Starting phenix.real_space_refine on Thu Jun 26 01:41:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oyu_17296/06_2025/8oyu_17296.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oyu_17296/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8oyu_17296/06_2025/8oyu_17296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oyu_17296/06_2025/8oyu_17296.map" model { file = "/net/cci-nas-00/data/ceres_data/8oyu_17296/06_2025/8oyu_17296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oyu_17296/06_2025/8oyu_17296.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.76s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.19, per 1000 atoms: 0.61 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: 6.80 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 3.55 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: 13.03 Time building geometry restraints manager: 8.22 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 1144 or resid 1301 thr \ ough 1303)) selection = (chain 'B' and (resid 19 through 441 or resid 444 through 1144 or resid 1301 thr \ ough 1303)) selection = (chain 'C' and (resid 19 through 837 or resid 848 through 1144 or resid 1301 thr \ ough 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 65.980 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.430 ------------------------------------------------------------------------------- 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 : 13.47 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (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 TRP 0.013 0.001 TRP B 102 HIS 0.009 0.001 HIS E 57 PHE 0.017 0.001 PHE C 830 TYR 0.018 0.001 TYR B 901 ARG 0.007 0.000 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00836 ( 25) link_NAG-ASN : angle 6.09566 ( 75) link_BETA1-4 : bond 0.01190 ( 11) link_BETA1-4 : angle 3.96777 ( 33) hydrogen bonds : bond 0.19807 ( 879) hydrogen bonds : angle 8.51718 ( 2518) SS BOND : bond 0.00214 ( 46) SS BOND : angle 0.68423 ( 92) covalent geometry : bond 0.00727 (28890) covalent geometry : angle 0.74727 (39314) *********************** 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 : 2.965 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: A 54 LEU cc_start: 0.7163 (mp) cc_final: 0.6766 (tt) REVERT: A 90 PHE cc_start: 0.4272 (t80) cc_final: 0.3901 (t80) REVERT: A 172 MET cc_start: 0.3576 (pmm) cc_final: 0.3048 (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: 0.7566 (p) REVERT: A 607 VAL cc_start: 0.6224 (t) cc_final: 0.5970 (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: 0.8450 (m110) REVERT: A 784 GLN cc_start: 0.6401 (mm-40) cc_final: 0.5851 (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: 0.2697 (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: 0.6328 (m) REVERT: A 990 ILE cc_start: 0.7441 (mt) cc_final: 0.7203 (mt) REVERT: A 991 ASP cc_start: 0.6370 (m-30) cc_final: 0.6056 (m-30) REVERT: A 1001 LEU cc_start: 0.8590 (mt) cc_final: 0.8219 (mt) REVERT: A 1064 TYR cc_start: 0.6753 (t80) cc_final: 0.6477 (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: 0.4255 (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: 0.7798 (m-80) REVERT: B 354 ARG cc_start: 0.4825 (mtt180) cc_final: 0.4064 (mmm-85) 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: 0.3794 (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: 0.4862 (p90) REVERT: B 604 GLN cc_start: 0.7262 (tt0) cc_final: 0.6930 (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: 0.5147 (tt0) REVERT: B 753 TYR cc_start: 0.4953 (m-80) cc_final: 0.4385 (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: 0.6895 (mt) REVERT: B 869 GLN cc_start: 0.7445 (mt0) cc_final: 0.7106 (mm-40) REVERT: B 880 THR cc_start: 0.7962 (p) cc_final: 0.7649 (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: 0.5749 (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: 0.7392 (ttmt) REVERT: C 320 THR cc_start: 0.5593 (p) cc_final: 0.5051 (p) REVERT: C 321 GLU cc_start: 0.6003 (pm20) cc_final: 0.4443 (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: 0.7317 (p) REVERT: C 607 VAL cc_start: 0.7532 (t) cc_final: 0.7314 (p) REVERT: C 631 ARG cc_start: 0.4713 (pmt170) cc_final: 0.4290 (mtm-85) REVERT: C 633 TYR cc_start: 0.4639 (p90) cc_final: 0.3892 (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: 0.5803 (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: 0.5520 (m-80) REVERT: C 820 PHE cc_start: 0.7401 (m-80) cc_final: 0.6696 (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: 0.6661 (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: 0.5826 (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: 0.1549 (t) REVERT: D 86 MET cc_start: 0.0924 (ptt) cc_final: 0.0440 (ptt) REVERT: D 97 TYR cc_start: 0.4118 (m-80) cc_final: 0.3855 (m-80) outliers start: 7 outliers final: 2 residues processed: 745 average time/residue: 0.4972 time to fit residues: 575.0853 Evaluate side-chains 360 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 356 time to evaluate : 4.677 ------------------------------------------------------------------------------- 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 296 optimal weight: 5.9990 chunk 266 optimal weight: 5.9990 chunk 147 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 275 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 204 optimal weight: 0.8980 chunk 318 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN 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 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN B1080 HIS ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.107446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.085537 restraints weight = 236003.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.086155 restraints weight = 178861.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.086425 restraints weight = 114109.810| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5803 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28972 Z= 0.167 Angle : 0.776 17.909 39514 Z= 0.379 Chirality : 0.052 0.606 4524 Planarity : 0.006 0.074 5046 Dihedral : 11.329 119.910 4608 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.82 % Favored : 93.87 % Rotamer: Outliers : 2.82 % Allowed : 16.50 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3510 helix: 1.83 (0.21), residues: 663 sheet: -0.05 (0.21), residues: 584 loop : -1.46 (0.12), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 630 HIS 0.010 0.001 HIS A 202 PHE 0.029 0.002 PHE C 326 TYR 0.040 0.002 TYR B 901 ARG 0.006 0.001 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00764 ( 25) link_NAG-ASN : angle 5.48452 ( 75) link_BETA1-4 : bond 0.01030 ( 11) link_BETA1-4 : angle 3.60400 ( 33) hydrogen bonds : bond 0.04643 ( 879) hydrogen bonds : angle 6.55950 ( 2518) SS BOND : bond 0.00526 ( 46) SS BOND : angle 2.09561 ( 92) covalent geometry : bond 0.00372 (28890) covalent geometry : angle 0.72623 (39314) *********************** 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: 87 poor density : 378 time to evaluate : 3.252 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 172 MET cc_start: 0.3934 (pmm) cc_final: 0.3496 (ptp) REVERT: A 211 GLU cc_start: 0.5736 (mm-30) cc_final: 0.5371 (tp30) REVERT: A 223 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.5557 (tp) REVERT: A 239 LEU cc_start: 0.2449 (mt) cc_final: 0.2086 (tt) REVERT: A 282 ILE cc_start: 0.5253 (mt) cc_final: 0.4727 (mm) REVERT: A 296 THR cc_start: 0.7745 (m) cc_final: 0.7384 (p) REVERT: A 321 GLU cc_start: 0.3507 (OUTLIER) cc_final: 0.3215 (pt0) REVERT: A 525 LYS cc_start: 0.6135 (tptp) cc_final: 0.5918 (tppp) REVERT: A 539 ASN cc_start: 0.3495 (t0) cc_final: 0.2888 (m-40) REVERT: A 607 VAL cc_start: 0.5590 (t) cc_final: 0.5281 (m) REVERT: A 634 SER cc_start: 0.3803 (t) cc_final: 0.3539 (p) REVERT: A 707 ASN cc_start: 0.5825 (p0) cc_final: 0.5606 (p0) REVERT: A 753 TYR cc_start: 0.4544 (m-80) cc_final: 0.4280 (m-80) REVERT: A 758 THR cc_start: 0.7332 (p) cc_final: 0.7033 (t) REVERT: A 834 TYR cc_start: 0.3117 (OUTLIER) cc_final: 0.2207 (t80) REVERT: A 914 TYR cc_start: 0.6647 (m-80) cc_final: 0.5783 (m-80) REVERT: A 990 ILE cc_start: 0.6728 (mt) cc_final: 0.6349 (mm) REVERT: A 997 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7581 (mtt-85) REVERT: A 1073 THR cc_start: 0.6666 (m) cc_final: 0.6036 (p) REVERT: B 66 HIS cc_start: 0.4222 (t-90) cc_final: 0.3882 (t70) REVERT: B 99 ILE cc_start: 0.4540 (mm) cc_final: 0.4242 (mm) REVERT: B 148 MET cc_start: -0.0210 (tpt) cc_final: -0.0778 (ttm) REVERT: B 354 ARG cc_start: 0.4084 (mtt180) cc_final: 0.3069 (mmm-85) REVERT: B 489 LEU cc_start: 0.3171 (OUTLIER) cc_final: 0.2896 (pp) REVERT: B 538 PHE cc_start: 0.4472 (p90) cc_final: 0.3316 (p90) REVERT: B 609 TYR cc_start: 0.7279 (m-80) cc_final: 0.6885 (m-10) REVERT: B 750 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.5894 (mt) REVERT: B 798 ASN cc_start: 0.6443 (OUTLIER) cc_final: 0.5807 (p0) REVERT: B 880 THR cc_start: 0.7661 (p) cc_final: 0.7227 (t) REVERT: B 884 THR cc_start: 0.8160 (p) cc_final: 0.7530 (t) REVERT: B 903 PHE cc_start: 0.7349 (m-10) cc_final: 0.7077 (m-80) REVERT: B 914 TYR cc_start: 0.5807 (m-80) cc_final: 0.5462 (m-10) REVERT: B 944 LYS cc_start: 0.8040 (mmtm) cc_final: 0.7735 (mttt) REVERT: B 1033 GLN cc_start: 0.7123 (tt0) cc_final: 0.6811 (tt0) REVERT: C 90 PHE cc_start: 0.5373 (t80) cc_final: 0.5063 (t80) REVERT: C 263 TYR cc_start: 0.5149 (m-80) cc_final: 0.4882 (m-10) REVERT: C 292 PRO cc_start: 0.6799 (Cg_exo) cc_final: 0.6417 (Cg_endo) REVERT: C 297 LYS cc_start: 0.8097 (mttt) cc_final: 0.7614 (ttmt) REVERT: C 320 THR cc_start: 0.5421 (p) cc_final: 0.4597 (t) REVERT: C 321 GLU cc_start: 0.5983 (pm20) cc_final: 0.3822 (mt-10) REVERT: C 494 PHE cc_start: -0.0058 (OUTLIER) cc_final: -0.0460 (m-10) REVERT: C 564 ARG cc_start: 0.4643 (mmt180) cc_final: 0.4074 (mmt180) REVERT: C 568 ASP cc_start: 0.6063 (t70) cc_final: 0.5811 (t70) REVERT: C 584 ILE cc_start: 0.3149 (OUTLIER) cc_final: 0.2925 (tp) REVERT: C 630 TRP cc_start: 0.4133 (m100) cc_final: 0.3495 (m-90) REVERT: C 633 TYR cc_start: 0.4846 (p90) cc_final: 0.4433 (p90) REVERT: C 714 ASN cc_start: 0.4713 (OUTLIER) cc_final: 0.4119 (m110) REVERT: C 737 MET cc_start: 0.7483 (ppp) cc_final: 0.7020 (ppp) REVERT: C 753 TYR cc_start: 0.6069 (m-80) cc_final: 0.4939 (m-80) REVERT: C 803 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.6078 (mp) REVERT: C 820 PHE cc_start: 0.6684 (m-80) cc_final: 0.6072 (m-80) REVERT: C 833 GLN cc_start: 0.3589 (mp10) cc_final: 0.2656 (pp30) REVERT: C 869 GLN cc_start: 0.7611 (mt0) cc_final: 0.7393 (mm110) REVERT: C 910 GLN cc_start: 0.7205 (pm20) cc_final: 0.6438 (mt0) REVERT: C 984 PRO cc_start: 0.6334 (Cg_exo) cc_final: 0.5772 (Cg_endo) REVERT: C 985 GLU cc_start: 0.5855 (tp30) cc_final: 0.5622 (mp0) REVERT: C 1099 TRP cc_start: 0.6652 (m100) cc_final: 0.6028 (m100) REVERT: D 81 THR cc_start: -0.0160 (m) cc_final: -0.0760 (m) REVERT: D 86 MET cc_start: 0.1329 (ptt) cc_final: 0.1105 (ptp) outliers start: 87 outliers final: 42 residues processed: 452 average time/residue: 0.3951 time to fit residues: 288.2556 Evaluate side-chains 332 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 280 time to evaluate : 3.550 ------------------------------------------------------------------------------- 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 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 688 SER 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 912 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 994 ILE 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 309 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 705 SER Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 750 LEU 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 B residue 1005 VAL Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 456 SER 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 688 SER Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 893 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 325 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 231 optimal weight: 8.9990 chunk 344 optimal weight: 9.9990 chunk 217 optimal weight: 0.9990 chunk 153 optimal weight: 0.4980 chunk 207 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 340 ASN A 752 GLN A 774 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN A1103 GLN A1116 ASN B 202 HIS ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 GLN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN C 610 GLN ** C 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 752 GLN C 922 ASN C 950 ASN ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 GLN D 77 ASN D 111 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.105180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.083295 restraints weight = 263447.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.082533 restraints weight = 170561.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.083087 restraints weight = 134757.134| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 28972 Z= 0.225 Angle : 0.869 19.058 39514 Z= 0.430 Chirality : 0.056 0.896 4524 Planarity : 0.006 0.070 5046 Dihedral : 10.405 131.808 4608 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.96 % Favored : 92.70 % Rotamer: Outliers : 4.54 % Allowed : 19.38 % Favored : 76.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3510 helix: 1.03 (0.20), residues: 662 sheet: -0.44 (0.21), residues: 606 loop : -1.69 (0.12), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 433 HIS 0.009 0.002 HIS A1098 PHE 0.029 0.003 PHE C 217 TYR 0.029 0.003 TYR B 348 ARG 0.010 0.001 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.02050 ( 25) link_NAG-ASN : angle 5.49902 ( 75) link_BETA1-4 : bond 0.00989 ( 11) link_BETA1-4 : angle 3.96727 ( 33) hydrogen bonds : bond 0.04852 ( 879) hydrogen bonds : angle 6.38420 ( 2518) SS BOND : bond 0.00453 ( 46) SS BOND : angle 1.66142 ( 92) covalent geometry : bond 0.00495 (28890) covalent geometry : angle 0.82612 (39314) *********************** 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 464 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 324 time to evaluate : 4.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 GLN cc_start: 0.3853 (pm20) cc_final: 0.2912 (tp-100) REVERT: A 172 MET cc_start: 0.4390 (pmm) cc_final: 0.3078 (tmm) REVERT: A 190 LYS cc_start: 0.5637 (ttpt) cc_final: 0.5432 (mmmt) REVERT: A 193 ASP cc_start: 0.5430 (OUTLIER) cc_final: 0.5122 (t70) REVERT: A 211 GLU cc_start: 0.6126 (mm-30) cc_final: 0.5909 (tt0) REVERT: A 374 PHE cc_start: 0.2512 (p90) cc_final: 0.1881 (p90) REVERT: A 446 TYR cc_start: 0.3727 (p90) cc_final: 0.3245 (p90) REVERT: A 525 LYS cc_start: 0.5713 (tptp) cc_final: 0.5509 (tmtt) REVERT: A 728 MET cc_start: 0.7881 (ptt) cc_final: 0.7478 (ptm) REVERT: A 834 TYR cc_start: 0.3132 (OUTLIER) cc_final: 0.2217 (t80) REVERT: A 878 THR cc_start: 0.8538 (m) cc_final: 0.8321 (p) REVERT: A 914 TYR cc_start: 0.7162 (m-80) cc_final: 0.6266 (m-80) REVERT: A 1033 GLN cc_start: 0.6014 (OUTLIER) cc_final: 0.5511 (tp40) REVERT: B 54 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6516 (mm) REVERT: B 148 MET cc_start: -0.0268 (tpt) cc_final: -0.1128 (ttm) REVERT: B 152 PHE cc_start: 0.3203 (m-80) cc_final: 0.2436 (p90) REVERT: B 405 ARG cc_start: 0.4381 (mpp80) cc_final: 0.4029 (mpp80) REVERT: B 538 PHE cc_start: 0.4703 (p90) cc_final: 0.3557 (p90) REVERT: B 556 PHE cc_start: 0.3512 (OUTLIER) cc_final: 0.2739 (m-10) REVERT: B 702 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7799 (m) REVERT: B 737 MET cc_start: 0.6303 (tmm) cc_final: 0.6017 (tmm) REVERT: B 750 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5674 (mt) REVERT: B 798 ASN cc_start: 0.6980 (OUTLIER) cc_final: 0.6402 (p0) REVERT: B 862 LEU cc_start: 0.8302 (mt) cc_final: 0.8084 (mp) REVERT: B 944 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7686 (mttt) REVERT: B 1016 ARG cc_start: 0.7466 (tpt170) cc_final: 0.6872 (tpt170) REVERT: B 1033 GLN cc_start: 0.7139 (tt0) cc_final: 0.6557 (tt0) REVERT: B 1047 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6700 (pmm) REVERT: C 90 PHE cc_start: 0.5440 (t80) cc_final: 0.5093 (t80) REVERT: C 187 PHE cc_start: 0.3188 (m-80) cc_final: 0.2603 (m-80) REVERT: C 297 LYS cc_start: 0.8092 (mttt) cc_final: 0.7528 (ttmt) REVERT: C 311 GLN cc_start: 0.6319 (mt0) cc_final: 0.5439 (tp-100) REVERT: C 541 ASN cc_start: 0.5630 (m-40) cc_final: 0.5320 (t0) REVERT: C 737 MET cc_start: 0.7562 (ppp) cc_final: 0.7205 (ppp) REVERT: C 899 MET cc_start: 0.8027 (tpp) cc_final: 0.7720 (tpp) REVERT: C 984 PRO cc_start: 0.6391 (Cg_exo) cc_final: 0.5745 (Cg_endo) REVERT: C 985 GLU cc_start: 0.5807 (tp30) cc_final: 0.5596 (mp0) REVERT: C 992 ARG cc_start: 0.7047 (ttm170) cc_final: 0.6762 (ttm-80) REVERT: D 79 LYS cc_start: 0.1914 (tptp) cc_final: 0.1252 (mtmm) REVERT: D 93 ASP cc_start: -0.0038 (t70) cc_final: -0.0407 (t70) outliers start: 140 outliers final: 76 residues processed: 442 average time/residue: 0.3786 time to fit residues: 273.1925 Evaluate side-chains 319 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 234 time to evaluate : 2.968 ------------------------------------------------------------------------------- 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 193 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 494 PHE 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 711 ILE Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 879 ILE 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 994 ILE Chi-restraints excluded: chain A residue 1033 GLN Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 213 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 498 TYR 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 705 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 823 VAL 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 990 ILE Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1047 MET 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 B residue 1119 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 172 MET 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 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 424 ASP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 548 VAL 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 607 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 752 GLN Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1142 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 86 optimal weight: 0.9990 chunk 271 optimal weight: 0.0370 chunk 208 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 154 optimal weight: 20.0000 overall best weight: 0.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 752 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.105738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.083413 restraints weight = 263170.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.083275 restraints weight = 159217.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.083642 restraints weight = 118455.007| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.094 | | 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) = 0.094 | | 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: 0.5968 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28972 Z= 0.138 Angle : 0.712 18.717 39514 Z= 0.346 Chirality : 0.049 0.544 4524 Planarity : 0.005 0.064 5046 Dihedral : 9.386 113.736 4607 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.70 % Favored : 93.98 % Rotamer: Outliers : 3.73 % Allowed : 21.17 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3510 helix: 1.37 (0.20), residues: 674 sheet: -0.38 (0.21), residues: 594 loop : -1.63 (0.12), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 630 HIS 0.008 0.001 HIS C 202 PHE 0.027 0.002 PHE A 138 TYR 0.036 0.002 TYR B1107 ARG 0.008 0.001 ARG C1104 Details of bonding type rmsd link_NAG-ASN : bond 0.00868 ( 25) link_NAG-ASN : angle 5.13936 ( 75) link_BETA1-4 : bond 0.01044 ( 11) link_BETA1-4 : angle 3.74616 ( 33) hydrogen bonds : bond 0.03903 ( 879) hydrogen bonds : angle 5.90535 ( 2518) SS BOND : bond 0.00283 ( 46) SS BOND : angle 1.27058 ( 92) covalent geometry : bond 0.00308 (28890) covalent geometry : angle 0.66619 (39314) *********************** 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 393 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 278 time to evaluate : 3.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 GLN cc_start: 0.3996 (pm20) cc_final: 0.3053 (tp-100) REVERT: A 172 MET cc_start: 0.4361 (pmm) cc_final: 0.3814 (ptt) REVERT: A 211 GLU cc_start: 0.6390 (mm-30) cc_final: 0.6025 (tt0) REVERT: A 276 TYR cc_start: 0.5343 (m-80) cc_final: 0.4767 (m-80) REVERT: A 374 PHE cc_start: 0.2872 (p90) cc_final: 0.2185 (p90) REVERT: A 446 TYR cc_start: 0.4020 (p90) cc_final: 0.3570 (p90) REVERT: A 525 LYS cc_start: 0.5921 (tptp) cc_final: 0.5677 (tmtt) REVERT: A 609 TYR cc_start: 0.6055 (m-80) cc_final: 0.5828 (m-80) REVERT: A 834 TYR cc_start: 0.3462 (OUTLIER) cc_final: 0.2225 (t80) REVERT: A 866 MET cc_start: 0.6471 (ptt) cc_final: 0.5903 (ptp) REVERT: A 914 TYR cc_start: 0.7123 (m-80) cc_final: 0.6180 (m-80) REVERT: A 915 GLU cc_start: 0.7260 (tt0) cc_final: 0.6970 (tm-30) REVERT: A 1111 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.8000 (tp) REVERT: A 1125 VAL cc_start: 0.5897 (m) cc_final: 0.4876 (p) REVERT: B 120 ASN cc_start: 0.2142 (p0) cc_final: 0.1596 (m-40) REVERT: B 148 MET cc_start: -0.0177 (tpt) cc_final: -0.0494 (ttm) REVERT: B 152 PHE cc_start: 0.2967 (m-80) cc_final: 0.2238 (p90) REVERT: B 172 MET cc_start: 0.5171 (OUTLIER) cc_final: 0.3978 (ttp) REVERT: B 187 PHE cc_start: 0.7204 (t80) cc_final: 0.6684 (t80) REVERT: B 405 ARG cc_start: 0.4399 (mpp80) cc_final: 0.4071 (mpp80) REVERT: B 526 LYS cc_start: 0.5052 (OUTLIER) cc_final: 0.4613 (ptpt) REVERT: B 538 PHE cc_start: 0.4405 (p90) cc_final: 0.3187 (p90) REVERT: B 702 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7838 (m) REVERT: B 737 MET cc_start: 0.6484 (tmm) cc_final: 0.6250 (tmm) REVERT: B 762 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.6737 (mtp85) REVERT: B 770 GLU cc_start: 0.7246 (tt0) cc_final: 0.6848 (tm-30) REVERT: B 798 ASN cc_start: 0.6590 (OUTLIER) cc_final: 0.5670 (p0) REVERT: B 862 LEU cc_start: 0.8213 (mt) cc_final: 0.7928 (mp) REVERT: B 915 GLU cc_start: 0.6778 (mt-10) cc_final: 0.5760 (mm-30) REVERT: B 944 LYS cc_start: 0.8018 (mmtm) cc_final: 0.7607 (mttm) REVERT: B 1033 GLN cc_start: 0.6966 (tt0) cc_final: 0.6640 (tt0) REVERT: B 1047 MET cc_start: 0.6958 (pmm) cc_final: 0.6449 (pmm) REVERT: B 1136 ASP cc_start: 0.7812 (t0) cc_final: 0.7543 (t0) REVERT: C 102 TRP cc_start: 0.2371 (m-10) cc_final: 0.1518 (m-10) REVERT: C 187 PHE cc_start: 0.3213 (m-80) cc_final: 0.2526 (m-80) REVERT: C 196 PHE cc_start: 0.7056 (m-80) cc_final: 0.6825 (m-80) REVERT: C 297 LYS cc_start: 0.7989 (mttt) cc_final: 0.7451 (ttmt) REVERT: C 311 GLN cc_start: 0.6506 (mt0) cc_final: 0.5607 (tp-100) REVERT: C 320 THR cc_start: 0.5274 (p) cc_final: 0.5006 (t) REVERT: C 492 TYR cc_start: 0.1303 (p90) cc_final: 0.0902 (p90) REVERT: C 541 ASN cc_start: 0.5516 (m-40) cc_final: 0.5302 (t0) REVERT: C 566 ILE cc_start: 0.5494 (OUTLIER) cc_final: 0.5118 (mm) REVERT: C 694 MET cc_start: 0.6071 (mmm) cc_final: 0.5809 (mmm) REVERT: C 737 MET cc_start: 0.7436 (ppp) cc_final: 0.7117 (ppp) REVERT: C 805 ASP cc_start: 0.4669 (p0) cc_final: 0.4391 (p0) REVERT: C 910 GLN cc_start: 0.7978 (pm20) cc_final: 0.6797 (mt0) REVERT: C 962 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7115 (tt0) REVERT: C 984 PRO cc_start: 0.6176 (Cg_exo) cc_final: 0.5675 (Cg_endo) REVERT: C 992 ARG cc_start: 0.7012 (ttm170) cc_final: 0.6701 (ttm-80) REVERT: D 68 LYS cc_start: 0.0832 (mtpt) cc_final: 0.0157 (mmmt) REVERT: D 79 LYS cc_start: 0.1742 (tptp) cc_final: 0.1116 (mtmm) outliers start: 115 outliers final: 62 residues processed: 377 average time/residue: 0.4844 time to fit residues: 316.4032 Evaluate side-chains 311 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 241 time to evaluate : 8.810 ------------------------------------------------------------------------------- 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 187 PHE Chi-restraints excluded: chain A residue 188 VAL 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 550 THR 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 718 SER 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 1060 LEU Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 125 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 347 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 750 LEU 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 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 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 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 221 GLU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 530 LEU 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 607 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 962 GLN Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 189 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 307 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 310 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 299 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 541 ASN A 752 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 HIS ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN 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** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.103190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.081834 restraints weight = 293748.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.081079 restraints weight = 200718.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.081533 restraints weight = 164306.758| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 28972 Z= 0.242 Angle : 0.887 19.870 39514 Z= 0.441 Chirality : 0.055 0.604 4524 Planarity : 0.007 0.080 5046 Dihedral : 9.993 99.560 4607 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.70 % Favored : 90.99 % Rotamer: Outliers : 5.90 % Allowed : 20.91 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3510 helix: 0.60 (0.19), residues: 672 sheet: -0.77 (0.21), residues: 602 loop : -1.97 (0.12), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 630 HIS 0.009 0.002 HIS A1080 PHE 0.028 0.003 PHE C 538 TYR 0.027 0.003 TYR B 348 ARG 0.015 0.001 ARG C 812 Details of bonding type rmsd link_NAG-ASN : bond 0.00898 ( 25) link_NAG-ASN : angle 5.29294 ( 75) link_BETA1-4 : bond 0.01198 ( 11) link_BETA1-4 : angle 4.33160 ( 33) hydrogen bonds : bond 0.04852 ( 879) hydrogen bonds : angle 6.44598 ( 2518) SS BOND : bond 0.00502 ( 46) SS BOND : angle 1.93136 ( 92) covalent geometry : bond 0.00543 (28890) covalent geometry : angle 0.84458 (39314) *********************** 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 451 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 269 time to evaluate : 3.129 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 44 ARG cc_start: 0.4413 (OUTLIER) cc_final: 0.4126 (ptm-80) REVERT: A 172 MET cc_start: 0.4375 (pmm) cc_final: 0.3749 (ptt) REVERT: A 193 ASP cc_start: 0.5460 (OUTLIER) cc_final: 0.5107 (t70) REVERT: A 446 TYR cc_start: 0.4061 (p90) cc_final: 0.3436 (p90) REVERT: A 449 LEU cc_start: 0.1378 (OUTLIER) cc_final: 0.1177 (pp) REVERT: A 526 LYS cc_start: 0.5340 (OUTLIER) cc_final: 0.4938 (mttp) REVERT: A 724 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8342 (mp) REVERT: A 834 TYR cc_start: 0.3254 (OUTLIER) cc_final: 0.1960 (t80) REVERT: A 866 MET cc_start: 0.7090 (ptt) cc_final: 0.6710 (ptp) REVERT: A 1098 HIS cc_start: 0.6294 (OUTLIER) cc_final: 0.6001 (m170) REVERT: A 1111 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7937 (tp) REVERT: B 120 ASN cc_start: 0.2292 (OUTLIER) cc_final: 0.2017 (m-40) REVERT: B 148 MET cc_start: 0.0796 (tpt) cc_final: 0.0368 (ttm) REVERT: B 152 PHE cc_start: 0.3528 (m-80) cc_final: 0.3273 (m-10) REVERT: B 172 MET cc_start: 0.5386 (OUTLIER) cc_final: 0.4317 (ttp) REVERT: B 405 ARG cc_start: 0.4300 (mpp80) cc_final: 0.3973 (mpp80) REVERT: B 526 LYS cc_start: 0.4931 (OUTLIER) cc_final: 0.4102 (mmtm) REVERT: B 538 PHE cc_start: 0.4376 (p90) cc_final: 0.3039 (p90) REVERT: B 556 PHE cc_start: 0.3322 (OUTLIER) cc_final: 0.2876 (m-10) REVERT: B 702 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.7839 (m) REVERT: B 798 ASN cc_start: 0.6231 (OUTLIER) cc_final: 0.5370 (p0) REVERT: B 944 LYS cc_start: 0.8059 (mmtm) cc_final: 0.7526 (mttt) REVERT: B 1047 MET cc_start: 0.7394 (pmm) cc_final: 0.7048 (pmm) REVERT: B 1106 PHE cc_start: 0.4978 (t80) cc_final: 0.4612 (t80) REVERT: B 1141 GLU cc_start: 0.3747 (OUTLIER) cc_final: 0.3336 (mp0) REVERT: C 175 GLU cc_start: 0.3340 (OUTLIER) cc_final: 0.2626 (mm-30) REVERT: C 187 PHE cc_start: 0.3547 (m-80) cc_final: 0.3086 (m-80) REVERT: C 311 GLN cc_start: 0.6650 (mt0) cc_final: 0.5507 (tp-100) REVERT: C 320 THR cc_start: 0.5766 (p) cc_final: 0.5128 (t) REVERT: C 321 GLU cc_start: 0.5992 (pm20) cc_final: 0.4031 (mt-10) REVERT: C 455 LYS cc_start: 0.0782 (OUTLIER) cc_final: -0.0342 (mmtp) REVERT: C 633 TYR cc_start: 0.5399 (OUTLIER) cc_final: 0.4674 (p90) REVERT: C 737 MET cc_start: 0.7535 (ppp) cc_final: 0.7217 (ppp) REVERT: C 748 ASN cc_start: 0.6798 (OUTLIER) cc_final: 0.6448 (t0) REVERT: C 1093 VAL cc_start: 0.7755 (m) cc_final: 0.7451 (p) REVERT: C 1104 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7075 (mtm-85) REVERT: E 37 TRP cc_start: -0.1295 (m100) cc_final: -0.1810 (m100) outliers start: 182 outliers final: 105 residues processed: 427 average time/residue: 0.3660 time to fit residues: 258.3953 Evaluate side-chains 357 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 232 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain A residue 449 LEU 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 580 GLU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 912 VAL 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 1106 PHE Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 348 TYR 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 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 513 GLU Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 775 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 906 ILE 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 1102 THR Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1141 GLU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 VAL 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 281 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 569 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 720 THR Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1062 VAL Chi-restraints excluded: chain C residue 1104 ARG Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1142 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 101 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 chunk 303 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 310 optimal weight: 0.9990 chunk 248 optimal weight: 0.0770 chunk 59 optimal weight: 7.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN A 774 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN B 560 GLN ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN C 641 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.104529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.082017 restraints weight = 242186.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.081926 restraints weight = 147946.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.082231 restraints weight = 106086.600| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28972 Z= 0.133 Angle : 0.716 18.845 39514 Z= 0.347 Chirality : 0.049 0.566 4524 Planarity : 0.005 0.063 5046 Dihedral : 8.710 89.711 4607 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.08 % Favored : 93.67 % Rotamer: Outliers : 3.37 % Allowed : 23.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3510 helix: 1.22 (0.20), residues: 671 sheet: -0.68 (0.21), residues: 601 loop : -1.80 (0.12), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 630 HIS 0.030 0.001 HIS A1098 PHE 0.025 0.002 PHE A 799 TYR 0.030 0.002 TYR B 348 ARG 0.006 0.001 ARG B 352 Details of bonding type rmsd link_NAG-ASN : bond 0.00814 ( 25) link_NAG-ASN : angle 5.09807 ( 75) link_BETA1-4 : bond 0.01097 ( 11) link_BETA1-4 : angle 3.94190 ( 33) hydrogen bonds : bond 0.03803 ( 879) hydrogen bonds : angle 5.80196 ( 2518) SS BOND : bond 0.00306 ( 46) SS BOND : angle 1.39014 ( 92) covalent geometry : bond 0.00293 (28890) covalent geometry : angle 0.66971 (39314) *********************** 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 368 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 264 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.4380 (OUTLIER) cc_final: 0.4057 (ptm-80) REVERT: A 168 GLN cc_start: 0.4120 (pm20) cc_final: 0.3229 (tp-100) REVERT: A 172 MET cc_start: 0.4644 (pmm) cc_final: 0.3906 (ptt) REVERT: A 446 TYR cc_start: 0.4141 (p90) cc_final: 0.3576 (p90) REVERT: A 526 LYS cc_start: 0.4905 (OUTLIER) cc_final: 0.4610 (mttp) REVERT: A 729 THR cc_start: 0.8143 (m) cc_final: 0.7769 (t) REVERT: A 834 TYR cc_start: 0.2946 (OUTLIER) cc_final: 0.1601 (t80) REVERT: A 866 MET cc_start: 0.6451 (ptt) cc_final: 0.5892 (ptp) REVERT: A 911 ASN cc_start: 0.7636 (p0) cc_final: 0.7287 (t0) REVERT: A 915 GLU cc_start: 0.7276 (tt0) cc_final: 0.6953 (tm-30) REVERT: A 1102 THR cc_start: 0.5140 (m) cc_final: 0.4870 (m) REVERT: B 40 ASP cc_start: 0.6017 (OUTLIER) cc_final: 0.5808 (t70) REVERT: B 116 LEU cc_start: 0.8051 (mt) cc_final: 0.7688 (tp) REVERT: B 120 ASN cc_start: 0.2418 (OUTLIER) cc_final: 0.1942 (m-40) REVERT: B 148 MET cc_start: 0.0760 (tpt) cc_final: 0.0506 (ttp) REVERT: B 172 MET cc_start: 0.5390 (OUTLIER) cc_final: 0.4297 (ttp) REVERT: B 405 ARG cc_start: 0.4565 (mpp80) cc_final: 0.4175 (mpp80) REVERT: B 526 LYS cc_start: 0.4767 (OUTLIER) cc_final: 0.4217 (mmtm) REVERT: B 538 PHE cc_start: 0.4498 (p90) cc_final: 0.2932 (p90) REVERT: B 556 PHE cc_start: 0.3278 (OUTLIER) cc_final: 0.2850 (m-10) REVERT: B 694 MET cc_start: 0.5905 (mmm) cc_final: 0.5299 (tpt) REVERT: B 762 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.6866 (mtp85) REVERT: B 798 ASN cc_start: 0.5977 (OUTLIER) cc_final: 0.5356 (p0) REVERT: B 944 LYS cc_start: 0.7915 (mmtm) cc_final: 0.7585 (mttt) REVERT: B 1047 MET cc_start: 0.6720 (pmm) cc_final: 0.6375 (pmm) REVERT: B 1106 PHE cc_start: 0.5160 (t80) cc_final: 0.4813 (t80) REVERT: B 1111 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6752 (mm) REVERT: B 1141 GLU cc_start: 0.3753 (OUTLIER) cc_final: 0.3267 (mp0) REVERT: C 187 PHE cc_start: 0.3593 (m-80) cc_final: 0.3272 (m-80) REVERT: C 255 TRP cc_start: 0.0950 (m100) cc_final: 0.0690 (m-10) REVERT: C 311 GLN cc_start: 0.6614 (mt0) cc_final: 0.5963 (tp-100) REVERT: C 455 LYS cc_start: 0.0704 (OUTLIER) cc_final: -0.0416 (mmtt) REVERT: C 494 PHE cc_start: 0.0241 (OUTLIER) cc_final: 0.0016 (m-80) REVERT: C 737 MET cc_start: 0.7340 (ppp) cc_final: 0.7084 (ppp) REVERT: C 899 MET cc_start: 0.7685 (tpp) cc_final: 0.7340 (tpp) REVERT: C 1093 VAL cc_start: 0.7542 (m) cc_final: 0.7248 (p) REVERT: C 1104 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6495 (mtm-85) REVERT: E 37 TRP cc_start: -0.1480 (m100) cc_final: -0.1956 (m100) REVERT: E 62 TYR cc_start: 0.1829 (m-80) cc_final: 0.1437 (m-80) REVERT: D 79 LYS cc_start: 0.2028 (tptp) cc_final: 0.1351 (mtmm) outliers start: 104 outliers final: 66 residues processed: 354 average time/residue: 0.4244 time to fit residues: 249.3663 Evaluate side-chains 305 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 225 time to evaluate : 3.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 396 SER 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 580 GLU 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 714 ASN Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 834 TYR 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 B residue 40 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 125 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 347 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 753 TYR 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 906 ILE Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1037 VAL 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 B residue 1141 GLU 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 221 GLU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 548 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 607 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 1104 ARG 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 191 optimal weight: 4.9990 chunk 321 optimal weight: 0.7980 chunk 303 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 139 optimal weight: 0.0020 chunk 154 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN A 774 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.103888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.082204 restraints weight = 244603.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.081753 restraints weight = 152636.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.082425 restraints weight = 116575.060| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.6394 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= 0.149 Angle : 0.727 18.950 39514 Z= 0.355 Chirality : 0.050 0.560 4524 Planarity : 0.005 0.063 5046 Dihedral : 8.546 82.804 4607 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.33 % Favored : 92.38 % Rotamer: Outliers : 3.99 % Allowed : 23.82 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3510 helix: 1.12 (0.20), residues: 681 sheet: -0.79 (0.21), residues: 594 loop : -1.80 (0.12), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 433 HIS 0.007 0.001 HIS C 202 PHE 0.038 0.002 PHE A 315 TYR 0.034 0.002 TYR B 348 ARG 0.006 0.001 ARG C 812 Details of bonding type rmsd link_NAG-ASN : bond 0.00792 ( 25) link_NAG-ASN : angle 4.96016 ( 75) link_BETA1-4 : bond 0.01008 ( 11) link_BETA1-4 : angle 3.95283 ( 33) hydrogen bonds : bond 0.03936 ( 879) hydrogen bonds : angle 5.78642 ( 2518) SS BOND : bond 0.00312 ( 46) SS BOND : angle 1.71771 ( 92) covalent geometry : bond 0.00336 (28890) covalent geometry : angle 0.68185 (39314) *********************** 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 372 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 249 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 GLN cc_start: 0.4432 (pm20) cc_final: 0.3677 (tp-100) REVERT: A 172 MET cc_start: 0.4553 (pmm) cc_final: 0.3649 (ptt) REVERT: A 193 ASP cc_start: 0.5513 (OUTLIER) cc_final: 0.4829 (t70) REVERT: A 276 TYR cc_start: 0.5312 (m-80) cc_final: 0.4641 (m-80) REVERT: A 446 TYR cc_start: 0.4042 (p90) cc_final: 0.3156 (p90) REVERT: A 525 LYS cc_start: 0.6258 (tptp) cc_final: 0.5784 (tppt) REVERT: A 617 VAL cc_start: 0.4978 (OUTLIER) cc_final: 0.4770 (m) REVERT: A 834 TYR cc_start: 0.2904 (OUTLIER) cc_final: 0.1573 (t80) REVERT: A 866 MET cc_start: 0.6169 (ptt) cc_final: 0.5631 (ptp) REVERT: A 911 ASN cc_start: 0.7241 (p0) cc_final: 0.6895 (t0) REVERT: B 40 ASP cc_start: 0.5989 (OUTLIER) cc_final: 0.5733 (t70) REVERT: B 120 ASN cc_start: 0.2249 (OUTLIER) cc_final: 0.1819 (m-40) REVERT: B 148 MET cc_start: 0.0986 (tpt) cc_final: 0.0711 (ttp) REVERT: B 172 MET cc_start: 0.5092 (OUTLIER) cc_final: 0.4046 (ttp) REVERT: B 405 ARG cc_start: 0.4574 (mpp80) cc_final: 0.4171 (mpp80) REVERT: B 526 LYS cc_start: 0.4744 (OUTLIER) cc_final: 0.4238 (mmtm) REVERT: B 538 PHE cc_start: 0.4354 (p90) cc_final: 0.2746 (p90) REVERT: B 556 PHE cc_start: 0.3462 (OUTLIER) cc_final: 0.2953 (m-10) REVERT: B 762 ARG cc_start: 0.7611 (mtm-85) cc_final: 0.6725 (mtp85) REVERT: B 798 ASN cc_start: 0.6229 (OUTLIER) cc_final: 0.5587 (p0) REVERT: B 944 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7494 (mttm) REVERT: B 1047 MET cc_start: 0.6698 (pmm) cc_final: 0.6411 (pmm) REVERT: B 1106 PHE cc_start: 0.5257 (t80) cc_final: 0.4997 (t80) REVERT: B 1111 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6714 (mm) REVERT: B 1141 GLU cc_start: 0.3745 (OUTLIER) cc_final: 0.3271 (mp0) REVERT: C 59 PHE cc_start: 0.5968 (m-80) cc_final: 0.5726 (m-80) REVERT: C 187 PHE cc_start: 0.3314 (m-80) cc_final: 0.3055 (m-80) REVERT: C 301 LYS cc_start: 0.7214 (tptm) cc_final: 0.6601 (tptp) REVERT: C 311 GLN cc_start: 0.6622 (mt0) cc_final: 0.6165 (tp-100) REVERT: C 455 LYS cc_start: 0.0415 (OUTLIER) cc_final: -0.0673 (mmtp) REVERT: C 494 PHE cc_start: 0.0493 (OUTLIER) cc_final: 0.0270 (m-80) REVERT: C 633 TYR cc_start: 0.5496 (OUTLIER) cc_final: 0.4725 (p90) REVERT: C 734 ASP cc_start: 0.6242 (t0) cc_final: 0.5879 (p0) REVERT: C 737 MET cc_start: 0.7390 (ppp) cc_final: 0.7147 (ppp) REVERT: C 910 GLN cc_start: 0.7731 (pm20) cc_final: 0.6327 (pt0) REVERT: C 1093 VAL cc_start: 0.7403 (m) cc_final: 0.7128 (p) REVERT: E 62 TYR cc_start: 0.1725 (m-80) cc_final: 0.1306 (m-80) REVERT: D 79 LYS cc_start: 0.2429 (tptp) cc_final: 0.1588 (mtmm) outliers start: 123 outliers final: 87 residues processed: 352 average time/residue: 0.4205 time to fit residues: 246.2525 Evaluate side-chains 321 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 220 time to evaluate : 3.652 ------------------------------------------------------------------------------- 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 124 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 617 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 714 ASN Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 834 TYR 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 1127 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 213 LEU 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 347 VAL 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 465 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 755 SER 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 864 ASP Chi-restraints excluded: chain B residue 906 ILE 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 1015 ILE Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1141 GLU 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 221 GLU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 489 LEU 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 566 ILE 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 694 MET Chi-restraints excluded: chain C residue 721 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 25 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 335 optimal weight: 0.5980 chunk 283 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** A 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.104349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.082483 restraints weight = 271779.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.081742 restraints weight = 175423.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.082519 restraints weight = 134411.548| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.6570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28972 Z= 0.130 Angle : 0.698 18.704 39514 Z= 0.339 Chirality : 0.049 0.550 4524 Planarity : 0.005 0.065 5046 Dihedral : 8.057 72.124 4607 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.56 % Favored : 93.15 % Rotamer: Outliers : 3.70 % Allowed : 24.38 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 3510 helix: 1.15 (0.20), residues: 688 sheet: -0.65 (0.21), residues: 617 loop : -1.74 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 255 HIS 0.005 0.001 HIS C 202 PHE 0.048 0.002 PHE C 152 TYR 0.033 0.001 TYR B 348 ARG 0.012 0.001 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00792 ( 25) link_NAG-ASN : angle 4.82668 ( 75) link_BETA1-4 : bond 0.00958 ( 11) link_BETA1-4 : angle 3.93369 ( 33) hydrogen bonds : bond 0.03614 ( 879) hydrogen bonds : angle 5.58840 ( 2518) SS BOND : bond 0.00507 ( 46) SS BOND : angle 1.39145 ( 92) covalent geometry : bond 0.00288 (28890) covalent geometry : angle 0.65358 (39314) *********************** 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 359 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 245 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 GLN cc_start: 0.4473 (pm20) cc_final: 0.3728 (tp-100) REVERT: A 172 MET cc_start: 0.4450 (pmm) cc_final: 0.3650 (ptt) REVERT: A 193 ASP cc_start: 0.5258 (OUTLIER) cc_final: 0.4934 (t70) REVERT: A 525 LYS cc_start: 0.6430 (tptp) cc_final: 0.5991 (tppt) REVERT: A 617 VAL cc_start: 0.5110 (OUTLIER) cc_final: 0.4897 (m) REVERT: A 834 TYR cc_start: 0.3233 (OUTLIER) cc_final: 0.1898 (t80) REVERT: A 866 MET cc_start: 0.6537 (ptt) cc_final: 0.6027 (ptp) REVERT: B 40 ASP cc_start: 0.5966 (t70) cc_final: 0.5730 (t70) REVERT: B 116 LEU cc_start: 0.7985 (mt) cc_final: 0.7670 (tp) REVERT: B 120 ASN cc_start: 0.2389 (OUTLIER) cc_final: 0.1874 (m-40) REVERT: B 148 MET cc_start: 0.0973 (tpt) cc_final: 0.0725 (ttp) REVERT: B 172 MET cc_start: 0.5224 (OUTLIER) cc_final: 0.4274 (ttp) REVERT: B 405 ARG cc_start: 0.4551 (mpp80) cc_final: 0.4176 (mpp80) REVERT: B 526 LYS cc_start: 0.4761 (OUTLIER) cc_final: 0.4282 (mmtm) REVERT: B 538 PHE cc_start: 0.4470 (p90) cc_final: 0.2787 (p90) REVERT: B 556 PHE cc_start: 0.3231 (OUTLIER) cc_final: 0.2796 (m-10) REVERT: B 750 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.4657 (mt) REVERT: B 762 ARG cc_start: 0.7630 (mtm-85) cc_final: 0.6711 (mtp85) REVERT: B 798 ASN cc_start: 0.5987 (OUTLIER) cc_final: 0.5339 (p0) REVERT: B 944 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7463 (mttt) REVERT: B 1047 MET cc_start: 0.6830 (pmm) cc_final: 0.6465 (pmm) REVERT: B 1106 PHE cc_start: 0.5336 (t80) cc_final: 0.5048 (t80) REVERT: B 1111 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6695 (mm) REVERT: B 1141 GLU cc_start: 0.3613 (OUTLIER) cc_final: 0.3249 (mp0) REVERT: C 136 ASP cc_start: 0.1938 (OUTLIER) cc_final: 0.0890 (p0) REVERT: C 187 PHE cc_start: 0.3415 (m-80) cc_final: 0.3170 (m-80) REVERT: C 311 GLN cc_start: 0.6654 (mt0) cc_final: 0.6230 (tp-100) REVERT: C 455 LYS cc_start: 0.0482 (OUTLIER) cc_final: -0.0566 (mmtp) REVERT: C 494 PHE cc_start: 0.0470 (OUTLIER) cc_final: 0.0192 (m-80) REVERT: C 584 ILE cc_start: 0.4715 (OUTLIER) cc_final: 0.4373 (tp) REVERT: C 899 MET cc_start: 0.7589 (tpp) cc_final: 0.7028 (tpp) REVERT: C 903 PHE cc_start: 0.7656 (m-80) cc_final: 0.7396 (m-80) REVERT: C 1093 VAL cc_start: 0.7426 (m) cc_final: 0.7153 (p) REVERT: E 62 TYR cc_start: 0.1700 (m-80) cc_final: 0.1316 (m-80) REVERT: D 79 LYS cc_start: 0.2950 (tptp) cc_final: 0.2164 (mtmm) outliers start: 114 outliers final: 77 residues processed: 343 average time/residue: 0.3514 time to fit residues: 202.7508 Evaluate side-chains 315 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 223 time to evaluate : 3.157 ------------------------------------------------------------------------------- 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 166 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 617 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 714 ASN Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 834 TYR 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 1127 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 750 LEU 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 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 906 ILE 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 1074 THR Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1141 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 136 ASP 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 262 TYR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 548 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 607 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 124 THR 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 186 optimal weight: 0.0470 chunk 116 optimal weight: 5.9990 chunk 156 optimal weight: 0.4980 chunk 155 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 264 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 260 optimal weight: 1.9990 chunk 55 optimal weight: 0.0040 chunk 281 optimal weight: 1.9990 overall best weight: 0.6892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.104462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.084061 restraints weight = 272801.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.083083 restraints weight = 193587.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.083913 restraints weight = 149837.152| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.6708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28972 Z= 0.125 Angle : 0.693 18.585 39514 Z= 0.336 Chirality : 0.049 0.543 4524 Planarity : 0.005 0.065 5046 Dihedral : 7.628 65.930 4607 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.96 % Favored : 92.76 % Rotamer: Outliers : 3.08 % Allowed : 25.09 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3510 helix: 1.16 (0.21), residues: 692 sheet: -0.63 (0.21), residues: 619 loop : -1.69 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 630 HIS 0.006 0.001 HIS B 502 PHE 0.049 0.002 PHE C 152 TYR 0.031 0.001 TYR B 348 ARG 0.008 0.000 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00791 ( 25) link_NAG-ASN : angle 4.72849 ( 75) link_BETA1-4 : bond 0.00910 ( 11) link_BETA1-4 : angle 3.96528 ( 33) hydrogen bonds : bond 0.03500 ( 879) hydrogen bonds : angle 5.48195 ( 2518) SS BOND : bond 0.00309 ( 46) SS BOND : angle 1.27751 ( 92) covalent geometry : bond 0.00279 (28890) covalent geometry : angle 0.65066 (39314) *********************** 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 344 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 249 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 GLN cc_start: 0.4287 (pm20) cc_final: 0.3578 (tp-100) REVERT: A 172 MET cc_start: 0.4492 (pmm) cc_final: 0.3605 (ptt) REVERT: A 193 ASP cc_start: 0.5238 (OUTLIER) cc_final: 0.4904 (t70) REVERT: A 266 TYR cc_start: 0.5325 (m-80) cc_final: 0.3934 (t80) REVERT: A 335 PHE cc_start: 0.0294 (p90) cc_final: -0.0779 (p90) REVERT: A 339 PHE cc_start: 0.1647 (m-10) cc_final: 0.1054 (m-80) REVERT: A 525 LYS cc_start: 0.6375 (tptp) cc_final: 0.5906 (tppt) REVERT: A 729 THR cc_start: 0.8118 (m) cc_final: 0.7825 (t) REVERT: A 776 GLN cc_start: 0.7942 (pt0) cc_final: 0.7474 (mt0) REVERT: A 777 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6948 (tt0) REVERT: A 834 TYR cc_start: 0.3205 (OUTLIER) cc_final: 0.1850 (t80) REVERT: A 866 MET cc_start: 0.6814 (ptt) cc_final: 0.6307 (ptp) REVERT: A 915 GLU cc_start: 0.7639 (tt0) cc_final: 0.7288 (tm-30) REVERT: B 40 ASP cc_start: 0.6045 (t70) cc_final: 0.5830 (t70) REVERT: B 116 LEU cc_start: 0.7948 (mt) cc_final: 0.7652 (tp) REVERT: B 120 ASN cc_start: 0.2747 (OUTLIER) cc_final: 0.2117 (m110) REVERT: B 148 MET cc_start: 0.1290 (tpt) cc_final: 0.0993 (ttp) REVERT: B 172 MET cc_start: 0.5137 (mmt) cc_final: 0.4188 (ttp) REVERT: B 196 PHE cc_start: 0.6997 (m-10) cc_final: 0.6554 (m-80) REVERT: B 405 ARG cc_start: 0.4573 (mpp80) cc_final: 0.4190 (mpp80) REVERT: B 526 LYS cc_start: 0.4952 (OUTLIER) cc_final: 0.4501 (mmtm) REVERT: B 538 PHE cc_start: 0.4529 (p90) cc_final: 0.2800 (p90) REVERT: B 556 PHE cc_start: 0.3187 (OUTLIER) cc_final: 0.2756 (m-10) REVERT: B 762 ARG cc_start: 0.7699 (mtm-85) cc_final: 0.6787 (mtp85) REVERT: B 798 ASN cc_start: 0.5709 (OUTLIER) cc_final: 0.5185 (p0) REVERT: B 944 LYS cc_start: 0.7911 (mmtm) cc_final: 0.7390 (mttt) REVERT: B 1047 MET cc_start: 0.6680 (pmm) cc_final: 0.6256 (pmm) REVERT: B 1106 PHE cc_start: 0.5300 (t80) cc_final: 0.5019 (t80) REVERT: B 1111 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6744 (mm) REVERT: B 1141 GLU cc_start: 0.3439 (OUTLIER) cc_final: 0.3064 (mp0) REVERT: C 90 PHE cc_start: 0.5128 (t80) cc_final: 0.4267 (t80) REVERT: C 187 PHE cc_start: 0.3305 (m-80) cc_final: 0.2471 (m-80) REVERT: C 311 GLN cc_start: 0.6784 (mt0) cc_final: 0.6307 (tp-100) REVERT: C 455 LYS cc_start: 0.0527 (OUTLIER) cc_final: -0.0552 (mmtp) REVERT: C 494 PHE cc_start: 0.0562 (OUTLIER) cc_final: 0.0247 (m-80) REVERT: C 584 ILE cc_start: 0.4631 (OUTLIER) cc_final: 0.4293 (tp) REVERT: C 899 MET cc_start: 0.7648 (tpp) cc_final: 0.6957 (tpp) REVERT: C 903 PHE cc_start: 0.7811 (m-80) cc_final: 0.7453 (m-80) REVERT: C 910 GLN cc_start: 0.7733 (pm20) cc_final: 0.6267 (pt0) REVERT: C 1093 VAL cc_start: 0.7556 (m) cc_final: 0.7275 (p) REVERT: E 62 TYR cc_start: 0.1597 (m-80) cc_final: 0.1180 (m-80) REVERT: D 79 LYS cc_start: 0.3134 (tptp) cc_final: 0.2377 (mtmm) outliers start: 95 outliers final: 73 residues processed: 329 average time/residue: 0.3741 time to fit residues: 205.0556 Evaluate side-chains 313 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 229 time to evaluate : 3.369 ------------------------------------------------------------------------------- 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 166 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 580 GLU 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 714 ASN Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 834 TYR 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 B residue 66 HIS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 238 LEU 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 440 SER Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 638 ASN 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 906 ILE 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 1015 ILE Chi-restraints excluded: chain B residue 1037 VAL 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 B residue 1141 GLU 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 221 GLU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 548 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 617 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain E residue 124 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 224 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 205 optimal weight: 0.8980 chunk 242 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 318 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN ** 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** E 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.103974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.082149 restraints weight = 232804.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.081472 restraints weight = 149383.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.082180 restraints weight = 115610.592| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6017 moved from start: 0.6990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28972 Z= 0.139 Angle : 0.708 18.828 39514 Z= 0.345 Chirality : 0.049 0.549 4524 Planarity : 0.005 0.065 5046 Dihedral : 7.605 63.751 4607 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.05 % Favored : 92.67 % Rotamer: Outliers : 2.85 % Allowed : 25.58 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3510 helix: 1.08 (0.20), residues: 691 sheet: -0.69 (0.21), residues: 603 loop : -1.72 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 64 HIS 0.003 0.001 HIS A 66 PHE 0.048 0.002 PHE C 152 TYR 0.032 0.002 TYR B 348 ARG 0.010 0.001 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00792 ( 25) link_NAG-ASN : angle 4.70820 ( 75) link_BETA1-4 : bond 0.00857 ( 11) link_BETA1-4 : angle 3.96136 ( 33) hydrogen bonds : bond 0.03587 ( 879) hydrogen bonds : angle 5.55485 ( 2518) SS BOND : bond 0.00303 ( 46) SS BOND : angle 1.33493 ( 92) covalent geometry : bond 0.00313 (28890) covalent geometry : angle 0.66652 (39314) ********************** 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 332 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 244 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 GLN cc_start: 0.4691 (pm20) cc_final: 0.3938 (tp-100) REVERT: A 172 MET cc_start: 0.4342 (pmm) cc_final: 0.3627 (ptt) REVERT: A 193 ASP cc_start: 0.5292 (OUTLIER) cc_final: 0.4973 (t70) REVERT: A 266 TYR cc_start: 0.5402 (m-80) cc_final: 0.3985 (t80) REVERT: A 389 PHE cc_start: 0.1410 (p90) cc_final: 0.1190 (p90) REVERT: A 446 TYR cc_start: 0.4730 (p90) cc_final: 0.3932 (p90) REVERT: A 525 LYS cc_start: 0.6603 (tptp) cc_final: 0.6202 (pttm) REVERT: A 602 SER cc_start: 0.5218 (t) cc_final: 0.4923 (p) REVERT: A 776 GLN cc_start: 0.7968 (pt0) cc_final: 0.7524 (mt0) REVERT: A 834 TYR cc_start: 0.3091 (OUTLIER) cc_final: 0.1779 (t80) REVERT: A 852 PHE cc_start: 0.7185 (m-10) cc_final: 0.6909 (m-10) REVERT: A 915 GLU cc_start: 0.7490 (tt0) cc_final: 0.7224 (tm-30) REVERT: B 97 ASN cc_start: 0.6362 (m-40) cc_final: 0.6052 (p0) REVERT: B 120 ASN cc_start: 0.2752 (OUTLIER) cc_final: 0.2145 (m110) REVERT: B 148 MET cc_start: 0.1406 (tpt) cc_final: 0.1126 (ttp) REVERT: B 172 MET cc_start: 0.5077 (mmt) cc_final: 0.4101 (ttp) REVERT: B 405 ARG cc_start: 0.4470 (mpp80) cc_final: 0.4085 (mpp80) REVERT: B 538 PHE cc_start: 0.4716 (p90) cc_final: 0.3140 (p90) REVERT: B 556 PHE cc_start: 0.3230 (OUTLIER) cc_final: 0.2836 (m-10) REVERT: B 750 LEU cc_start: 0.6219 (tp) cc_final: 0.5932 (mt) REVERT: B 762 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.6799 (mtp85) REVERT: B 798 ASN cc_start: 0.5875 (OUTLIER) cc_final: 0.5218 (p0) REVERT: B 944 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7425 (mttt) REVERT: B 1047 MET cc_start: 0.6659 (pmm) cc_final: 0.6336 (pmm) REVERT: B 1106 PHE cc_start: 0.5489 (t80) cc_final: 0.5244 (t80) REVERT: B 1111 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6899 (mm) REVERT: B 1141 GLU cc_start: 0.3674 (OUTLIER) cc_final: 0.3232 (mp0) REVERT: C 90 PHE cc_start: 0.5302 (t80) cc_final: 0.4426 (t80) REVERT: C 187 PHE cc_start: 0.3391 (m-80) cc_final: 0.2605 (m-80) REVERT: C 196 PHE cc_start: 0.7195 (m-80) cc_final: 0.6977 (m-80) REVERT: C 290 LEU cc_start: 0.6829 (mt) cc_final: 0.6436 (mt) REVERT: C 311 GLN cc_start: 0.7093 (mt0) cc_final: 0.6569 (tp-100) REVERT: C 455 LYS cc_start: 0.0513 (OUTLIER) cc_final: -0.0421 (mmtp) REVERT: C 494 PHE cc_start: 0.0364 (OUTLIER) cc_final: -0.0075 (m-80) REVERT: C 584 ILE cc_start: 0.4678 (OUTLIER) cc_final: 0.4351 (tp) REVERT: C 899 MET cc_start: 0.7813 (tpp) cc_final: 0.7213 (tpp) REVERT: C 903 PHE cc_start: 0.7716 (m-80) cc_final: 0.7390 (m-80) REVERT: C 1093 VAL cc_start: 0.7549 (m) cc_final: 0.7270 (p) REVERT: E 62 TYR cc_start: 0.1655 (m-80) cc_final: 0.1286 (m-80) REVERT: D 79 LYS cc_start: 0.3084 (tptp) cc_final: 0.2333 (mtmm) outliers start: 88 outliers final: 75 residues processed: 320 average time/residue: 0.3347 time to fit residues: 179.3051 Evaluate side-chains 315 residues out of total 3085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 230 time to evaluate : 2.838 ------------------------------------------------------------------------------- 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 166 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 580 GLU 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 714 ASN Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 834 TYR 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 B residue 66 HIS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 988 VAL 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 1074 THR Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1141 GLU 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 221 GLU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 548 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 617 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 124 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 173 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 323 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 237 optimal weight: 0.5980 chunk 324 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 752 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.103838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.082242 restraints weight = 257076.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.081560 restraints weight = 167315.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.082402 restraints weight = 125296.298| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.7215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28972 Z= 0.140 Angle : 0.712 18.946 39514 Z= 0.347 Chirality : 0.049 0.546 4524 Planarity : 0.005 0.068 5046 Dihedral : 7.601 63.761 4607 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.33 % Favored : 92.38 % Rotamer: Outliers : 3.01 % Allowed : 25.67 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.14), residues: 3510 helix: 1.04 (0.20), residues: 692 sheet: -0.72 (0.21), residues: 601 loop : -1.76 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 102 HIS 0.005 0.001 HIS C 242 PHE 0.047 0.002 PHE C 152 TYR 0.029 0.002 TYR B 348 ARG 0.010 0.001 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00795 ( 25) link_NAG-ASN : angle 4.68071 ( 75) link_BETA1-4 : bond 0.00845 ( 11) link_BETA1-4 : angle 3.96420 ( 33) hydrogen bonds : bond 0.03584 ( 879) hydrogen bonds : angle 5.58022 ( 2518) SS BOND : bond 0.00285 ( 46) SS BOND : angle 1.28190 ( 92) covalent geometry : bond 0.00316 (28890) covalent geometry : angle 0.67108 (39314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12061.05 seconds wall clock time: 216 minutes 14.68 seconds (12974.68 seconds total)