Starting phenix.real_space_refine on Mon Aug 25 19:00:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oyu_17296/08_2025/8oyu_17296.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oyu_17296/08_2025/8oyu_17296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oyu_17296/08_2025/8oyu_17296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oyu_17296/08_2025/8oyu_17296.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oyu_17296/08_2025/8oyu_17296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oyu_17296/08_2025/8oyu_17296.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1924 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 17974 2.51 5 N 4674 2.21 5 O 5446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28223 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8596 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 60, 'TRANS': 1037} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8589 Classifications: {'peptide': 1096} Link IDs: {'CIS': 1, 'PTRANS': 60, 'TRANS': 1034} Chain breaks: 4 Chain: "C" Number of atoms: 8596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8596 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 60, 'TRANS': 1037} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 962 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 126, 955 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Conformer: "B" Number of residues, atoms: 126, 955 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} bond proxies already assigned to first conformer: 968 Chain: "D" Number of atoms: 962 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 126, 955 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Conformer: "B" Number of residues, atoms: 126, 955 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} bond proxies already assigned to first conformer: 968 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.33, per 1000 atoms: 0.22 Number of scatterers: 28223 At special positions: 0 Unit cell: (172.8, 172.8, 148.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5446 8.00 N 4674 7.00 C 17974 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.04 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 51 " - pdb=" SG CYS E 107 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 51 " - pdb=" SG CYS D 107 " 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 279 " " NAG A1302 " - " ASN A 706 " " NAG B1301 " - " ASN B1131 " " NAG B1302 " - " ASN B 706 " " NAG B1303 " - " ASN B 279 " " NAG B1304 " - " ASN B 120 " " NAG C1301 " - " ASN C 600 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 613 " " NAG C1304 " - " ASN C 654 " " NAG C1305 " - " ASN C 279 " " NAG C1306 " - " ASN C 706 " " NAG C1307 " - " ASN C1131 " " NAG C1308 " - " ASN C1071 " " NAG F 1 " - " ASN A1131 " " NAG G 1 " - " ASN A1095 " " NAG H 1 " - " ASN A 714 " " NAG I 1 " - " ASN A 798 " " NAG J 1 " - " ASN B1071 " " NAG K 1 " - " ASN B 798 " " NAG L 1 " - " ASN B 714 " " NAG M 1 " - " ASN B1095 " " NAG N 1 " - " ASN C1095 " " NAG O 1 " - " ASN C 714 " " NAG P 1 " - " ASN C 798 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6634 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 56 sheets defined 21.4% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 removed outlier: 4.329A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 445 through 449 removed outlier: 4.180A pdb=" N TYR A 448 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.930A pdb=" N ALA A 623 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.565A pdb=" N CYS A 740 " --> pdb=" O THR A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.601A pdb=" N LEU A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 780 Processing helix chain 'A' and resid 813 through 824 Processing helix chain 'A' and resid 846 through 852 removed outlier: 3.578A pdb=" N GLN A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.600A pdb=" N GLY A 888 " --> pdb=" O PHE A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 909 through 937 removed outlier: 4.174A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.836A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 980 Processing helix chain 'A' and resid 982 through 1031 removed outlier: 5.051A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 362 through 368 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 4.201A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 4.482A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 824 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 909 through 937 removed outlier: 4.114A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS B 918 " --> pdb=" O TYR B 914 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU B 919 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 963 removed outlier: 3.503A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 980 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.956A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 removed outlier: 4.035A pdb=" N PHE C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.288A pdb=" N ALA C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 445 through 449 removed outlier: 4.359A pdb=" N TYR C 448 " --> pdb=" O ASN C 445 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 449 " --> pdb=" O TYR C 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 445 through 449' Processing helix chain 'C' and resid 539 through 543 Processing helix chain 'C' and resid 620 through 624 removed outlier: 3.863A pdb=" N ALA C 623 " --> pdb=" O ALA C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 removed outlier: 3.634A pdb=" N CYS C 740 " --> pdb=" O THR C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 752 Processing helix chain 'C' and resid 757 through 780 Processing helix chain 'C' and resid 813 through 824 Processing helix chain 'C' and resid 846 through 852 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.744A pdb=" N GLY C 888 " --> pdb=" O PHE C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 909 through 937 removed outlier: 4.251A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS C 918 " --> pdb=" O TYR C 914 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.756A pdb=" N GLN C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 980 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 5.034A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 61 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'D' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.814A pdb=" N GLN A 268 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 114 removed outlier: 3.803A pdb=" N CYS A 129 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 163 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLU A 130 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N CYS A 161 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N GLN A 132 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N ASN A 159 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 192 removed outlier: 6.280A pdb=" N PHE A 196 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP A 225 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE A 198 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.746A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 355 removed outlier: 3.896A pdb=" N LYS A 353 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 392 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N SER A 511 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ALA A 394 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL A 509 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A 507 " --> pdb=" O PHE A 397 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 397 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 353 through 355 removed outlier: 3.896A pdb=" N LYS A 353 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 392 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N SER A 511 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ALA A 394 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL A 509 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 510 " --> pdb=" O CYS A 429 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS A 429 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 535 through 536 removed outlier: 4.136A pdb=" N VAL A 536 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 547 " --> pdb=" O VAL A 536 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.152A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 698 through 701 removed outlier: 6.545A pdb=" N ALA A 698 " --> pdb=" O ILE B 785 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS B 787 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASN A 700 " --> pdb=" O LYS B 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 725 removed outlier: 6.421A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 725 removed outlier: 6.421A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AB6, first strand: chain 'A' and resid 784 through 786 removed outlier: 5.804A pdb=" N ILE A 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.088A pdb=" N VAL B 36 " --> pdb=" O LEU B 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.977A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AC3, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.665A pdb=" N ARG B 234 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY B 105 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.609A pdb=" N LYS B 201 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE B 196 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP B 225 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B 198 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.565A pdb=" N LYS B 127 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLU B 130 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS B 161 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLN B 132 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N ASN B 159 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 308 through 316 removed outlier: 7.229A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 322 through 323 removed outlier: 3.664A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 352 through 355 Processing sheet with id=AC9, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.398A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 375 through 376 removed outlier: 4.043A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.191A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR B 692 " --> pdb=" O CYS B 668 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS B 668 " --> pdb=" O TYR B 692 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 661 " --> pdb=" O ALA B 669 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 698 through 700 Processing sheet with id=AD4, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.862A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.862A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD7, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.767A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.752A pdb=" N GLN C 268 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 114 removed outlier: 3.676A pdb=" N CYS C 129 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLU C 130 " --> pdb=" O CYS C 161 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N CYS C 161 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N GLN C 132 " --> pdb=" O ASN C 159 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ASN C 159 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AE4, first strand: chain 'C' and resid 186 through 192 removed outlier: 3.588A pdb=" N ILE C 198 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL C 224 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N SER C 200 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.246A pdb=" N GLU C 306 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY C 598 " --> pdb=" O GLU C 306 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.246A pdb=" N GLU C 306 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY C 598 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 610 " --> pdb=" O GLY C 591 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.182A pdb=" N LYS C 353 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL C 392 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N SER C 511 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA C 394 " --> pdb=" O VAL C 509 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C 509 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 507 " --> pdb=" O PHE C 397 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE C 397 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.182A pdb=" N LYS C 353 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL C 392 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N SER C 511 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA C 394 " --> pdb=" O VAL C 509 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C 509 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU C 510 " --> pdb=" O CYS C 429 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS C 429 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 535 through 537 removed outlier: 3.601A pdb=" N VAL C 536 " --> pdb=" O GLY C 547 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY C 547 " --> pdb=" O VAL C 536 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.028A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.620A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.620A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AF5, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AF6, first strand: chain 'E' and resid 4 through 8 removed outlier: 3.718A pdb=" N VAL E 82 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 12 through 13 removed outlier: 3.539A pdb=" N SER E 50 " --> pdb=" O TRP E 37 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG E 39 " --> pdb=" O GLY E 48 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLY E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 12 through 13 Processing sheet with id=AF9, first strand: chain 'D' and resid 4 through 8 removed outlier: 3.541A pdb=" N SER D 74 " --> pdb=" O TYR D 83 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AG2, first strand: chain 'D' and resid 62 through 63 removed outlier: 5.251A pdb=" N GLY D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ARG D 39 " --> pdb=" O GLY D 48 " (cutoff:3.500A) 932 hydrogen bonds defined for protein. 2518 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: 4.62 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.92: 1 0.92 - 1.22: 0 1.22 - 1.51: 17966 1.51 - 1.81: 10895 1.81 - 2.10: 28 Bond restraints: 28890 Sorted by residual: bond pdb=" CG PRO E 32 " pdb=" CD PRO E 32 " ideal model delta sigma weight residual 1.503 0.625 0.878 3.40e-02 8.65e+02 6.66e+02 bond pdb=" CB PRO E 32 " pdb=" CG PRO E 32 " ideal model delta sigma weight residual 1.492 2.104 -0.612 5.00e-02 4.00e+02 1.50e+02 bond pdb=" N PRO E 32 " pdb=" CD PRO E 32 " ideal model delta sigma weight residual 1.473 1.631 -0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" N PRO E 32 " pdb=" CA PRO E 32 " ideal model delta sigma weight residual 1.469 1.384 0.085 1.28e-02 6.10e+03 4.43e+01 bond pdb=" CA PRO E 32 " pdb=" CB PRO E 32 " ideal model delta sigma weight residual 1.533 1.468 0.065 1.42e-02 4.96e+03 2.10e+01 ... (remaining 28885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.18: 39296 8.18 - 16.36: 13 16.36 - 24.54: 4 24.54 - 32.73: 0 32.73 - 40.91: 1 Bond angle restraints: 39314 Sorted by residual: angle pdb=" CA PRO E 32 " pdb=" N PRO E 32 " pdb=" CD PRO E 32 " ideal model delta sigma weight residual 112.00 89.68 22.32 1.40e+00 5.10e-01 2.54e+02 angle pdb=" N PRO E 32 " pdb=" CD PRO E 32 " pdb=" CG PRO E 32 " ideal model delta sigma weight residual 103.20 82.83 20.37 1.50e+00 4.44e-01 1.84e+02 angle pdb=" CB PRO E 32 " pdb=" CG PRO E 32 " pdb=" CD PRO E 32 " ideal model delta sigma weight residual 106.10 65.19 40.91 3.20e+00 9.77e-02 1.63e+02 angle pdb=" N PRO E 32 " pdb=" CA PRO E 32 " pdb=" CB PRO E 32 " ideal model delta sigma weight residual 103.25 90.82 12.43 1.05e+00 9.07e-01 1.40e+02 angle pdb=" CA PRO E 32 " pdb=" CB PRO E 32 " pdb=" CG PRO E 32 " ideal model delta sigma weight residual 104.50 84.60 19.90 1.90e+00 2.77e-01 1.10e+02 ... (remaining 39309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.20: 16600 25.20 - 50.41: 957 50.41 - 75.61: 120 75.61 - 100.81: 44 100.81 - 126.02: 27 Dihedral angle restraints: 17748 sinusoidal: 7418 harmonic: 10330 Sorted by residual: dihedral pdb=" CB CYS C 837 " pdb=" SG CYS C 837 " pdb=" SG CYS C 848 " pdb=" CB CYS C 848 " ideal model delta sinusoidal sigma weight residual -86.00 -175.79 89.79 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS A 837 " pdb=" SG CYS A 837 " pdb=" SG CYS A 848 " pdb=" CB CYS A 848 " ideal model delta sinusoidal sigma weight residual 93.00 178.19 -85.19 1 1.00e+01 1.00e-02 8.79e+01 dihedral pdb=" CB CYS B 535 " pdb=" SG CYS B 535 " pdb=" SG CYS B 587 " pdb=" CB CYS B 587 " ideal model delta sinusoidal sigma weight residual -86.00 -26.16 -59.84 1 1.00e+01 1.00e-02 4.78e+01 ... (remaining 17745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 4510 0.199 - 0.399: 6 0.399 - 0.598: 5 0.598 - 0.797: 0 0.797 - 0.997: 3 Chirality restraints: 4524 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B1071 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.40 -1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 279 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A1131 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.66e+01 ... (remaining 4521 not shown) Planarity restraints: 5071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 31 " -0.070 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO E 32 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO E 32 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 32 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 24 " 0.064 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO A 25 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 369 " 0.050 5.00e-02 4.00e+02 7.60e-02 9.23e+00 pdb=" N PRO B 370 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 370 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 370 " 0.042 5.00e-02 4.00e+02 ... (remaining 5068 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 992 2.70 - 3.25: 28818 3.25 - 3.80: 45926 3.80 - 4.35: 57762 4.35 - 4.90: 94815 Nonbonded interactions: 228313 Sorted by model distance: nonbonded pdb=" NH2 ARG B 354 " pdb=" O PRO C 227 " model vdw 2.147 3.120 nonbonded pdb=" O GLU B 658 " pdb=" OH TYR B 692 " model vdw 2.173 3.040 nonbonded pdb=" O GLU A 658 " pdb=" OH TYR A 692 " model vdw 2.179 3.040 nonbonded pdb=" OD1 ASP B 464 " pdb=" OG SER B 466 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR A1113 " pdb=" OD1 ASP A1115 " model vdw 2.197 3.040 ... (remaining 228308 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 19 through 837 or resid 848 through 1303)) selection = (chain 'B' and (resid 19 through 441 or resid 444 through 1303)) selection = (chain 'C' and (resid 19 through 837 or resid 848 through 1303)) } ncs_group { reference = (chain 'D' and (resid 2 through 25 or resid 27 through 63 or resid 65 through 12 \ 7)) selection = (chain 'E' and (resid 2 through 25 or resid 27 through 63 or resid 65 through 12 \ 7)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.870 Find NCS groups from input model: 0.630 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 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 0.878 28972 Z= 0.251 Angle : 0.800 40.906 39514 Z= 0.403 Chirality : 0.052 0.997 4524 Planarity : 0.005 0.090 5046 Dihedral : 16.409 126.017 10976 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.68 % Favored : 93.98 % Rotamer: Outliers : 0.23 % Allowed : 11.73 % Favored : 88.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.14), residues: 3510 helix: 1.88 (0.21), residues: 677 sheet: -0.14 (0.22), residues: 583 loop : -1.35 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 325 TYR 0.018 0.001 TYR B 901 PHE 0.017 0.001 PHE C 830 TRP 0.013 0.001 TRP B 102 HIS 0.009 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00727 (28890) covalent geometry : angle 0.74727 (39314) SS BOND : bond 0.00214 ( 46) SS BOND : angle 0.68423 ( 92) hydrogen bonds : bond 0.19807 ( 879) hydrogen bonds : angle 8.51718 ( 2518) link_BETA1-4 : bond 0.01190 ( 11) link_BETA1-4 : angle 3.96777 ( 33) link_NAG-ASN : bond 0.00836 ( 25) link_NAG-ASN : angle 6.09566 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 739 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7163 (mp) cc_final: 0.6763 (tt) REVERT: A 90 PHE cc_start: 0.4272 (t80) cc_final: 0.3900 (t80) REVERT: A 172 MET cc_start: 0.3576 (pmm) cc_final: 0.3035 (ptp) REVERT: A 211 GLU cc_start: 0.5660 (mm-30) cc_final: 0.5243 (tp30) REVERT: A 239 LEU cc_start: 0.2566 (mt) cc_final: 0.2131 (tt) REVERT: A 272 PHE cc_start: 0.6760 (m-80) cc_final: 0.6321 (m-10) REVERT: A 276 TYR cc_start: 0.5311 (m-80) cc_final: 0.5104 (m-10) REVERT: A 296 THR cc_start: 0.7967 (m) cc_final: 0.7568 (p) REVERT: A 607 VAL cc_start: 0.6224 (t) cc_final: 0.5969 (m) REVERT: A 707 ASN cc_start: 0.6826 (p0) cc_final: 0.6507 (p0) REVERT: A 718 SER cc_start: 0.7936 (t) cc_final: 0.7527 (p) REVERT: A 774 ASN cc_start: 0.8839 (m-40) cc_final: 0.8451 (m110) REVERT: A 784 GLN cc_start: 0.6401 (mm-40) cc_final: 0.5850 (mm-40) REVERT: A 797 PHE cc_start: 0.6617 (m-80) cc_final: 0.6287 (m-80) REVERT: A 834 TYR cc_start: 0.3822 (OUTLIER) cc_final: 0.2698 (t80) REVERT: A 903 PHE cc_start: 0.7180 (m-10) cc_final: 0.6864 (m-80) REVERT: A 908 VAL cc_start: 0.6558 (t) cc_final: 0.6321 (m) REVERT: A 990 ILE cc_start: 0.7441 (mt) cc_final: 0.7204 (mt) REVERT: A 991 ASP cc_start: 0.6370 (m-30) cc_final: 0.6057 (m-30) REVERT: A 1001 LEU cc_start: 0.8590 (mt) cc_final: 0.8218 (mt) REVERT: A 1064 TYR cc_start: 0.6753 (t80) cc_final: 0.6469 (t80) REVERT: A 1073 THR cc_start: 0.6945 (m) cc_final: 0.6679 (p) REVERT: A 1117 THR cc_start: 0.6575 (p) cc_final: 0.6109 (t) REVERT: B 66 HIS cc_start: 0.4024 (t-90) cc_final: 0.3701 (t70) REVERT: B 102 TRP cc_start: 0.4625 (m-90) cc_final: 0.4256 (m-90) REVERT: B 148 MET cc_start: -0.0354 (tpt) cc_final: -0.0804 (ttm) REVERT: B 187 PHE cc_start: 0.8175 (m-80) cc_final: 0.7803 (m-80) REVERT: B 354 ARG cc_start: 0.4825 (mtt180) cc_final: 0.4064 (mmm-85) REVERT: B 383 LYS cc_start: 0.5085 (mttp) cc_final: 0.4804 (mmtt) REVERT: B 391 ASN cc_start: 0.3696 (p0) cc_final: 0.2917 (p0) REVERT: B 397 PHE cc_start: 0.4031 (m-10) cc_final: 0.3793 (m-80) REVERT: B 538 PHE cc_start: 0.4995 (p90) cc_final: 0.4131 (p90) REVERT: B 584 ILE cc_start: 0.3765 (mt) cc_final: 0.3314 (mm) REVERT: B 589 PHE cc_start: 0.5193 (p90) cc_final: 0.4863 (p90) REVERT: B 604 GLN cc_start: 0.7262 (tt0) cc_final: 0.6931 (pt0) REVERT: B 657 TYR cc_start: 0.6195 (m-10) cc_final: 0.5834 (m-80) REVERT: B 671 TYR cc_start: 0.5499 (t80) cc_final: 0.4385 (t80) REVERT: B 672 GLN cc_start: 0.5551 (mm-40) cc_final: 0.5148 (tt0) REVERT: B 753 TYR cc_start: 0.4953 (m-80) cc_final: 0.4382 (m-80) REVERT: B 770 GLU cc_start: 0.8193 (tt0) cc_final: 0.7287 (tt0) REVERT: B 793 TYR cc_start: 0.7165 (t80) cc_final: 0.6910 (t80) REVERT: B 798 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.6903 (p0) REVERT: B 861 LEU cc_start: 0.7356 (tp) cc_final: 0.6894 (mt) REVERT: B 869 GLN cc_start: 0.7445 (mt0) cc_final: 0.7107 (mm-40) REVERT: B 880 THR cc_start: 0.7962 (p) cc_final: 0.7648 (t) REVERT: B 884 THR cc_start: 0.7467 (p) cc_final: 0.7035 (t) REVERT: B 914 TYR cc_start: 0.5813 (m-80) cc_final: 0.5250 (m-80) REVERT: B 918 LYS cc_start: 0.7756 (mttp) cc_final: 0.7500 (tptt) REVERT: B 980 ARG cc_start: 0.6071 (ttm110) cc_final: 0.5732 (tmm160) REVERT: B 1033 GLN cc_start: 0.6543 (tt0) cc_final: 0.5748 (tt0) REVERT: B 1111 ILE cc_start: 0.7058 (mm) cc_final: 0.6828 (mp) REVERT: B 1112 ILE cc_start: 0.7619 (mt) cc_final: 0.7327 (pt) REVERT: B 1119 VAL cc_start: 0.7085 (t) cc_final: 0.6581 (m) REVERT: C 90 PHE cc_start: 0.6150 (t80) cc_final: 0.5944 (t80) REVERT: C 172 MET cc_start: 0.4339 (pmm) cc_final: 0.3872 (ppp) REVERT: C 297 LYS cc_start: 0.7768 (mttt) cc_final: 0.7390 (ttmt) REVERT: C 307 LYS cc_start: 0.4793 (ttpp) cc_final: 0.4476 (ttpt) REVERT: C 320 THR cc_start: 0.5593 (p) cc_final: 0.5052 (p) REVERT: C 321 GLU cc_start: 0.6003 (pm20) cc_final: 0.4444 (mt-10) REVERT: C 564 ARG cc_start: 0.5472 (mmt180) cc_final: 0.4447 (mmt180) REVERT: C 568 ASP cc_start: 0.6273 (t70) cc_final: 0.6012 (t70) REVERT: C 592 VAL cc_start: 0.7631 (m) cc_final: 0.7314 (p) REVERT: C 607 VAL cc_start: 0.7532 (t) cc_final: 0.7315 (p) REVERT: C 631 ARG cc_start: 0.4713 (pmt170) cc_final: 0.4314 (mtm-85) REVERT: C 633 TYR cc_start: 0.4639 (p90) cc_final: 0.3897 (p90) REVERT: C 655 ASN cc_start: 0.7291 (m-40) cc_final: 0.6874 (p0) REVERT: C 658 GLU cc_start: 0.6654 (tt0) cc_final: 0.6363 (pm20) REVERT: C 660 ASP cc_start: 0.6079 (t0) cc_final: 0.5841 (t0) REVERT: C 694 MET cc_start: 0.6642 (tpp) cc_final: 0.5980 (tpt) REVERT: C 704 TYR cc_start: 0.5807 (t80) cc_final: 0.5426 (t80) REVERT: C 753 TYR cc_start: 0.5963 (m-80) cc_final: 0.5519 (m-80) REVERT: C 820 PHE cc_start: 0.7401 (m-80) cc_final: 0.6694 (m-80) REVERT: C 831 ILE cc_start: 0.0705 (tp) cc_final: 0.0505 (pt) REVERT: C 833 GLN cc_start: 0.4253 (mp10) cc_final: 0.2935 (pm20) REVERT: C 864 ASP cc_start: 0.7270 (m-30) cc_final: 0.6660 (t70) REVERT: C 869 GLN cc_start: 0.8233 (mt0) cc_final: 0.7572 (mm110) REVERT: C 922 ASN cc_start: 0.8303 (m-40) cc_final: 0.7942 (t0) REVERT: C 970 ILE cc_start: 0.5189 (mt) cc_final: 0.4919 (mm) REVERT: C 984 PRO cc_start: 0.6524 (Cg_exo) cc_final: 0.5827 (Cg_endo) REVERT: C 985 GLU cc_start: 0.6127 (tp30) cc_final: 0.5780 (mp0) REVERT: C 990 ILE cc_start: 0.7754 (mt) cc_final: 0.7544 (mm) REVERT: C 1015 ILE cc_start: 0.8280 (mm) cc_final: 0.7887 (tp) REVERT: C 1021 LEU cc_start: 0.8741 (tp) cc_final: 0.8434 (mt) REVERT: C 1033 GLN cc_start: 0.5426 (tt0) cc_final: 0.4992 (tp-100) REVERT: C 1099 TRP cc_start: 0.7200 (m100) cc_final: 0.6760 (m100) REVERT: C 1126 VAL cc_start: 0.7368 (t) cc_final: 0.7139 (p) REVERT: D 46 ARG cc_start: 0.0026 (mtt180) cc_final: -0.0702 (mtp85) REVERT: D 53 SER cc_start: 0.1953 (m) cc_final: 0.1550 (t) REVERT: D 86 MET cc_start: 0.0924 (ptt) cc_final: 0.0442 (ptt) REVERT: D 97 TYR cc_start: 0.4118 (m-80) cc_final: 0.3854 (m-80) outliers start: 7 outliers final: 2 residues processed: 745 average time/residue: 0.1777 time to fit residues: 204.5751 Evaluate side-chains 362 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 358 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain B residue 798 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.0470 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.0470 chunk 248 optimal weight: 0.0040 chunk 207 optimal weight: 0.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN A 989 GLN A1007 GLN A1008 GLN A1033 GLN A1103 GLN ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 759 GLN B 925 ASN B 952 ASN B1080 HIS B1103 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 ASN ** C 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 GLN ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN E 122 GLN D 77 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.108846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.087324 restraints weight = 275436.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.087641 restraints weight = 160186.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.088181 restraints weight = 116835.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.088481 restraints weight = 98809.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.088558 restraints weight = 92559.555| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5700 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 28972 Z= 0.144 Angle : 0.746 17.505 39514 Z= 0.362 Chirality : 0.051 0.647 4524 Planarity : 0.005 0.075 5046 Dihedral : 11.230 116.722 4608 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.42 % Favored : 94.24 % Rotamer: Outliers : 2.20 % Allowed : 16.08 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -0.71 (0.14), residues: 3510 helix: 1.81 (0.21), residues: 675 sheet: -0.08 (0.20), residues: 633 loop : -1.41 (0.12), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 34 TYR 0.038 0.001 TYR B 901 PHE 0.029 0.002 PHE C 326 TRP 0.016 0.001 TRP C 102 HIS 0.006 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00316 (28890) covalent geometry : angle 0.69713 (39314) SS BOND : bond 0.00448 ( 46) SS BOND : angle 1.71827 ( 92) hydrogen bonds : bond 0.04517 ( 879) hydrogen bonds : angle 6.49185 ( 2518) link_BETA1-4 : bond 0.01009 ( 11) link_BETA1-4 : angle 3.52604 ( 33) link_NAG-ASN : bond 0.00977 ( 25) link_NAG-ASN : angle 5.43431 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 397 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7052 (mp) cc_final: 0.6778 (tt) REVERT: A 172 MET cc_start: 0.3931 (pmm) cc_final: 0.3482 (ptp) REVERT: A 211 GLU cc_start: 0.5795 (mm-30) cc_final: 0.5423 (tp30) REVERT: A 223 LEU cc_start: 0.5720 (OUTLIER) cc_final: 0.5474 (tp) REVERT: A 239 LEU cc_start: 0.2669 (mt) cc_final: 0.2273 (tt) REVERT: A 272 PHE cc_start: 0.6170 (m-80) cc_final: 0.5960 (m-80) REVERT: A 282 ILE cc_start: 0.5051 (mt) cc_final: 0.4561 (mt) REVERT: A 296 THR cc_start: 0.7666 (m) cc_final: 0.7365 (p) REVERT: A 321 GLU cc_start: 0.3473 (OUTLIER) cc_final: 0.3214 (pt0) REVERT: A 525 LYS cc_start: 0.6091 (tptp) cc_final: 0.5849 (tppp) REVERT: A 539 ASN cc_start: 0.3410 (t0) cc_final: 0.2867 (m-40) REVERT: A 607 VAL cc_start: 0.5379 (t) cc_final: 0.5140 (m) REVERT: A 753 TYR cc_start: 0.4344 (m-80) cc_final: 0.4051 (m-80) REVERT: A 758 THR cc_start: 0.7181 (p) cc_final: 0.6928 (t) REVERT: A 834 TYR cc_start: 0.3080 (OUTLIER) cc_final: 0.2187 (t80) REVERT: A 914 TYR cc_start: 0.6249 (m-80) cc_final: 0.5694 (m-80) REVERT: A 945 LEU cc_start: 0.7704 (mt) cc_final: 0.7397 (mt) REVERT: A 997 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7429 (mtt-85) REVERT: A 1073 THR cc_start: 0.6669 (m) cc_final: 0.6328 (p) REVERT: B 66 HIS cc_start: 0.4370 (t-90) cc_final: 0.3964 (t70) REVERT: B 84 PHE cc_start: 0.6355 (t80) cc_final: 0.5986 (t80) REVERT: B 99 ILE cc_start: 0.4377 (mm) cc_final: 0.4138 (mm) REVERT: B 293 LEU cc_start: 0.7749 (mt) cc_final: 0.7526 (mp) REVERT: B 354 ARG cc_start: 0.4227 (mtt180) cc_final: 0.3276 (mmm-85) REVERT: B 391 ASN cc_start: 0.3147 (p0) cc_final: 0.2374 (p0) REVERT: B 397 PHE cc_start: 0.4603 (m-10) cc_final: 0.3924 (m-80) REVERT: B 538 PHE cc_start: 0.4761 (p90) cc_final: 0.3967 (p90) REVERT: B 584 ILE cc_start: 0.4157 (mt) cc_final: 0.3905 (mp) REVERT: B 737 MET cc_start: 0.5950 (tmm) cc_final: 0.5534 (ppp) REVERT: B 798 ASN cc_start: 0.6178 (OUTLIER) cc_final: 0.5443 (p0) REVERT: B 880 THR cc_start: 0.7525 (p) cc_final: 0.7044 (t) REVERT: B 884 THR cc_start: 0.7949 (p) cc_final: 0.7393 (t) REVERT: B 930 LYS cc_start: 0.7981 (mttt) cc_final: 0.7730 (mtpp) REVERT: B 944 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7830 (mttt) REVERT: B 1033 GLN cc_start: 0.6817 (tt0) cc_final: 0.6594 (tt0) REVERT: B 1107 TYR cc_start: 0.5501 (t80) cc_final: 0.5236 (t80) REVERT: C 59 PHE cc_start: 0.6501 (m-80) cc_final: 0.6202 (m-80) REVERT: C 90 PHE cc_start: 0.5366 (t80) cc_final: 0.5077 (t80) REVERT: C 297 LYS cc_start: 0.8018 (mttt) cc_final: 0.7581 (ttmt) REVERT: C 320 THR cc_start: 0.5363 (p) cc_final: 0.4518 (t) REVERT: C 321 GLU cc_start: 0.5835 (pm20) cc_final: 0.3788 (mt-10) REVERT: C 455 LYS cc_start: 0.0403 (OUTLIER) cc_final: -0.0876 (mmtt) REVERT: C 494 PHE cc_start: -0.0130 (OUTLIER) cc_final: -0.0584 (m-10) REVERT: C 564 ARG cc_start: 0.4462 (mmt180) cc_final: 0.3908 (mmt180) REVERT: C 568 ASP cc_start: 0.5916 (t70) cc_final: 0.5607 (t70) REVERT: C 584 ILE cc_start: 0.3058 (OUTLIER) cc_final: 0.2830 (tp) REVERT: C 633 TYR cc_start: 0.4580 (p90) cc_final: 0.4176 (p90) REVERT: C 737 MET cc_start: 0.7470 (ppp) cc_final: 0.7029 (ppp) REVERT: C 753 TYR cc_start: 0.5718 (m-80) cc_final: 0.4799 (m-80) REVERT: C 820 PHE cc_start: 0.6754 (m-80) cc_final: 0.6200 (m-80) REVERT: C 833 GLN cc_start: 0.3279 (mp10) cc_final: 0.2677 (pm20) REVERT: C 910 GLN cc_start: 0.6846 (pm20) cc_final: 0.6299 (mt0) REVERT: C 984 PRO cc_start: 0.6255 (Cg_exo) cc_final: 0.5575 (Cg_endo) REVERT: C 1033 GLN cc_start: 0.5843 (tt0) cc_final: 0.5522 (tp-100) REVERT: C 1099 TRP cc_start: 0.6394 (m100) cc_final: 0.5917 (m100) outliers start: 68 outliers final: 25 residues processed: 455 average time/residue: 0.1703 time to fit residues: 125.0056 Evaluate side-chains 308 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 276 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 746 CYS Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1099 TRP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 204 optimal weight: 0.9990 chunk 319 optimal weight: 2.9990 chunk 271 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 55 optimal weight: 0.2980 chunk 59 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 268 optimal weight: 0.0980 chunk 257 optimal weight: 0.9990 chunk 152 optimal weight: 0.0060 chunk 88 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 HIS A 752 GLN A 774 ASN A 801 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 GLN ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 752 GLN ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 922 ASN C 989 GLN E 2 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.109007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.087081 restraints weight = 289350.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.087616 restraints weight = 166200.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.087965 restraints weight = 132156.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.087858 restraints weight = 121301.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.088157 restraints weight = 112246.239| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 28972 Z= 0.132 Angle : 0.723 17.726 39514 Z= 0.344 Chirality : 0.051 0.953 4524 Planarity : 0.005 0.075 5046 Dihedral : 9.865 119.908 4608 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.50 % Favored : 94.21 % Rotamer: Outliers : 2.66 % Allowed : 17.21 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -0.72 (0.14), residues: 3510 helix: 1.78 (0.21), residues: 667 sheet: -0.00 (0.21), residues: 612 loop : -1.41 (0.12), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 631 TYR 0.030 0.001 TYR B 348 PHE 0.026 0.001 PHE A 138 TRP 0.028 0.001 TRP C 630 HIS 0.006 0.001 HIS A1098 Details of bonding type rmsd covalent geometry : bond 0.00287 (28890) covalent geometry : angle 0.67390 (39314) SS BOND : bond 0.00358 ( 46) SS BOND : angle 1.42270 ( 92) hydrogen bonds : bond 0.04027 ( 879) hydrogen bonds : angle 5.99116 ( 2518) link_BETA1-4 : bond 0.01116 ( 11) link_BETA1-4 : angle 3.55436 ( 33) link_NAG-ASN : bond 0.01392 ( 25) link_NAG-ASN : angle 5.43677 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 304 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6967 (mp) cc_final: 0.6654 (tt) REVERT: A 172 MET cc_start: 0.4470 (pmm) cc_final: 0.2547 (mpp) REVERT: A 211 GLU cc_start: 0.5718 (mm-30) cc_final: 0.5383 (tp30) REVERT: A 223 LEU cc_start: 0.5707 (OUTLIER) cc_final: 0.5484 (tp) REVERT: A 239 LEU cc_start: 0.2652 (mt) cc_final: 0.2302 (tt) REVERT: A 321 GLU cc_start: 0.3502 (OUTLIER) cc_final: 0.3215 (pt0) REVERT: A 834 TYR cc_start: 0.2956 (OUTLIER) cc_final: 0.2005 (t80) REVERT: A 865 GLU cc_start: 0.6747 (mp0) cc_final: 0.6411 (mp0) REVERT: A 893 ILE cc_start: 0.8370 (tt) cc_final: 0.8146 (mm) REVERT: A 914 TYR cc_start: 0.6073 (m-80) cc_final: 0.5644 (m-80) REVERT: A 945 LEU cc_start: 0.7656 (mt) cc_final: 0.7310 (mt) REVERT: A 1073 THR cc_start: 0.6003 (m) cc_final: 0.5776 (p) REVERT: A 1141 GLU cc_start: 0.5449 (pm20) cc_final: 0.5210 (pm20) REVERT: B 66 HIS cc_start: 0.4294 (t-90) cc_final: 0.3752 (t-90) REVERT: B 99 ILE cc_start: 0.4561 (mm) cc_final: 0.4310 (mm) REVERT: B 148 MET cc_start: -0.0316 (tpt) cc_final: -0.0805 (ttm) REVERT: B 187 PHE cc_start: 0.6870 (t80) cc_final: 0.6588 (t80) REVERT: B 228 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6544 (tt) REVERT: B 391 ASN cc_start: 0.3112 (p0) cc_final: 0.2737 (p0) REVERT: B 489 LEU cc_start: 0.3008 (OUTLIER) cc_final: 0.2743 (pp) REVERT: B 526 LYS cc_start: 0.4561 (pptt) cc_final: 0.4239 (tptt) REVERT: B 538 PHE cc_start: 0.4656 (p90) cc_final: 0.3696 (p90) REVERT: B 584 ILE cc_start: 0.4005 (mt) cc_final: 0.3682 (mt) REVERT: B 609 TYR cc_start: 0.6895 (m-80) cc_final: 0.6476 (m-10) REVERT: B 750 LEU cc_start: 0.5868 (mt) cc_final: 0.5606 (mt) REVERT: B 798 ASN cc_start: 0.6464 (OUTLIER) cc_final: 0.6017 (p0) REVERT: B 880 THR cc_start: 0.7276 (p) cc_final: 0.6859 (t) REVERT: B 884 THR cc_start: 0.7827 (p) cc_final: 0.7285 (t) REVERT: B 897 MET cc_start: 0.5798 (mmt) cc_final: 0.5536 (mpp) REVERT: B 1016 ARG cc_start: 0.7319 (tpt170) cc_final: 0.6872 (tpt170) REVERT: C 90 PHE cc_start: 0.5422 (t80) cc_final: 0.5051 (t80) REVERT: C 297 LYS cc_start: 0.7998 (mttt) cc_final: 0.7570 (ttmt) REVERT: C 320 THR cc_start: 0.5422 (p) cc_final: 0.4500 (t) REVERT: C 321 GLU cc_start: 0.5964 (pm20) cc_final: 0.3956 (mt-10) REVERT: C 455 LYS cc_start: 0.0369 (OUTLIER) cc_final: -0.0867 (mmtp) REVERT: C 494 PHE cc_start: -0.0172 (OUTLIER) cc_final: -0.0636 (m-10) REVERT: C 564 ARG cc_start: 0.4378 (mmt180) cc_final: 0.3910 (mmt180) REVERT: C 568 ASP cc_start: 0.5904 (t70) cc_final: 0.5638 (t70) REVERT: C 633 TYR cc_start: 0.4766 (p90) cc_final: 0.4481 (p90) REVERT: C 737 MET cc_start: 0.7373 (ppp) cc_final: 0.7094 (ppp) REVERT: C 833 GLN cc_start: 0.2881 (mp10) cc_final: 0.2425 (pp30) REVERT: C 910 GLN cc_start: 0.6750 (pm20) cc_final: 0.6351 (mt0) REVERT: C 1099 TRP cc_start: 0.6399 (m100) cc_final: 0.5868 (m100) REVERT: E 62 TYR cc_start: 0.1992 (m-80) cc_final: 0.1716 (m-80) REVERT: D 116 TRP cc_start: 0.3728 (m-90) cc_final: 0.3164 (m100) outliers start: 82 outliers final: 46 residues processed: 374 average time/residue: 0.1548 time to fit residues: 94.6589 Evaluate side-chains 301 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 247 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1099 TRP Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 32 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 ASN ** 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 = 0.4316 r_free = 0.4316 target = 0.108278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.085896 restraints weight = 234504.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.085831 restraints weight = 191122.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.086514 restraints weight = 124512.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.086722 restraints weight = 111082.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.086835 restraints weight = 97706.693| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28972 Z= 0.133 Angle : 0.695 18.276 39514 Z= 0.333 Chirality : 0.050 0.762 4524 Planarity : 0.005 0.073 5046 Dihedral : 8.521 89.651 4608 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.59 % Favored : 94.15 % Rotamer: Outliers : 2.76 % Allowed : 18.41 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -0.79 (0.14), residues: 3510 helix: 1.69 (0.21), residues: 670 sheet: -0.08 (0.21), residues: 613 loop : -1.44 (0.12), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 354 TYR 0.038 0.002 TYR B 901 PHE 0.018 0.002 PHE A 138 TRP 0.023 0.001 TRP C 102 HIS 0.007 0.001 HIS A1080 Details of bonding type rmsd covalent geometry : bond 0.00289 (28890) covalent geometry : angle 0.64817 (39314) SS BOND : bond 0.00264 ( 46) SS BOND : angle 1.38453 ( 92) hydrogen bonds : bond 0.03634 ( 879) hydrogen bonds : angle 5.63194 ( 2518) link_BETA1-4 : bond 0.01184 ( 11) link_BETA1-4 : angle 3.60878 ( 33) link_NAG-ASN : bond 0.00835 ( 25) link_NAG-ASN : angle 5.12153 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 293 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6792 (mp) cc_final: 0.6553 (tt) REVERT: A 172 MET cc_start: 0.4310 (pmm) cc_final: 0.3814 (ptt) REVERT: A 239 LEU cc_start: 0.2417 (mt) cc_final: 0.2061 (tt) REVERT: A 266 TYR cc_start: 0.5229 (m-80) cc_final: 0.4242 (t80) REVERT: A 374 PHE cc_start: 0.3368 (p90) cc_final: 0.2656 (p90) REVERT: A 707 ASN cc_start: 0.5758 (p0) cc_final: 0.5554 (p0) REVERT: A 834 TYR cc_start: 0.3131 (OUTLIER) cc_final: 0.2099 (t80) REVERT: A 893 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8259 (mm) REVERT: A 914 TYR cc_start: 0.6402 (m-80) cc_final: 0.5793 (m-80) REVERT: A 945 LEU cc_start: 0.8016 (mt) cc_final: 0.7715 (mt) REVERT: A 1049 PHE cc_start: 0.8199 (m-80) cc_final: 0.7938 (m-80) REVERT: A 1073 THR cc_start: 0.6951 (m) cc_final: 0.6299 (p) REVERT: A 1125 VAL cc_start: 0.5776 (m) cc_final: 0.4525 (p) REVERT: B 66 HIS cc_start: 0.4057 (t-90) cc_final: 0.3573 (t70) REVERT: B 99 ILE cc_start: 0.4603 (mm) cc_final: 0.4399 (mm) REVERT: B 489 LEU cc_start: 0.3582 (OUTLIER) cc_final: 0.3215 (pp) REVERT: B 526 LYS cc_start: 0.5026 (pptt) cc_final: 0.4562 (tptt) REVERT: B 538 PHE cc_start: 0.4389 (p90) cc_final: 0.3126 (p90) REVERT: B 584 ILE cc_start: 0.4449 (mt) cc_final: 0.4214 (mt) REVERT: B 702 VAL cc_start: 0.8041 (OUTLIER) cc_final: 0.7602 (m) REVERT: B 750 LEU cc_start: 0.6120 (mt) cc_final: 0.5797 (mt) REVERT: B 798 ASN cc_start: 0.6277 (OUTLIER) cc_final: 0.5890 (p0) REVERT: B 880 THR cc_start: 0.7536 (p) cc_final: 0.7105 (t) REVERT: B 884 THR cc_start: 0.8191 (p) cc_final: 0.7493 (t) REVERT: B 914 TYR cc_start: 0.5668 (m-80) cc_final: 0.5147 (m-10) REVERT: B 915 GLU cc_start: 0.6500 (mt-10) cc_final: 0.5552 (mm-30) REVERT: B 1016 ARG cc_start: 0.7511 (tpt170) cc_final: 0.6905 (tpt170) REVERT: B 1047 MET cc_start: 0.6533 (pmm) cc_final: 0.6222 (pmm) REVERT: C 90 PHE cc_start: 0.5805 (t80) cc_final: 0.5477 (t80) REVERT: C 196 PHE cc_start: 0.7191 (m-80) cc_final: 0.6921 (m-80) REVERT: C 263 TYR cc_start: 0.5317 (m-10) cc_final: 0.5066 (m-10) REVERT: C 297 LYS cc_start: 0.7913 (mttt) cc_final: 0.7416 (ttmt) REVERT: C 320 THR cc_start: 0.5509 (p) cc_final: 0.4806 (p) REVERT: C 321 GLU cc_start: 0.6203 (pm20) cc_final: 0.4390 (mt-10) REVERT: C 455 LYS cc_start: 0.0111 (OUTLIER) cc_final: -0.0975 (mmtt) REVERT: C 494 PHE cc_start: -0.0086 (OUTLIER) cc_final: -0.0472 (m-10) REVERT: C 564 ARG cc_start: 0.4617 (mmt180) cc_final: 0.4263 (mmt180) REVERT: C 568 ASP cc_start: 0.6158 (t70) cc_final: 0.5904 (t70) REVERT: C 569 THR cc_start: 0.5155 (OUTLIER) cc_final: 0.4879 (m) REVERT: C 633 TYR cc_start: 0.4698 (p90) cc_final: 0.4294 (p90) REVERT: C 833 GLN cc_start: 0.3652 (mp10) cc_final: 0.2761 (pp30) REVERT: C 910 GLN cc_start: 0.7156 (pm20) cc_final: 0.6305 (mt0) REVERT: C 1015 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8198 (tt) REVERT: C 1099 TRP cc_start: 0.6893 (m100) cc_final: 0.6241 (m100) REVERT: E 62 TYR cc_start: 0.2151 (m-80) cc_final: 0.1948 (m-80) REVERT: D 81 THR cc_start: 0.1493 (m) cc_final: 0.1154 (m) REVERT: D 86 MET cc_start: 0.0012 (ptt) cc_final: -0.0371 (ptp) REVERT: D 116 TRP cc_start: 0.3385 (m-90) cc_final: 0.2972 (m100) outliers start: 85 outliers final: 53 residues processed: 361 average time/residue: 0.1596 time to fit residues: 95.0055 Evaluate side-chains 294 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 232 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1000 SER Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1099 TRP Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain E residue 124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 260 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 296 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN A 311 GLN A 340 ASN A 752 GLN A1098 HIS B 66 HIS ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN B 989 GLN C 79 ASN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN C 610 GLN ** C 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN E 122 GLN D 111 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.104679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.082422 restraints weight = 223865.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.081789 restraints weight = 149505.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.082350 restraints weight = 114536.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.082498 restraints weight = 91267.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.082604 restraints weight = 85990.666| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28972 Z= 0.229 Angle : 0.871 19.519 39514 Z= 0.432 Chirality : 0.055 0.659 4524 Planarity : 0.006 0.069 5046 Dihedral : 8.927 87.955 4607 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.70 % Favored : 91.99 % Rotamer: Outliers : 4.51 % Allowed : 19.00 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -1.43 (0.13), residues: 3510 helix: 1.01 (0.20), residues: 654 sheet: -0.58 (0.21), residues: 597 loop : -1.76 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 454 TYR 0.033 0.003 TYR B 348 PHE 0.032 0.003 PHE C 217 TRP 0.034 0.003 TRP C 102 HIS 0.010 0.002 HIS A1080 Details of bonding type rmsd covalent geometry : bond 0.00501 (28890) covalent geometry : angle 0.82845 (39314) SS BOND : bond 0.00448 ( 46) SS BOND : angle 1.86354 ( 92) hydrogen bonds : bond 0.04640 ( 879) hydrogen bonds : angle 6.13182 ( 2518) link_BETA1-4 : bond 0.01025 ( 11) link_BETA1-4 : angle 3.78887 ( 33) link_NAG-ASN : bond 0.00918 ( 25) link_NAG-ASN : angle 5.38217 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 289 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 GLN cc_start: 0.4019 (pm20) cc_final: 0.3096 (tp-100) REVERT: A 172 MET cc_start: 0.4218 (pmm) cc_final: 0.3655 (ptt) REVERT: A 193 ASP cc_start: 0.5427 (OUTLIER) cc_final: 0.5106 (t70) REVERT: A 525 LYS cc_start: 0.7014 (tppp) cc_final: 0.6720 (tmtt) REVERT: A 526 LYS cc_start: 0.5276 (OUTLIER) cc_final: 0.4774 (mptt) REVERT: A 834 TYR cc_start: 0.3386 (OUTLIER) cc_final: 0.2308 (t80) REVERT: A 866 MET cc_start: 0.7660 (ptp) cc_final: 0.7401 (ptp) REVERT: A 1098 HIS cc_start: 0.6186 (OUTLIER) cc_final: 0.5872 (m170) REVERT: B 152 PHE cc_start: 0.3378 (m-80) cc_final: 0.2479 (p90) REVERT: B 172 MET cc_start: 0.5193 (mmt) cc_final: 0.3994 (ttp) REVERT: B 189 PHE cc_start: 0.4500 (t80) cc_final: 0.4230 (t80) REVERT: B 405 ARG cc_start: 0.4417 (mpp80) cc_final: 0.4046 (mpp80) REVERT: B 526 LYS cc_start: 0.4854 (OUTLIER) cc_final: 0.3908 (mmtm) REVERT: B 538 PHE cc_start: 0.4718 (p90) cc_final: 0.3534 (p90) REVERT: B 556 PHE cc_start: 0.3722 (OUTLIER) cc_final: 0.3249 (m-10) REVERT: B 702 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.7974 (m) REVERT: B 1106 PHE cc_start: 0.4649 (t80) cc_final: 0.4338 (t80) REVERT: B 1135 TYR cc_start: 0.5536 (t80) cc_final: 0.5324 (t80) REVERT: C 187 PHE cc_start: 0.3526 (m-80) cc_final: 0.2856 (m-80) REVERT: C 263 TYR cc_start: 0.5608 (m-10) cc_final: 0.5352 (m-10) REVERT: C 297 LYS cc_start: 0.8020 (mttt) cc_final: 0.7629 (ttmt) REVERT: C 311 GLN cc_start: 0.6332 (mt0) cc_final: 0.5383 (tp-100) REVERT: C 541 ASN cc_start: 0.5807 (m-40) cc_final: 0.5518 (t0) REVERT: C 564 ARG cc_start: 0.4797 (mmt180) cc_final: 0.4580 (mmp80) REVERT: C 587 CYS cc_start: 0.1355 (p) cc_final: 0.1042 (p) REVERT: C 633 TYR cc_start: 0.5273 (OUTLIER) cc_final: 0.4476 (p90) REVERT: C 753 TYR cc_start: 0.6698 (OUTLIER) cc_final: 0.6092 (m-10) REVERT: C 805 ASP cc_start: 0.4369 (p0) cc_final: 0.4154 (p0) REVERT: C 865 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: D 68 LYS cc_start: 0.0851 (mtpt) cc_final: 0.0160 (mmmt) REVERT: D 79 LYS cc_start: 0.2066 (tptp) cc_final: 0.1439 (mtmm) outliers start: 139 outliers final: 78 residues processed: 411 average time/residue: 0.1481 time to fit residues: 100.9785 Evaluate side-chains 314 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 226 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1000 SER Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1098 HIS Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 938 THR Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1005 VAL Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 633 TYR Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 753 TYR Chi-restraints excluded: chain C residue 865 GLU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 125 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 154 optimal weight: 0.5980 chunk 322 optimal weight: 5.9990 chunk 333 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 193 optimal weight: 0.6980 chunk 182 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 774 ASN A 951 HIS A 999 GLN B 66 HIS B 202 HIS B 311 GLN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.105928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.084485 restraints weight = 287608.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.083861 restraints weight = 198120.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.084286 restraints weight = 158289.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.084532 restraints weight = 119827.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.084722 restraints weight = 120566.094| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28972 Z= 0.132 Angle : 0.703 19.129 39514 Z= 0.341 Chirality : 0.049 0.558 4524 Planarity : 0.005 0.064 5046 Dihedral : 8.084 77.229 4607 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.82 % Favored : 93.90 % Rotamer: Outliers : 2.79 % Allowed : 21.65 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -1.20 (0.14), residues: 3510 helix: 1.37 (0.21), residues: 662 sheet: -0.52 (0.21), residues: 625 loop : -1.66 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 234 TYR 0.033 0.002 TYR A 448 PHE 0.024 0.002 PHE B1072 TRP 0.030 0.002 TRP B 630 HIS 0.024 0.001 HIS A1098 Details of bonding type rmsd covalent geometry : bond 0.00292 (28890) covalent geometry : angle 0.65550 (39314) SS BOND : bond 0.00276 ( 46) SS BOND : angle 1.33153 ( 92) hydrogen bonds : bond 0.03720 ( 879) hydrogen bonds : angle 5.68521 ( 2518) link_BETA1-4 : bond 0.01054 ( 11) link_BETA1-4 : angle 3.72472 ( 33) link_NAG-ASN : bond 0.00843 ( 25) link_NAG-ASN : angle 5.15153 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 260 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 GLN cc_start: 0.4032 (pm20) cc_final: 0.3074 (tp-100) REVERT: A 172 MET cc_start: 0.4152 (pmm) cc_final: 0.3450 (ptt) REVERT: A 266 TYR cc_start: 0.5225 (m-80) cc_final: 0.3731 (t80) REVERT: A 321 GLU cc_start: 0.4379 (OUTLIER) cc_final: 0.3835 (tp30) REVERT: A 526 LYS cc_start: 0.5061 (mmtt) cc_final: 0.4804 (mptt) REVERT: A 834 TYR cc_start: 0.2819 (OUTLIER) cc_final: 0.1533 (t80) REVERT: A 866 MET cc_start: 0.7643 (ptp) cc_final: 0.7365 (ptp) REVERT: A 914 TYR cc_start: 0.7019 (m-80) cc_final: 0.6057 (m-80) REVERT: B 84 PHE cc_start: 0.6479 (t80) cc_final: 0.6121 (t80) REVERT: B 152 PHE cc_start: 0.2692 (m-80) cc_final: 0.2106 (p90) REVERT: B 172 MET cc_start: 0.5141 (mmt) cc_final: 0.3967 (ttp) REVERT: B 405 ARG cc_start: 0.4424 (mpp80) cc_final: 0.4035 (mpp80) REVERT: B 489 LEU cc_start: 0.3068 (OUTLIER) cc_final: 0.2838 (pp) REVERT: B 526 LYS cc_start: 0.4921 (OUTLIER) cc_final: 0.4144 (mmtm) REVERT: B 538 PHE cc_start: 0.4130 (p90) cc_final: 0.2940 (p90) REVERT: B 556 PHE cc_start: 0.3563 (OUTLIER) cc_final: 0.2970 (m-10) REVERT: B 702 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.7864 (m) REVERT: B 762 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.6660 (mtp85) REVERT: B 776 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7177 (tt0) REVERT: B 798 ASN cc_start: 0.6287 (OUTLIER) cc_final: 0.5560 (p0) REVERT: B 1047 MET cc_start: 0.6653 (pmm) cc_final: 0.6166 (pmm) REVERT: B 1135 TYR cc_start: 0.5569 (t80) cc_final: 0.5317 (t80) REVERT: C 90 PHE cc_start: 0.5227 (t80) cc_final: 0.4928 (t80) REVERT: C 187 PHE cc_start: 0.3335 (m-80) cc_final: 0.2900 (m-80) REVERT: C 202 HIS cc_start: 0.2087 (t70) cc_final: 0.1629 (m-70) REVERT: C 263 TYR cc_start: 0.5505 (m-10) cc_final: 0.5298 (m-10) REVERT: C 297 LYS cc_start: 0.7975 (mttt) cc_final: 0.7553 (ttmt) REVERT: C 311 GLN cc_start: 0.6471 (mt0) cc_final: 0.5684 (tp-100) REVERT: C 321 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.4312 (mt-10) REVERT: C 414 ASN cc_start: 0.1681 (m-40) cc_final: 0.1386 (t0) REVERT: C 541 ASN cc_start: 0.5980 (m-40) cc_final: 0.5732 (t0) REVERT: C 584 ILE cc_start: 0.3702 (OUTLIER) cc_final: 0.3388 (tp) REVERT: C 587 CYS cc_start: 0.1321 (OUTLIER) cc_final: 0.1008 (p) REVERT: C 734 ASP cc_start: 0.6467 (t0) cc_final: 0.6260 (t0) REVERT: C 833 GLN cc_start: 0.3006 (mp10) cc_final: 0.2246 (pp30) REVERT: C 910 GLN cc_start: 0.7762 (pm20) cc_final: 0.6488 (mt0) REVERT: C 1015 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8548 (tt) REVERT: D 68 LYS cc_start: 0.1415 (mtpt) cc_final: 0.0586 (mmmt) REVERT: D 79 LYS cc_start: 0.1997 (tptp) cc_final: 0.1363 (mtmm) REVERT: D 116 TRP cc_start: 0.3539 (m-90) cc_final: 0.2957 (m-90) outliers start: 86 outliers final: 49 residues processed: 332 average time/residue: 0.1583 time to fit residues: 86.7208 Evaluate side-chains 274 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 213 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1000 SER Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1099 TRP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 776 GLN Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain D residue 53 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 316 optimal weight: 0.8980 chunk 240 optimal weight: 10.0000 chunk 304 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 284 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 293 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 311 GLN A 367 ASN A 419 ASN A 951 HIS A 999 GLN A1098 HIS A1103 GLN A1116 ASN B 311 GLN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN C 610 GLN ** C 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.102442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.079168 restraints weight = 196383.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.079519 restraints weight = 146616.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.079283 restraints weight = 103199.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.079572 restraints weight = 107715.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.079618 restraints weight = 94679.418| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.6615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 28972 Z= 0.293 Angle : 0.983 20.372 39514 Z= 0.492 Chirality : 0.059 0.613 4524 Planarity : 0.007 0.082 5046 Dihedral : 9.177 82.820 4607 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.10 % Favored : 90.62 % Rotamer: Outliers : 4.57 % Allowed : 21.85 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.52 % 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 aren not related in a simple way. whole: -2.10 (0.13), residues: 3510 helix: 0.21 (0.19), residues: 658 sheet: -0.91 (0.21), residues: 579 loop : -2.15 (0.12), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 631 TYR 0.037 0.004 TYR A 420 PHE 0.040 0.004 PHE A 315 TRP 0.036 0.004 TRP E 117 HIS 0.028 0.003 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00645 (28890) covalent geometry : angle 0.94121 (39314) SS BOND : bond 0.00681 ( 46) SS BOND : angle 2.14122 ( 92) hydrogen bonds : bond 0.05392 ( 879) hydrogen bonds : angle 6.55449 ( 2518) link_BETA1-4 : bond 0.01116 ( 11) link_BETA1-4 : angle 4.09280 ( 33) link_NAG-ASN : bond 0.00970 ( 25) link_NAG-ASN : angle 5.58986 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 235 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6072 (tt) cc_final: 0.5596 (pt) REVERT: A 172 MET cc_start: 0.4397 (pmm) cc_final: 0.3904 (ptt) REVERT: A 193 ASP cc_start: 0.5501 (OUTLIER) cc_final: 0.5171 (t70) REVERT: A 321 GLU cc_start: 0.5068 (OUTLIER) cc_final: 0.4810 (pm20) REVERT: A 389 PHE cc_start: 0.1560 (p90) cc_final: 0.1359 (p90) REVERT: A 525 LYS cc_start: 0.7111 (tppp) cc_final: 0.6887 (tmtt) REVERT: A 834 TYR cc_start: 0.3423 (OUTLIER) cc_final: 0.2099 (t80) REVERT: A 1047 MET cc_start: 0.6330 (ppp) cc_final: 0.6104 (ptm) REVERT: A 1098 HIS cc_start: 0.6283 (OUTLIER) cc_final: 0.5931 (m170) REVERT: B 152 PHE cc_start: 0.3939 (m-80) cc_final: 0.3052 (p90) REVERT: B 172 MET cc_start: 0.5122 (mmt) cc_final: 0.3845 (ttp) REVERT: B 235 PHE cc_start: 0.5389 (t80) cc_final: 0.4323 (t80) REVERT: B 386 ASP cc_start: 0.3162 (t70) cc_final: 0.2927 (t70) REVERT: B 405 ARG cc_start: 0.4322 (mpp80) cc_final: 0.4013 (mpp80) REVERT: B 526 LYS cc_start: 0.4916 (OUTLIER) cc_final: 0.4187 (mmtm) REVERT: B 538 PHE cc_start: 0.4681 (p90) cc_final: 0.3020 (p90) REVERT: B 556 PHE cc_start: 0.3686 (OUTLIER) cc_final: 0.3277 (m-10) REVERT: B 702 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7815 (m) REVERT: B 728 MET cc_start: 0.7582 (ttm) cc_final: 0.7249 (ttp) REVERT: B 737 MET cc_start: 0.6063 (tmm) cc_final: 0.5779 (tmm) REVERT: B 762 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7051 (mtp85) REVERT: B 1047 MET cc_start: 0.6706 (pmm) cc_final: 0.6253 (pmm) REVERT: B 1111 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6864 (mm) REVERT: C 175 GLU cc_start: 0.3460 (OUTLIER) cc_final: 0.2680 (mm-30) REVERT: C 301 LYS cc_start: 0.7300 (mmmm) cc_final: 0.6879 (tptp) REVERT: C 311 GLN cc_start: 0.6552 (mt0) cc_final: 0.5757 (tp-100) REVERT: C 584 ILE cc_start: 0.4574 (OUTLIER) cc_final: 0.4242 (tp) REVERT: C 587 CYS cc_start: 0.1588 (OUTLIER) cc_final: 0.1275 (p) REVERT: C 633 TYR cc_start: 0.5401 (OUTLIER) cc_final: 0.4699 (p90) REVERT: C 737 MET cc_start: 0.7456 (ppp) cc_final: 0.7019 (ppp) REVERT: C 753 TYR cc_start: 0.6738 (OUTLIER) cc_final: 0.6124 (m-10) REVERT: C 865 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6949 (pm20) REVERT: C 991 ASP cc_start: 0.6441 (OUTLIER) cc_final: 0.6229 (t0) REVERT: E 2 GLN cc_start: 0.4018 (OUTLIER) cc_final: 0.3799 (mm110) REVERT: D 79 LYS cc_start: 0.2616 (tptp) cc_final: 0.1858 (mtmm) outliers start: 141 outliers final: 92 residues processed: 360 average time/residue: 0.1508 time to fit residues: 89.9356 Evaluate side-chains 312 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 204 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1000 SER Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1098 HIS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 938 THR Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1005 VAL Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1064 TYR Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 633 TYR Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 753 TYR Chi-restraints excluded: chain C residue 865 GLU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain C residue 1100 PHE Chi-restraints excluded: chain C residue 1107 TYR Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain D residue 53 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 317 optimal weight: 0.0060 chunk 346 optimal weight: 0.9990 chunk 239 optimal weight: 0.9980 chunk 344 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 170 optimal weight: 0.5980 chunk 192 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 311 GLN A 951 HIS A1098 HIS A1116 ASN B 311 GLN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.104363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.082940 restraints weight = 284400.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.082686 restraints weight = 185742.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.083180 restraints weight = 144369.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.083366 restraints weight = 109695.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.083554 restraints weight = 112767.183| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 28972 Z= 0.140 Angle : 0.737 19.374 39514 Z= 0.360 Chirality : 0.050 0.581 4524 Planarity : 0.005 0.064 5046 Dihedral : 8.061 71.553 4607 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.10 % Favored : 93.61 % Rotamer: Outliers : 2.50 % Allowed : 24.05 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -1.65 (0.13), residues: 3510 helix: 1.06 (0.20), residues: 665 sheet: -0.94 (0.20), residues: 595 loop : -1.92 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 495 TYR 0.033 0.002 TYR B 498 PHE 0.029 0.002 PHE C 187 TRP 0.025 0.002 TRP B 630 HIS 0.011 0.001 HIS A1098 Details of bonding type rmsd covalent geometry : bond 0.00314 (28890) covalent geometry : angle 0.69295 (39314) SS BOND : bond 0.00420 ( 46) SS BOND : angle 1.46836 ( 92) hydrogen bonds : bond 0.03827 ( 879) hydrogen bonds : angle 5.74294 ( 2518) link_BETA1-4 : bond 0.00967 ( 11) link_BETA1-4 : angle 3.91324 ( 33) link_NAG-ASN : bond 0.00866 ( 25) link_NAG-ASN : angle 4.99069 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 262 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.5863 (tt) cc_final: 0.5247 (pt) REVERT: A 172 MET cc_start: 0.4446 (pmm) cc_final: 0.3601 (ptt) REVERT: A 321 GLU cc_start: 0.4196 (OUTLIER) cc_final: 0.3983 (pm20) REVERT: A 339 PHE cc_start: 0.2151 (m-80) cc_final: 0.0844 (m-80) REVERT: A 776 GLN cc_start: 0.8082 (pt0) cc_final: 0.7512 (mt0) REVERT: A 834 TYR cc_start: 0.3052 (OUTLIER) cc_final: 0.1647 (t80) REVERT: A 911 ASN cc_start: 0.7603 (p0) cc_final: 0.7394 (t0) REVERT: B 97 ASN cc_start: 0.6145 (m-40) cc_final: 0.5894 (p0) REVERT: B 172 MET cc_start: 0.5250 (mmt) cc_final: 0.3960 (ttp) REVERT: B 235 PHE cc_start: 0.5325 (t80) cc_final: 0.4168 (t80) REVERT: B 354 ARG cc_start: 0.2998 (mmt90) cc_final: 0.2373 (mmm-85) REVERT: B 405 ARG cc_start: 0.4635 (mpp80) cc_final: 0.4252 (mpp80) REVERT: B 441 LYS cc_start: 0.4088 (tptm) cc_final: 0.3668 (tppt) REVERT: B 538 PHE cc_start: 0.4425 (p90) cc_final: 0.2710 (p90) REVERT: B 556 PHE cc_start: 0.3784 (OUTLIER) cc_final: 0.3130 (m-10) REVERT: B 694 MET cc_start: 0.5637 (mmm) cc_final: 0.4905 (tpt) REVERT: B 702 VAL cc_start: 0.8117 (OUTLIER) cc_final: 0.7750 (m) REVERT: B 728 MET cc_start: 0.7798 (ttm) cc_final: 0.7198 (ttp) REVERT: B 762 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.6668 (mtp85) REVERT: B 1047 MET cc_start: 0.6499 (pmm) cc_final: 0.5756 (pmm) REVERT: B 1111 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6759 (mm) REVERT: C 59 PHE cc_start: 0.5927 (m-80) cc_final: 0.5654 (m-80) REVERT: C 195 TYR cc_start: 0.5071 (OUTLIER) cc_final: 0.4860 (t80) REVERT: C 201 LYS cc_start: 0.6538 (tptt) cc_final: 0.5883 (ptmm) REVERT: C 311 GLN cc_start: 0.6599 (mt0) cc_final: 0.5875 (tp-100) REVERT: C 494 PHE cc_start: 0.0597 (OUTLIER) cc_final: 0.0336 (m-80) REVERT: C 584 ILE cc_start: 0.4347 (OUTLIER) cc_final: 0.4043 (tp) REVERT: C 587 CYS cc_start: 0.1779 (OUTLIER) cc_final: 0.1461 (p) REVERT: C 737 MET cc_start: 0.7541 (ppp) cc_final: 0.7167 (ppp) REVERT: C 753 TYR cc_start: 0.6353 (OUTLIER) cc_final: 0.5848 (m-80) REVERT: C 863 THR cc_start: 0.6655 (p) cc_final: 0.6259 (t) REVERT: C 865 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6532 (pm20) REVERT: C 866 MET cc_start: 0.6505 (ptp) cc_final: 0.6227 (ptp) REVERT: C 903 PHE cc_start: 0.7631 (m-80) cc_final: 0.7260 (m-80) REVERT: D 79 LYS cc_start: 0.2643 (tptp) cc_final: 0.1922 (mtmm) outliers start: 77 outliers final: 48 residues processed: 320 average time/residue: 0.1599 time to fit residues: 83.9324 Evaluate side-chains 272 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 753 TYR Chi-restraints excluded: chain C residue 865 GLU Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain D residue 53 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 184 optimal weight: 0.1980 chunk 180 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 0.0470 chunk 347 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 266 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 951 HIS B 123 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.104525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.082602 restraints weight = 263213.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.082138 restraints weight = 165467.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.082975 restraints weight = 121419.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.082812 restraints weight = 102424.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.083136 restraints weight = 100363.938| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28972 Z= 0.130 Angle : 0.713 18.973 39514 Z= 0.346 Chirality : 0.049 0.549 4524 Planarity : 0.005 0.065 5046 Dihedral : 7.393 63.732 4607 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.96 % Favored : 92.76 % Rotamer: Outliers : 1.91 % Allowed : 24.96 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -1.47 (0.14), residues: 3510 helix: 1.10 (0.20), residues: 681 sheet: -0.71 (0.21), residues: 576 loop : -1.82 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 980 TYR 0.035 0.001 TYR B 348 PHE 0.029 0.001 PHE C 397 TRP 0.033 0.002 TRP C 255 HIS 0.015 0.001 HIS A 951 Details of bonding type rmsd covalent geometry : bond 0.00290 (28890) covalent geometry : angle 0.67043 (39314) SS BOND : bond 0.00310 ( 46) SS BOND : angle 1.35430 ( 92) hydrogen bonds : bond 0.03600 ( 879) hydrogen bonds : angle 5.51714 ( 2518) link_BETA1-4 : bond 0.00912 ( 11) link_BETA1-4 : angle 3.80164 ( 33) link_NAG-ASN : bond 0.00821 ( 25) link_NAG-ASN : angle 4.82704 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 244 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6082 (tt) cc_final: 0.5418 (pt) REVERT: A 168 GLN cc_start: 0.4487 (pm20) cc_final: 0.3728 (tp-100) REVERT: A 172 MET cc_start: 0.4612 (pmm) cc_final: 0.3629 (ptt) REVERT: A 339 PHE cc_start: 0.2356 (m-80) cc_final: 0.1199 (m-80) REVERT: A 389 PHE cc_start: 0.1623 (p90) cc_final: 0.1362 (p90) REVERT: A 525 LYS cc_start: 0.7186 (tppp) cc_final: 0.6976 (pptt) REVERT: A 729 THR cc_start: 0.8231 (m) cc_final: 0.7933 (t) REVERT: A 834 TYR cc_start: 0.2906 (OUTLIER) cc_final: 0.1432 (t80) REVERT: A 911 ASN cc_start: 0.7436 (p0) cc_final: 0.7210 (t0) REVERT: A 914 TYR cc_start: 0.7093 (m-80) cc_final: 0.6268 (m-80) REVERT: A 992 ARG cc_start: 0.5858 (ttm-80) cc_final: 0.5515 (ptm160) REVERT: B 97 ASN cc_start: 0.6268 (m-40) cc_final: 0.5942 (p0) REVERT: B 172 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.4281 (ttp) REVERT: B 189 PHE cc_start: 0.5140 (t80) cc_final: 0.4861 (t80) REVERT: B 235 PHE cc_start: 0.5449 (t80) cc_final: 0.4305 (t80) REVERT: B 405 ARG cc_start: 0.4472 (mpp80) cc_final: 0.4108 (mpp80) REVERT: B 441 LYS cc_start: 0.4133 (tptm) cc_final: 0.3677 (tppt) REVERT: B 538 PHE cc_start: 0.4628 (p90) cc_final: 0.3047 (p90) REVERT: B 556 PHE cc_start: 0.3769 (OUTLIER) cc_final: 0.3216 (m-10) REVERT: B 728 MET cc_start: 0.7325 (ttm) cc_final: 0.6675 (ttp) REVERT: B 866 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6519 (mtp) REVERT: B 1047 MET cc_start: 0.6448 (pmm) cc_final: 0.5802 (pmm) REVERT: B 1111 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6821 (mm) REVERT: C 59 PHE cc_start: 0.6041 (m-80) cc_final: 0.5764 (m-80) REVERT: C 90 PHE cc_start: 0.4978 (t80) cc_final: 0.4394 (t80) REVERT: C 255 TRP cc_start: 0.0043 (m-10) cc_final: -0.0495 (m100) REVERT: C 270 ARG cc_start: 0.2505 (ttm-80) cc_final: 0.2180 (ttm-80) REVERT: C 301 LYS cc_start: 0.7084 (tptm) cc_final: 0.6493 (tptp) REVERT: C 311 GLN cc_start: 0.6472 (mt0) cc_final: 0.5963 (tp-100) REVERT: C 320 THR cc_start: 0.5410 (p) cc_final: 0.5191 (t) REVERT: C 321 GLU cc_start: 0.5359 (pm20) cc_final: 0.5028 (pm20) REVERT: C 494 PHE cc_start: 0.0510 (OUTLIER) cc_final: 0.0190 (m-80) REVERT: C 587 CYS cc_start: 0.1755 (OUTLIER) cc_final: 0.1395 (p) REVERT: C 737 MET cc_start: 0.7485 (ppp) cc_final: 0.7275 (ppp) REVERT: C 753 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.6030 (m-80) REVERT: C 863 THR cc_start: 0.6728 (p) cc_final: 0.6398 (t) REVERT: C 866 MET cc_start: 0.6601 (ptp) cc_final: 0.6348 (ptp) REVERT: C 910 GLN cc_start: 0.7622 (pm20) cc_final: 0.6294 (pt0) REVERT: E 2 GLN cc_start: 0.3363 (tp40) cc_final: 0.2648 (pm20) REVERT: D 79 LYS cc_start: 0.3038 (tptp) cc_final: 0.2307 (mtmm) outliers start: 59 outliers final: 40 residues processed: 286 average time/residue: 0.1467 time to fit residues: 69.7770 Evaluate side-chains 272 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 753 TYR Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 218 optimal weight: 9.9990 chunk 337 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 279 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 158 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN A 999 GLN B 314 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.104311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.081813 restraints weight = 241009.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.081696 restraints weight = 141053.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.082233 restraints weight = 104138.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.082325 restraints weight = 90704.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.082423 restraints weight = 86872.215| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.6858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28972 Z= 0.131 Angle : 0.709 18.997 39514 Z= 0.344 Chirality : 0.048 0.546 4524 Planarity : 0.005 0.067 5046 Dihedral : 7.189 59.062 4607 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.53 % Favored : 93.18 % Rotamer: Outliers : 1.85 % Allowed : 25.09 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -1.42 (0.14), residues: 3510 helix: 1.11 (0.20), residues: 679 sheet: -0.66 (0.21), residues: 611 loop : -1.79 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C1016 TYR 0.035 0.002 TYR B 348 PHE 0.019 0.002 PHE A 189 TRP 0.016 0.001 TRP C 102 HIS 0.004 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00294 (28890) covalent geometry : angle 0.66789 (39314) SS BOND : bond 0.00328 ( 46) SS BOND : angle 1.23898 ( 92) hydrogen bonds : bond 0.03520 ( 879) hydrogen bonds : angle 5.45860 ( 2518) link_BETA1-4 : bond 0.00903 ( 11) link_BETA1-4 : angle 3.77859 ( 33) link_NAG-ASN : bond 0.00817 ( 25) link_NAG-ASN : angle 4.77268 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6129 (tt) cc_final: 0.5418 (pt) REVERT: A 168 GLN cc_start: 0.4682 (pm20) cc_final: 0.3911 (tp-100) REVERT: A 172 MET cc_start: 0.4714 (pmm) cc_final: 0.3743 (ptt) REVERT: A 339 PHE cc_start: 0.2330 (m-80) cc_final: 0.1505 (m-80) REVERT: A 389 PHE cc_start: 0.1440 (p90) cc_final: 0.1218 (p90) REVERT: A 834 TYR cc_start: 0.2771 (OUTLIER) cc_final: 0.1468 (t80) REVERT: A 992 ARG cc_start: 0.5823 (ttm-80) cc_final: 0.5498 (ptm160) REVERT: B 84 PHE cc_start: 0.7057 (t80) cc_final: 0.6600 (t80) REVERT: B 97 ASN cc_start: 0.6321 (m-40) cc_final: 0.5989 (p0) REVERT: B 172 MET cc_start: 0.5354 (mmt) cc_final: 0.4302 (ttp) REVERT: B 189 PHE cc_start: 0.4930 (t80) cc_final: 0.4444 (t80) REVERT: B 235 PHE cc_start: 0.5403 (t80) cc_final: 0.4247 (t80) REVERT: B 386 ASP cc_start: 0.3874 (t70) cc_final: 0.3637 (m-30) REVERT: B 405 ARG cc_start: 0.4451 (mpp80) cc_final: 0.4083 (mpp80) REVERT: B 441 LYS cc_start: 0.4085 (tptm) cc_final: 0.3663 (tppt) REVERT: B 538 PHE cc_start: 0.4639 (p90) cc_final: 0.3187 (p90) REVERT: B 556 PHE cc_start: 0.3898 (OUTLIER) cc_final: 0.3404 (m-10) REVERT: B 728 MET cc_start: 0.7287 (ttm) cc_final: 0.6640 (ttp) REVERT: B 749 LEU cc_start: 0.6481 (mm) cc_final: 0.6195 (mm) REVERT: B 866 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.5973 (mtp) REVERT: B 1047 MET cc_start: 0.6627 (pmm) cc_final: 0.6123 (pmm) REVERT: B 1111 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6746 (mm) REVERT: C 59 PHE cc_start: 0.6104 (m-80) cc_final: 0.5859 (m-80) REVERT: C 90 PHE cc_start: 0.5052 (t80) cc_final: 0.4504 (t80) REVERT: C 201 LYS cc_start: 0.6546 (tptt) cc_final: 0.5923 (ttpp) REVERT: C 241 LEU cc_start: 0.3851 (mt) cc_final: 0.3483 (mt) REVERT: C 255 TRP cc_start: 0.0086 (m-10) cc_final: -0.0456 (m100) REVERT: C 301 LYS cc_start: 0.7224 (tptm) cc_final: 0.6597 (tptp) REVERT: C 311 GLN cc_start: 0.6654 (mt0) cc_final: 0.6225 (tp-100) REVERT: C 494 PHE cc_start: 0.0508 (OUTLIER) cc_final: 0.0220 (m-80) REVERT: C 584 ILE cc_start: 0.4562 (OUTLIER) cc_final: 0.4262 (tp) REVERT: C 587 CYS cc_start: 0.1717 (p) cc_final: 0.1382 (p) REVERT: C 737 MET cc_start: 0.7544 (ppp) cc_final: 0.7277 (ppp) REVERT: C 753 TYR cc_start: 0.6277 (OUTLIER) cc_final: 0.5936 (m-80) REVERT: C 899 MET cc_start: 0.7339 (tpp) cc_final: 0.7020 (tpp) REVERT: E 2 GLN cc_start: 0.3371 (tp40) cc_final: 0.2917 (pm20) REVERT: E 62 TYR cc_start: 0.2000 (m-80) cc_final: 0.1661 (m-80) REVERT: D 79 LYS cc_start: 0.2977 (tptp) cc_final: 0.2255 (mtmm) outliers start: 57 outliers final: 42 residues processed: 277 average time/residue: 0.1506 time to fit residues: 69.7996 Evaluate side-chains 263 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 753 TYR Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain D residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 233 optimal weight: 0.0030 chunk 163 optimal weight: 3.9990 chunk 35 optimal weight: 0.0670 chunk 185 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 282 optimal weight: 0.9990 overall best weight: 0.7132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN A1105 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.104465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.081500 restraints weight = 211818.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.081392 restraints weight = 168386.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.081324 restraints weight = 118194.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.081689 restraints weight = 114215.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.081779 restraints weight = 98529.773| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.6980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28972 Z= 0.127 Angle : 0.698 18.936 39514 Z= 0.339 Chirality : 0.049 0.540 4524 Planarity : 0.005 0.065 5046 Dihedral : 7.011 57.914 4607 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.85 % Favored : 92.87 % Rotamer: Outliers : 1.88 % Allowed : 25.25 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -1.36 (0.14), residues: 3510 helix: 1.12 (0.21), residues: 686 sheet: -0.62 (0.20), residues: 624 loop : -1.75 (0.12), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 574 TYR 0.033 0.001 TYR B 348 PHE 0.022 0.001 PHE B 540 TRP 0.018 0.002 TRP B 64 HIS 0.006 0.001 HIS A 951 Details of bonding type rmsd covalent geometry : bond 0.00285 (28890) covalent geometry : angle 0.65761 (39314) SS BOND : bond 0.00282 ( 46) SS BOND : angle 1.19043 ( 92) hydrogen bonds : bond 0.03452 ( 879) hydrogen bonds : angle 5.39165 ( 2518) link_BETA1-4 : bond 0.00910 ( 11) link_BETA1-4 : angle 3.75254 ( 33) link_NAG-ASN : bond 0.00816 ( 25) link_NAG-ASN : angle 4.71860 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5063.30 seconds wall clock time: 88 minutes 18.61 seconds (5298.61 seconds total)