpt) REVERT: D 480 MET cc_start: 0.8172 (mmp) cc_final: 0.7501 (ptt) REVERT: D 516 TYR cc_start: 0.8982 (t80) cc_final: 0.8186 (m-80) outliers start: 45 outliers final: 20 residues processed: 138 average time/residue: 0.1577 time to fit residues: 38.9658 Evaluate side-chains 123 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 455 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 267 optimal weight: 0.9980 chunk 300 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 310 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 353 optimal weight: 4.9990 chunk 225 optimal weight: 0.0870 chunk 13 optimal weight: 20.0000 chunk 371 optimal weight: 10.0000 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 280 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN D 58 ASN D 305 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.086710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.054741 restraints weight = 142859.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.054118 restraints weight = 99214.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.053920 restraints weight = 91630.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.054208 restraints weight = 75253.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.054415 restraints weight = 64198.726| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31260 Z= 0.157 Angle : 0.580 10.715 42598 Z= 0.300 Chirality : 0.043 0.191 4810 Planarity : 0.004 0.045 5468 Dihedral : 5.504 54.780 4598 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.55 % Allowed : 8.53 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.13), residues: 3785 helix: 0.80 (0.17), residues: 1001 sheet: 0.32 (0.18), residues: 780 loop : -1.07 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.023 0.001 TYR D 183 PHE 0.022 0.001 PHE B 392 TRP 0.024 0.001 TRP C 633 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00357 (31190) covalent geometry : angle 0.57318 (42439) SS BOND : bond 0.00329 ( 45) SS BOND : angle 1.11682 ( 90) hydrogen bonds : bond 0.04594 ( 1226) hydrogen bonds : angle 5.53547 ( 3378) metal coordination : bond 0.00171 ( 2) link_NAG-ASN : bond 0.00218 ( 23) link_NAG-ASN : angle 1.92927 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 100 time to evaluate : 1.213 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 106 PHE cc_start: 0.8675 (m-80) cc_final: 0.8354 (m-80) REVERT: A 338 PHE cc_start: 0.8580 (t80) cc_final: 0.8147 (m-80) REVERT: A 1017 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: B 177 MET cc_start: 0.8365 (mmm) cc_final: 0.7356 (mpp) REVERT: B 633 TRP cc_start: 0.8316 (OUTLIER) cc_final: 0.7818 (m-90) REVERT: B 1050 MET cc_start: 0.8343 (ptp) cc_final: 0.8124 (ptp) REVERT: C 118 LEU cc_start: 0.9561 (tp) cc_final: 0.9339 (mt) REVERT: C 135 PHE cc_start: 0.8160 (m-80) cc_final: 0.7877 (m-80) REVERT: C 238 PHE cc_start: 0.8392 (p90) cc_final: 0.8025 (p90) REVERT: C 275 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8742 (m-10) REVERT: C 338 PHE cc_start: 0.7930 (m-80) cc_final: 0.7713 (m-10) REVERT: C 505 TYR cc_start: 0.9653 (m-80) cc_final: 0.9158 (t80) REVERT: C 736 VAL cc_start: 0.9543 (OUTLIER) cc_final: 0.9222 (m) REVERT: D 62 MET cc_start: 0.8876 (ptt) cc_final: 0.8617 (ptm) REVERT: D 270 MET cc_start: 0.4215 (ptm) cc_final: 0.3627 (tpp) REVERT: D 297 MET cc_start: 0.8536 (ppp) cc_final: 0.8197 (ppp) REVERT: D 516 TYR cc_start: 0.8957 (t80) cc_final: 0.8147 (m-80) outliers start: 52 outliers final: 28 residues processed: 142 average time/residue: 0.1490 time to fit residues: 38.3043 Evaluate side-chains 129 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 455 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 324 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 334 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 265 optimal weight: 0.0970 chunk 208 optimal weight: 0.7980 chunk 345 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 356 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A1048 HIS ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.086503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.054554 restraints weight = 144579.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.053744 restraints weight = 101281.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053893 restraints weight = 88956.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.054083 restraints weight = 71348.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.054314 restraints weight = 63529.322| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31260 Z= 0.158 Angle : 0.572 11.764 42598 Z= 0.296 Chirality : 0.043 0.207 4810 Planarity : 0.004 0.047 5468 Dihedral : 5.279 55.253 4598 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.40 % Allowed : 9.34 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.13), residues: 3785 helix: 0.99 (0.17), residues: 996 sheet: 0.26 (0.18), residues: 782 loop : -1.07 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.020 0.001 TYR A1067 PHE 0.017 0.001 PHE B 133 TRP 0.008 0.001 TRP D 459 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00359 (31190) covalent geometry : angle 0.56623 (42439) SS BOND : bond 0.00363 ( 45) SS BOND : angle 1.02248 ( 90) hydrogen bonds : bond 0.04462 ( 1226) hydrogen bonds : angle 5.44254 ( 3378) metal coordination : bond 0.00433 ( 2) link_NAG-ASN : bond 0.00213 ( 23) link_NAG-ASN : angle 1.82663 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 94 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.5856 (mm) REVERT: A 106 PHE cc_start: 0.8675 (m-80) cc_final: 0.8277 (m-10) REVERT: A 177 MET cc_start: 0.5021 (mtt) cc_final: 0.2192 (mpp) REVERT: A 215 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8515 (t0) REVERT: A 338 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8176 (m-80) REVERT: A 1017 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: B 633 TRP cc_start: 0.8331 (OUTLIER) cc_final: 0.7799 (m-90) REVERT: B 1050 MET cc_start: 0.8344 (ptp) cc_final: 0.8110 (ptp) REVERT: B 1101 HIS cc_start: 0.6410 (OUTLIER) cc_final: 0.4952 (m90) REVERT: C 118 LEU cc_start: 0.9530 (tp) cc_final: 0.9326 (mt) REVERT: C 135 PHE cc_start: 0.8055 (m-80) cc_final: 0.7826 (m-80) REVERT: C 238 PHE cc_start: 0.8353 (p90) cc_final: 0.8005 (p90) REVERT: C 275 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8746 (m-10) REVERT: C 338 PHE cc_start: 0.7971 (m-80) cc_final: 0.7739 (m-10) REVERT: C 505 TYR cc_start: 0.9665 (m-80) cc_final: 0.9181 (t80) REVERT: D 62 MET cc_start: 0.8939 (ptt) cc_final: 0.8690 (ptm) REVERT: D 249 MET cc_start: 0.6088 (tpt) cc_final: 0.4968 (mmt) REVERT: D 270 MET cc_start: 0.4211 (ptm) cc_final: 0.3629 (tpp) REVERT: D 297 MET cc_start: 0.8108 (ppp) cc_final: 0.7806 (ppp) REVERT: D 360 MET cc_start: 0.7688 (tpt) cc_final: 0.7423 (tpt) REVERT: D 455 MET cc_start: 0.7512 (tpt) cc_final: 0.7148 (tpt) REVERT: D 480 MET cc_start: 0.8036 (mmm) cc_final: 0.7361 (ptt) REVERT: D 516 TYR cc_start: 0.9005 (t80) cc_final: 0.8249 (m-80) outliers start: 47 outliers final: 30 residues processed: 133 average time/residue: 0.1531 time to fit residues: 36.9818 Evaluate side-chains 127 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 152 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 297 optimal weight: 0.5980 chunk 315 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 348 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.085524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.052518 restraints weight = 144379.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.053090 restraints weight = 97367.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.052735 restraints weight = 68525.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.052952 restraints weight = 67192.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.053110 restraints weight = 59408.526| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 31260 Z= 0.217 Angle : 0.606 10.805 42598 Z= 0.313 Chirality : 0.043 0.216 4810 Planarity : 0.004 0.047 5468 Dihedral : 5.312 55.972 4598 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.49 % Allowed : 10.00 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.13), residues: 3785 helix: 0.99 (0.17), residues: 1002 sheet: 0.16 (0.17), residues: 792 loop : -1.13 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.020 0.001 TYR A1067 PHE 0.017 0.002 PHE B 133 TRP 0.009 0.001 TRP B 64 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00496 (31190) covalent geometry : angle 0.60123 (42439) SS BOND : bond 0.00362 ( 45) SS BOND : angle 1.04888 ( 90) hydrogen bonds : bond 0.04766 ( 1226) hydrogen bonds : angle 5.53898 ( 3378) metal coordination : bond 0.00232 ( 2) link_NAG-ASN : bond 0.00224 ( 23) link_NAG-ASN : angle 1.82250 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 94 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8769 (m-80) cc_final: 0.8509 (m-80) REVERT: A 215 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8425 (t0) REVERT: A 823 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8550 (m-10) REVERT: A 979 ASP cc_start: 0.8956 (m-30) cc_final: 0.8616 (p0) REVERT: A 1017 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8285 (tm-30) REVERT: A 1067 TYR cc_start: 0.9488 (OUTLIER) cc_final: 0.9062 (t80) REVERT: A 1084 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8642 (p0) REVERT: B 633 TRP cc_start: 0.8357 (OUTLIER) cc_final: 0.8086 (m-90) REVERT: B 1050 MET cc_start: 0.8429 (ptp) cc_final: 0.8190 (ptp) REVERT: B 1101 HIS cc_start: 0.6620 (OUTLIER) cc_final: 0.5475 (m90) REVERT: C 195 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8228 (mtmt) REVERT: C 238 PHE cc_start: 0.8378 (p90) cc_final: 0.8051 (p90) REVERT: C 275 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8738 (m-10) REVERT: C 338 PHE cc_start: 0.8080 (m-80) cc_final: 0.7835 (m-10) REVERT: C 505 TYR cc_start: 0.9710 (m-80) cc_final: 0.9235 (t80) REVERT: C 736 VAL cc_start: 0.9590 (OUTLIER) cc_final: 0.9332 (m) REVERT: D 62 MET cc_start: 0.9013 (ptt) cc_final: 0.8760 (ptm) REVERT: D 249 MET cc_start: 0.6512 (tpt) cc_final: 0.5996 (mmt) REVERT: D 270 MET cc_start: 0.4175 (ptm) cc_final: 0.3576 (tpp) REVERT: D 297 MET cc_start: 0.8095 (ppp) cc_final: 0.7853 (ppp) REVERT: D 360 MET cc_start: 0.7628 (tpt) cc_final: 0.7362 (tpt) REVERT: D 455 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7093 (tpt) REVERT: D 480 MET cc_start: 0.8035 (mmm) cc_final: 0.7323 (ptt) REVERT: D 516 TYR cc_start: 0.9112 (t80) cc_final: 0.8327 (m-80) outliers start: 50 outliers final: 33 residues processed: 134 average time/residue: 0.1576 time to fit residues: 37.9538 Evaluate side-chains 133 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 90 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 253 optimal weight: 0.9990 chunk 368 optimal weight: 7.9990 chunk 350 optimal weight: 9.9990 chunk 307 optimal weight: 1.9990 chunk 343 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 345 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.085899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.052303 restraints weight = 142983.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.053044 restraints weight = 108032.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.053154 restraints weight = 74000.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053203 restraints weight = 63292.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.053408 restraints weight = 58687.170| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31260 Z= 0.164 Angle : 0.562 10.270 42598 Z= 0.290 Chirality : 0.043 0.210 4810 Planarity : 0.004 0.045 5468 Dihedral : 5.169 57.459 4598 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.70 % Allowed : 10.41 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.14), residues: 3785 helix: 1.13 (0.17), residues: 1000 sheet: 0.18 (0.17), residues: 797 loop : -1.15 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.018 0.001 TYR A1067 PHE 0.017 0.001 PHE B 133 TRP 0.008 0.001 TRP A 152 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00374 (31190) covalent geometry : angle 0.55696 (42439) SS BOND : bond 0.00239 ( 45) SS BOND : angle 0.94807 ( 90) hydrogen bonds : bond 0.04411 ( 1226) hydrogen bonds : angle 5.39080 ( 3378) metal coordination : bond 0.00182 ( 2) link_NAG-ASN : bond 0.00202 ( 23) link_NAG-ASN : angle 1.79395 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 95 time to evaluate : 0.873 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 24 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.5895 (mt) REVERT: A 117 LEU cc_start: 0.9726 (tp) cc_final: 0.9508 (pp) REVERT: A 177 MET cc_start: 0.5303 (mtt) cc_final: 0.2968 (mpp) REVERT: A 215 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8352 (t0) REVERT: A 979 ASP cc_start: 0.8897 (m-30) cc_final: 0.8613 (p0) REVERT: A 1017 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: A 1067 TYR cc_start: 0.9456 (OUTLIER) cc_final: 0.9005 (t80) REVERT: A 1084 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8638 (p0) REVERT: B 633 TRP cc_start: 0.8351 (OUTLIER) cc_final: 0.8128 (m-90) REVERT: B 1050 MET cc_start: 0.8298 (ptp) cc_final: 0.8023 (ptp) REVERT: B 1101 HIS cc_start: 0.6564 (OUTLIER) cc_final: 0.5434 (m90) REVERT: C 195 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8299 (mtmt) REVERT: C 238 PHE cc_start: 0.8358 (p90) cc_final: 0.8014 (p90) REVERT: C 275 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8699 (m-10) REVERT: C 338 PHE cc_start: 0.8021 (m-80) cc_final: 0.7798 (m-10) REVERT: C 505 TYR cc_start: 0.9670 (m-80) cc_final: 0.9233 (t80) REVERT: C 736 VAL cc_start: 0.9591 (OUTLIER) cc_final: 0.9326 (m) REVERT: D 249 MET cc_start: 0.6280 (tpt) cc_final: 0.5726 (mmt) REVERT: D 270 MET cc_start: 0.4178 (ptm) cc_final: 0.3497 (tpp) REVERT: D 297 MET cc_start: 0.8137 (ppp) cc_final: 0.7924 (ppp) REVERT: D 360 MET cc_start: 0.7744 (tpt) cc_final: 0.7452 (tpt) REVERT: D 455 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7087 (tpt) REVERT: D 480 MET cc_start: 0.8098 (mmm) cc_final: 0.7379 (ptt) REVERT: D 516 TYR cc_start: 0.9041 (t80) cc_final: 0.8277 (m-80) outliers start: 57 outliers final: 35 residues processed: 142 average time/residue: 0.1526 time to fit residues: 38.6502 Evaluate side-chains 134 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 89 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 181 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 313 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN C 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.086427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.053752 restraints weight = 142928.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.053958 restraints weight = 94896.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.053988 restraints weight = 76940.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.054035 restraints weight = 66651.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.054199 restraints weight = 61384.327| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31260 Z= 0.124 Angle : 0.546 11.105 42598 Z= 0.281 Chirality : 0.042 0.199 4810 Planarity : 0.004 0.046 5468 Dihedral : 4.983 58.522 4598 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.40 % Allowed : 10.83 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3785 helix: 1.27 (0.17), residues: 1001 sheet: 0.28 (0.17), residues: 802 loop : -1.07 (0.14), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.020 0.001 TYR D 50 PHE 0.016 0.001 PHE B 133 TRP 0.008 0.001 TRP D 48 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00279 (31190) covalent geometry : angle 0.54111 (42439) SS BOND : bond 0.00281 ( 45) SS BOND : angle 0.83345 ( 90) hydrogen bonds : bond 0.04147 ( 1226) hydrogen bonds : angle 5.23061 ( 3378) metal coordination : bond 0.00119 ( 2) link_NAG-ASN : bond 0.00231 ( 23) link_NAG-ASN : angle 1.77635 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 95 time to evaluate : 1.423 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 24 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.5929 (mt) REVERT: A 177 MET cc_start: 0.5669 (mtt) cc_final: 0.5469 (mtt) REVERT: A 215 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8350 (t0) REVERT: A 239 GLN cc_start: 0.9151 (tt0) cc_final: 0.8926 (mp10) REVERT: A 441 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8924 (pp) REVERT: A 979 ASP cc_start: 0.8883 (m-30) cc_final: 0.8609 (p0) REVERT: A 1017 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8317 (tm-30) REVERT: B 633 TRP cc_start: 0.8339 (OUTLIER) cc_final: 0.7854 (m-90) REVERT: B 1050 MET cc_start: 0.8330 (ptp) cc_final: 0.8107 (ptp) REVERT: C 195 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8343 (mtmt) REVERT: C 238 PHE cc_start: 0.8316 (p90) cc_final: 0.7998 (p90) REVERT: C 275 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8763 (m-10) REVERT: C 338 PHE cc_start: 0.8061 (m-80) cc_final: 0.7820 (m-10) REVERT: C 505 TYR cc_start: 0.9703 (m-80) cc_final: 0.9234 (t80) REVERT: C 736 VAL cc_start: 0.9579 (OUTLIER) cc_final: 0.9318 (m) REVERT: D 62 MET cc_start: 0.9123 (ptt) cc_final: 0.8908 (mtm) REVERT: D 249 MET cc_start: 0.6533 (tpt) cc_final: 0.6022 (mmt) REVERT: D 270 MET cc_start: 0.4029 (ptm) cc_final: 0.3307 (tpp) REVERT: D 297 MET cc_start: 0.8065 (ppp) cc_final: 0.7840 (ppp) REVERT: D 360 MET cc_start: 0.7681 (tpt) cc_final: 0.7399 (tpt) REVERT: D 376 MET cc_start: 0.9192 (tpt) cc_final: 0.8439 (ptm) REVERT: D 455 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7092 (tpt) REVERT: D 480 MET cc_start: 0.8118 (mmm) cc_final: 0.7369 (ptt) REVERT: D 516 TYR cc_start: 0.9085 (t80) cc_final: 0.8366 (m-80) outliers start: 47 outliers final: 34 residues processed: 133 average time/residue: 0.1634 time to fit residues: 38.6715 Evaluate side-chains 135 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 177 optimal weight: 0.1980 chunk 307 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 184 optimal weight: 0.0570 chunk 246 optimal weight: 3.9990 chunk 275 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 232 optimal weight: 5.9990 chunk 142 optimal weight: 0.0000 chunk 281 optimal weight: 0.9990 overall best weight: 0.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.087288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.054777 restraints weight = 143095.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.055422 restraints weight = 95211.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055130 restraints weight = 68946.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.055470 restraints weight = 62346.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.055502 restraints weight = 56504.941| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 31260 Z= 0.093 Angle : 0.520 11.072 42598 Z= 0.266 Chirality : 0.042 0.194 4810 Planarity : 0.004 0.048 5468 Dihedral : 4.723 59.926 4598 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.25 % Allowed : 11.07 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 3785 helix: 1.44 (0.17), residues: 1003 sheet: 0.44 (0.18), residues: 788 loop : -0.99 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.027 0.001 TYR A 904 PHE 0.016 0.001 PHE B 133 TRP 0.010 0.001 TRP A 152 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00200 (31190) covalent geometry : angle 0.51438 (42439) SS BOND : bond 0.00240 ( 45) SS BOND : angle 0.80393 ( 90) hydrogen bonds : bond 0.03641 ( 1226) hydrogen bonds : angle 5.01112 ( 3378) metal coordination : bond 0.00108 ( 2) link_NAG-ASN : bond 0.00263 ( 23) link_NAG-ASN : angle 1.75956 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.5950 (mm) REVERT: A 106 PHE cc_start: 0.8932 (m-10) cc_final: 0.8412 (m-10) REVERT: A 177 MET cc_start: 0.5490 (mtt) cc_final: 0.5253 (mtt) REVERT: A 215 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8375 (t0) REVERT: A 441 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8916 (pp) REVERT: A 979 ASP cc_start: 0.8859 (m-30) cc_final: 0.8575 (p0) REVERT: B 633 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.7456 (m-90) REVERT: B 1050 MET cc_start: 0.8273 (ptp) cc_final: 0.8061 (ptp) REVERT: B 1101 HIS cc_start: 0.6524 (OUTLIER) cc_final: 0.5445 (m90) REVERT: C 238 PHE cc_start: 0.8293 (p90) cc_final: 0.7990 (p90) REVERT: C 338 PHE cc_start: 0.7998 (m-80) cc_final: 0.7786 (m-80) REVERT: C 505 TYR cc_start: 0.9701 (m-80) cc_final: 0.9222 (t80) REVERT: C 819 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8554 (mt-10) REVERT: D 90 ASN cc_start: 0.6969 (OUTLIER) cc_final: 0.6316 (p0) REVERT: D 249 MET cc_start: 0.6476 (tpt) cc_final: 0.5949 (mmt) REVERT: D 270 MET cc_start: 0.3929 (ptm) cc_final: 0.3241 (tpp) REVERT: D 297 MET cc_start: 0.8049 (ppp) cc_final: 0.7805 (ppp) REVERT: D 360 MET cc_start: 0.7753 (tpt) cc_final: 0.7424 (tpt) REVERT: D 455 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6788 (tpt) REVERT: D 462 MET cc_start: 0.8014 (pmm) cc_final: 0.7791 (pmm) REVERT: D 480 MET cc_start: 0.8055 (mmm) cc_final: 0.7207 (ptt) REVERT: D 516 TYR cc_start: 0.9028 (t80) cc_final: 0.8357 (m-80) outliers start: 42 outliers final: 24 residues processed: 133 average time/residue: 0.1549 time to fit residues: 37.3746 Evaluate side-chains 124 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 220 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 87 optimal weight: 0.4980 chunk 190 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 304 optimal weight: 0.6980 chunk 53 optimal weight: 0.1980 chunk 327 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 chunk 340 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.087053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.054930 restraints weight = 143315.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.054969 restraints weight = 98184.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.054820 restraints weight = 75717.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055087 restraints weight = 67016.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.055206 restraints weight = 58709.975| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 31260 Z= 0.105 Angle : 0.531 11.812 42598 Z= 0.269 Chirality : 0.042 0.197 4810 Planarity : 0.004 0.047 5468 Dihedral : 4.666 59.519 4596 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.87 % Allowed : 11.76 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.14), residues: 3785 helix: 1.46 (0.17), residues: 1007 sheet: 0.45 (0.18), residues: 785 loop : -0.95 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1107 TYR 0.029 0.001 TYR A 904 PHE 0.018 0.001 PHE A 823 TRP 0.010 0.001 TRP A 152 HIS 0.006 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00236 (31190) covalent geometry : angle 0.52585 (42439) SS BOND : bond 0.00233 ( 45) SS BOND : angle 0.75975 ( 90) hydrogen bonds : bond 0.03689 ( 1226) hydrogen bonds : angle 5.00144 ( 3378) metal coordination : bond 0.00141 ( 2) link_NAG-ASN : bond 0.00227 ( 23) link_NAG-ASN : angle 1.75949 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.5971 (mm) REVERT: A 106 PHE cc_start: 0.8825 (m-10) cc_final: 0.8337 (m-10) REVERT: A 215 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8375 (t0) REVERT: A 441 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8891 (pp) REVERT: A 979 ASP cc_start: 0.8915 (m-30) cc_final: 0.8618 (p0) REVERT: B 365 TYR cc_start: 0.7256 (p90) cc_final: 0.6862 (p90) REVERT: B 633 TRP cc_start: 0.8305 (OUTLIER) cc_final: 0.7800 (m-90) REVERT: B 697 MET cc_start: 0.8654 (mmm) cc_final: 0.7794 (mmm) REVERT: B 1050 MET cc_start: 0.8257 (ptp) cc_final: 0.8044 (ptp) REVERT: B 1101 HIS cc_start: 0.6569 (OUTLIER) cc_final: 0.5463 (m90) REVERT: C 238 PHE cc_start: 0.8288 (p90) cc_final: 0.7988 (p90) REVERT: C 338 PHE cc_start: 0.8004 (m-80) cc_final: 0.7798 (m-10) REVERT: C 505 TYR cc_start: 0.9675 (m-80) cc_final: 0.9224 (t80) REVERT: C 819 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8571 (mt-10) REVERT: D 90 ASN cc_start: 0.6995 (OUTLIER) cc_final: 0.6320 (p0) REVERT: D 249 MET cc_start: 0.6467 (tpt) cc_final: 0.5918 (mmt) REVERT: D 270 MET cc_start: 0.3979 (ptm) cc_final: 0.3311 (tpp) REVERT: D 297 MET cc_start: 0.8040 (ppp) cc_final: 0.7805 (ppp) REVERT: D 360 MET cc_start: 0.7754 (tpt) cc_final: 0.7522 (tpt) REVERT: D 455 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.6787 (tpt) REVERT: D 462 MET cc_start: 0.8115 (pmm) cc_final: 0.7913 (pmm) REVERT: D 480 MET cc_start: 0.8079 (mmm) cc_final: 0.7193 (ptt) REVERT: D 516 TYR cc_start: 0.8971 (t80) cc_final: 0.8302 (m-80) outliers start: 29 outliers final: 20 residues processed: 117 average time/residue: 0.1509 time to fit residues: 32.0470 Evaluate side-chains 118 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 317 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 316 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 240 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 chunk 369 optimal weight: 3.9990 chunk 262 optimal weight: 10.0000 chunk 206 optimal weight: 0.7980 chunk 345 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.086753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053367 restraints weight = 143385.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.054692 restraints weight = 89620.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.054699 restraints weight = 54253.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055056 restraints weight = 51267.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.055041 restraints weight = 46989.885| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31260 Z= 0.119 Angle : 0.538 11.310 42598 Z= 0.274 Chirality : 0.042 0.197 4810 Planarity : 0.004 0.046 5468 Dihedral : 4.646 59.533 4596 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.10 % Allowed : 11.73 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3785 helix: 1.49 (0.17), residues: 997 sheet: 0.49 (0.18), residues: 779 loop : -0.95 (0.14), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.022 0.001 TYR A 904 PHE 0.019 0.001 PHE A 823 TRP 0.010 0.001 TRP A 152 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00269 (31190) covalent geometry : angle 0.53335 (42439) SS BOND : bond 0.00236 ( 45) SS BOND : angle 0.77714 ( 90) hydrogen bonds : bond 0.03815 ( 1226) hydrogen bonds : angle 5.02125 ( 3378) metal coordination : bond 0.00067 ( 2) link_NAG-ASN : bond 0.00219 ( 23) link_NAG-ASN : angle 1.75075 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5049.69 seconds wall clock time: 88 minutes 14.39 seconds (5294.39 seconds total)