Starting phenix.real_space_refine on Sun Oct 12 09:39:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8upx_42456/10_2025/8upx_42456.cif Found real_map, /net/cci-nas-00/data/ceres_data/8upx_42456/10_2025/8upx_42456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8upx_42456/10_2025/8upx_42456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8upx_42456/10_2025/8upx_42456.map" model { file = "/net/cci-nas-00/data/ceres_data/8upx_42456/10_2025/8upx_42456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8upx_42456/10_2025/8upx_42456.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 14809 2.51 5 N 3806 2.21 5 O 4512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23232 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7082 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 906, 7066 Classifications: {'peptide': 906} Link IDs: {'PTRANS': 49, 'TRANS': 856} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 906, 7066 Classifications: {'peptide': 906} Link IDs: {'PTRANS': 49, 'TRANS': 856} Chain breaks: 4 bond proxies already assigned to first conformer: 7207 Chain: "B" Number of atoms: 8530 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1092, 8514 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 62, 'TRANS': 1029} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1092, 8514 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 62, 'TRANS': 1029} Chain breaks: 6 bond proxies already assigned to first conformer: 8691 Chain: "C" Number of atoms: 7088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 906, 7072 Classifications: {'peptide': 906} Link IDs: {'PTRANS': 48, 'TRANS': 857} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 906, 7072 Classifications: {'peptide': 906} Link IDs: {'PTRANS': 48, 'TRANS': 857} Chain breaks: 4 bond proxies already assigned to first conformer: 7213 Chain: "D" 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: "E" 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: "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: "A" 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: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 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 Time building chain proxies: 9.56, per 1000 atoms: 0.41 Number of scatterers: 23232 At special positions: 0 Unit cell: (143, 160.6, 174.9, 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 105 16.00 O 4512 8.00 N 3806 7.00 C 14809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, 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 553 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 632 " - pdb=" SG CYS A 664 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 686 " distance=2.03 Simple disulfide: pdb=" SG CYS A 753 " - pdb=" SG CYS A 775 " distance=2.03 Simple disulfide: pdb=" SG CYS A 758 " - pdb=" SG CYS A 764 " distance=2.03 Simple disulfide: pdb=" SG CYS A1047 " - pdb=" SG CYS A1058 " distance=2.03 Simple disulfide: pdb=" SG CYS A1097 " - pdb=" SG CYS A1141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - 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 454 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 632 " - pdb=" SG CYS B 664 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 686 " distance=2.03 Simple disulfide: pdb=" SG CYS B 753 " - pdb=" SG CYS B 775 " distance=2.03 Simple disulfide: pdb=" SG CYS B 758 " - pdb=" SG CYS B 764 " distance=2.03 Simple disulfide: pdb=" SG CYS B1047 " - pdb=" SG CYS B1058 " distance=2.03 Simple disulfide: pdb=" SG CYS B1097 " - pdb=" SG CYS B1141 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 134 " 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 553 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 632 " - pdb=" SG CYS C 664 " distance=2.03 Simple disulfide: pdb=" SG CYS C 677 " - pdb=" SG CYS C 686 " distance=2.03 Simple disulfide: pdb=" SG CYS C 753 " - pdb=" SG CYS C 775 " distance=2.03 Simple disulfide: pdb=" SG CYS C 758 " - pdb=" SG CYS C 764 " distance=2.03 Simple disulfide: pdb=" SG CYS C 855 " - pdb=" SG CYS C 866 " distance=2.03 Simple disulfide: pdb=" SG CYS C1047 " - pdb=" SG CYS C1058 " distance=2.03 Simple disulfide: pdb=" SG CYS C1097 " - pdb=" SG CYS C1141 " distance=2.04 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " 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-ASN " NAG A1301 " - " ASN A 631 " " NAG A1302 " - " ASN A 672 " " NAG A1303 " - " ASN A 724 " " NAG A1304 " - " ASN A1089 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 631 " " NAG B1303 " - " ASN B 279 " " NAG B1304 " - " ASN B 672 " " NAG B1305 " - " ASN B 724 " " NAG B1306 " - " ASN B1089 " " NAG C1301 " - " ASN C 631 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 724 " " NAG C1304 " - " ASN C1089 " " NAG D 1 " - " ASN C 732 " " NAG E 1 " - " ASN A 732 " " NAG F 1 " - " ASN A 816 " " NAG G 1 " - " ASN A1113 " " NAG H 1 " - " ASN A1149 " " NAG I 1 " - " ASN B 732 " " NAG J 1 " - " ASN B 816 " " NAG K 1 " - " ASN B1113 " " NAG L 1 " - " ASN B1149 " " NAG M 1 " - " ASN C 816 " " NAG N 1 " - " ASN C1113 " " NAG O 1 " - " ASN C1149 " Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5464 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 40 sheets defined 24.8% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 648 through 653 Processing helix chain 'A' and resid 752 through 757 removed outlier: 3.584A pdb=" N TYR A 756 " --> pdb=" O ASP A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 770 removed outlier: 4.030A pdb=" N GLN A 770 " --> pdb=" O ASN A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 798 removed outlier: 3.507A pdb=" N GLN A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 840 Processing helix chain 'A' and resid 864 through 870 Processing helix chain 'A' and resid 883 through 899 Processing helix chain 'A' and resid 901 through 905 Processing helix chain 'A' and resid 912 through 924 removed outlier: 3.644A pdb=" N ILE A 924 " --> pdb=" O ARG A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 955 removed outlier: 3.529A pdb=" N TYR A 932 " --> pdb=" O GLN A 928 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS A 936 " --> pdb=" O TYR A 932 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 980 removed outlier: 3.590A pdb=" N GLN A 964 " --> pdb=" O LEU A 960 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 966 " --> pdb=" O LYS A 962 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 967 " --> pdb=" O LEU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 removed outlier: 4.128A pdb=" N ARG A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1048 removed outlier: 4.583A pdb=" N VAL A1006 " --> pdb=" O PRO A1002 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A1048 " --> pdb=" O MET A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1161 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 336 through 341 removed outlier: 3.740A pdb=" N LEU B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 361 through 369 removed outlier: 3.842A pdb=" N LEU B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.964A pdb=" N ALA B 385 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 removed outlier: 4.021A pdb=" N MET B 403 " --> pdb=" O PRO B 400 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER B 405 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 475 through 480 removed outlier: 4.067A pdb=" N SER B 479 " --> pdb=" O PRO B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.583A pdb=" N GLY B 560 " --> pdb=" O ASN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 757 Processing helix chain 'B' and resid 761 through 769 Processing helix chain 'B' and resid 770 through 772 No H-bonds generated for 'chain 'B' and resid 770 through 772' Processing helix chain 'B' and resid 774 through 798 removed outlier: 3.689A pdb=" N ASP B 790 " --> pdb=" O ALA B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 841 removed outlier: 3.538A pdb=" N VAL B 841 " --> pdb=" O LEU B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 870 Processing helix chain 'B' and resid 881 through 899 removed outlier: 3.758A pdb=" N ILE B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 886 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN B 887 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 905 removed outlier: 3.619A pdb=" N ALA B 905 " --> pdb=" O THR B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 925 removed outlier: 3.634A pdb=" N ALA B 918 " --> pdb=" O PRO B 914 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR B 919 " --> pdb=" O MET B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 934 removed outlier: 3.624A pdb=" N TYR B 932 " --> pdb=" O GLN B 928 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 933 " --> pdb=" O ASN B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 955 removed outlier: 4.340A pdb=" N SER B 954 " --> pdb=" O GLN B 950 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 980 removed outlier: 4.204A pdb=" N VAL B 966 " --> pdb=" O LYS B 962 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 983 No H-bonds generated for 'chain 'B' and resid 981 through 983' Processing helix chain 'B' and resid 991 through 997 Processing helix chain 'B' and resid 1000 through 1047 removed outlier: 4.550A pdb=" N VAL B1006 " --> pdb=" O PRO B1002 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN B1007 " --> pdb=" O GLU B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1156 through 1161 Processing helix chain 'C' and resid 291 through 300 Processing helix chain 'C' and resid 752 through 758 removed outlier: 3.934A pdb=" N CYS C 758 " --> pdb=" O THR C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 770 Processing helix chain 'C' and resid 775 through 798 removed outlier: 3.670A pdb=" N ASP C 790 " --> pdb=" O ALA C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 840 Processing helix chain 'C' and resid 856 through 860 Processing helix chain 'C' and resid 863 through 870 Processing helix chain 'C' and resid 881 through 899 removed outlier: 3.739A pdb=" N ILE C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA C 886 " --> pdb=" O ASP C 882 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN C 887 " --> pdb=" O GLU C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 905 removed outlier: 3.762A pdb=" N ALA C 905 " --> pdb=" O THR C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 925 removed outlier: 3.951A pdb=" N ALA C 918 " --> pdb=" O PRO C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 934 Processing helix chain 'C' and resid 934 through 953 Processing helix chain 'C' and resid 960 through 980 removed outlier: 4.068A pdb=" N VAL C 966 " --> pdb=" O LYS C 962 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C 967 " --> pdb=" O LEU C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 983 No H-bonds generated for 'chain 'C' and resid 981 through 983' Processing helix chain 'C' and resid 991 through 995 Processing helix chain 'C' and resid 1000 through 1048 removed outlier: 4.974A pdb=" N VAL C1006 " --> pdb=" O PRO C1002 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C1048 " --> pdb=" O MET C1044 " (cutoff:3.500A) Processing helix chain 'C' and resid 1156 through 1161 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 8.093A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 183 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.623A pdb=" N ALA C 590 " --> pdb=" O GLY C 581 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASP C 589 " --> pdb=" O ILE C 602 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 53 removed outlier: 3.817A pdb=" N ASP A 53 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 83 removed outlier: 3.681A pdb=" N LEU A 139 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 153 " --> pdb=" O PHE A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 83 removed outlier: 6.985A pdb=" N ARG A 234 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE A 104 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN A 236 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP A 102 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU A 238 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE A 163 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 307 through 313 removed outlier: 5.690A pdb=" N ILE A 309 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR A 614 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLN A 311 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 612 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 313 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323 removed outlier: 3.789A pdb=" N VAL A 554 " --> pdb=" O GLY A 565 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 669 through 670 removed outlier: 6.146A pdb=" N GLU A 669 " --> pdb=" O ALA A 709 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR A 711 " --> pdb=" O GLU A 669 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 706 " --> pdb=" O GLN A 690 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN A 690 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 687 " --> pdb=" O PRO A 680 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 716 through 717 removed outlier: 6.894A pdb=" N ALA A 716 " --> pdb=" O ILE B 803 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 726 through 730 removed outlier: 3.701A pdb=" N ILE A 727 " --> pdb=" O PHE A1090 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A1093 " --> pdb=" O PHE A1110 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE A1110 " --> pdb=" O ALA A1093 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 743 removed outlier: 5.951A pdb=" N TYR A1082 " --> pdb=" O HIS A1063 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1063 " --> pdb=" O TYR A1082 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 749 through 750 Processing sheet with id=AB4, first strand: chain 'A' and resid 802 through 803 Processing sheet with id=AB5, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.802A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N SER B 200 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N HIS B 202 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N LEU B 220 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL B 36 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.725A pdb=" N VAL B 47 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AB9, first strand: chain 'B' and resid 131 through 133 removed outlier: 5.017A pdb=" N SER B 157 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 308 through 316 removed outlier: 4.511A pdb=" N VAL B 610 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN B 314 " --> pdb=" O GLY B 608 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLY B 608 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS B 664 " --> pdb=" O TYR B 627 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY B 663 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.785A pdb=" N LEU B 392 " --> pdb=" O PHE B 355 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER B 391 " --> pdb=" O GLN B 527 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 518 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B 428 " --> pdb=" O CYS B 376 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N CYS B 376 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 430 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE B 374 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 432 " --> pdb=" O ASN B 372 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 464 through 466 removed outlier: 5.177A pdb=" N SER B 449 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 512 " --> pdb=" O SER B 449 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE B 451 " --> pdb=" O SER B 510 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER B 510 " --> pdb=" O ILE B 451 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 554 through 556 removed outlier: 3.638A pdb=" N VAL B 554 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY B 565 " --> pdb=" O VAL B 554 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 590 through 592 Processing sheet with id=AC6, first strand: chain 'B' and resid 669 through 670 removed outlier: 6.075A pdb=" N GLU B 669 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR B 711 " --> pdb=" O GLU B 669 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA B 687 " --> pdb=" O PRO B 680 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 716 through 719 removed outlier: 3.618A pdb=" N LYS C 805 " --> pdb=" O ASN B 718 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 726 through 743 removed outlier: 6.209A pdb=" N GLN B1086 " --> pdb=" O THR B 731 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B 733 " --> pdb=" O PRO B1084 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE B 735 " --> pdb=" O TYR B1082 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR B1082 " --> pdb=" O ILE B 735 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 737 " --> pdb=" O VAL B1080 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B1080 " --> pdb=" O VAL B 737 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR B 739 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B1078 " --> pdb=" O THR B 739 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 741 " --> pdb=" O VAL B1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B1076 " --> pdb=" O ILE B 741 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLY B1074 " --> pdb=" O PRO B 743 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR B1082 " --> pdb=" O HIS B1063 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N HIS B1063 " --> pdb=" O TYR B1082 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AD1, first strand: chain 'B' and resid 1135 through 1140 removed outlier: 4.715A pdb=" N ALA B1102 " --> pdb=" O SER B1138 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1109 through 1112 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.820A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N SER C 200 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 9.855A pdb=" N HIS C 202 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N LEU C 220 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.249A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 161 through 166 removed outlier: 4.272A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY C 101 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 147 through 152 removed outlier: 5.957A pdb=" N GLU C 149 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS C 142 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS C 141 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C 243 " --> pdb=" O HIS C 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 308 through 314 removed outlier: 5.460A pdb=" N ILE C 309 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR C 614 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN C 311 " --> pdb=" O VAL C 612 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 612 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER C 313 " --> pdb=" O VAL C 610 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 669 through 670 removed outlier: 6.086A pdb=" N GLU C 669 " --> pdb=" O ALA C 709 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR C 711 " --> pdb=" O GLU C 669 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA C 687 " --> pdb=" O PRO C 680 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 726 through 730 Processing sheet with id=AE1, first strand: chain 'C' and resid 733 through 743 removed outlier: 5.976A pdb=" N TYR C1082 " --> pdb=" O HIS C1063 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N HIS C1063 " --> pdb=" O TYR C1082 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 749 through 750 Processing sheet with id=AE3, first strand: chain 'C' and resid 1135 through 1137 Processing sheet with id=AE4, first strand: chain 'C' and resid 1109 through 1112 884 hydrogen bonds defined for protein. 2433 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: 5.67 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7361 1.34 - 1.46: 5469 1.46 - 1.58: 10789 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 23757 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" CA GLU B 278 " pdb=" C GLU B 278 " ideal model delta sigma weight residual 1.524 1.575 -0.051 1.66e-02 3.63e+03 9.36e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" CG PRO B 594 " pdb=" CD PRO B 594 " ideal model delta sigma weight residual 1.503 1.413 0.090 3.40e-02 8.65e+02 6.99e+00 ... (remaining 23752 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 31935 2.57 - 5.15: 359 5.15 - 7.72: 29 7.72 - 10.29: 6 10.29 - 12.87: 4 Bond angle restraints: 32333 Sorted by residual: angle pdb=" N PRO B 594 " pdb=" CD PRO B 594 " pdb=" CG PRO B 594 " ideal model delta sigma weight residual 103.20 94.06 9.14 1.50e+00 4.44e-01 3.71e+01 angle pdb=" C ASN A1089 " pdb=" CA ASN A1089 " pdb=" CB ASN A1089 " ideal model delta sigma weight residual 110.14 118.73 -8.59 1.54e+00 4.22e-01 3.11e+01 angle pdb=" CA CYS B 161 " pdb=" CB CYS B 161 " pdb=" SG CYS B 161 " ideal model delta sigma weight residual 114.40 125.30 -10.90 2.30e+00 1.89e-01 2.24e+01 angle pdb=" CA PRO B 594 " pdb=" CB PRO B 594 " pdb=" CG PRO B 594 " ideal model delta sigma weight residual 104.50 96.56 7.94 1.90e+00 2.77e-01 1.75e+01 angle pdb=" CA PRO B 594 " pdb=" N PRO B 594 " pdb=" CD PRO B 594 " ideal model delta sigma weight residual 112.00 106.49 5.51 1.40e+00 5.10e-01 1.55e+01 ... (remaining 32328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.08: 13391 23.08 - 46.16: 1066 46.16 - 69.23: 181 69.23 - 92.31: 74 92.31 - 115.39: 40 Dihedral angle restraints: 14752 sinusoidal: 6278 harmonic: 8474 Sorted by residual: dihedral pdb=" CB CYS C 632 " pdb=" SG CYS C 632 " pdb=" SG CYS C 664 " pdb=" CB CYS C 664 " ideal model delta sinusoidal sigma weight residual -86.00 3.39 -89.39 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS C1097 " pdb=" SG CYS C1097 " pdb=" SG CYS C1141 " pdb=" CB CYS C1141 " ideal model delta sinusoidal sigma weight residual 93.00 4.42 88.58 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS B 334 " pdb=" SG CYS B 334 " pdb=" SG CYS B 358 " pdb=" CB CYS B 358 " ideal model delta sinusoidal sigma weight residual 93.00 28.02 64.98 1 1.00e+01 1.00e-02 5.54e+01 ... (remaining 14749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 3785 0.155 - 0.310: 21 0.310 - 0.465: 1 0.465 - 0.620: 0 0.620 - 0.775: 2 Chirality restraints: 3809 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A1089 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 724 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 3806 not shown) Planarity restraints: 4149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1089 " 0.043 2.00e-02 2.50e+03 4.08e-02 2.08e+01 pdb=" CG ASN A1089 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN A1089 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A1089 " -0.043 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 221 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO A 222 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 222 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 222 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 816 " 0.038 2.00e-02 2.50e+03 3.44e-02 1.48e+01 pdb=" CG ASN A 816 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 816 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 816 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.041 2.00e-02 2.50e+03 ... (remaining 4146 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 433 2.67 - 3.23: 21397 3.23 - 3.79: 33690 3.79 - 4.34: 44199 4.34 - 4.90: 76000 Nonbonded interactions: 175719 Sorted by model distance: nonbonded pdb=" OG SER A 302 " pdb=" O THR A 304 " model vdw 2.118 3.040 nonbonded pdb=" O ALA B 894 " pdb=" OG1 THR B 898 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.240 3.040 nonbonded pdb=" NE2 GLN A 819 " pdb=" OE1 GLN A 950 " model vdw 2.246 3.120 nonbonded pdb=" OH TYR B 399 " pdb=" O MET B 403 " model vdw 2.247 3.040 ... (remaining 175714 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 325 or resid 542 through 637 or resid 648 throu \ gh 837 or resid 839 through 1033 or resid 1035 through 1304)) selection = (chain 'C' and (resid 14 through 325 or resid 327 through 837 or resid 839 throu \ gh 851 or resid 863 through 1033 or resid 1035 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 29.690 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.004 0.090 23828 Z= 0.174 Angle : 0.705 13.328 32513 Z= 0.344 Chirality : 0.051 0.775 3809 Planarity : 0.005 0.103 4123 Dihedral : 18.281 115.389 9189 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.55 % Favored : 93.34 % Rotamer: Outliers : 0.20 % Allowed : 18.12 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.16), residues: 2876 helix: 2.24 (0.23), residues: 598 sheet: 0.28 (0.21), residues: 600 loop : -2.24 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 44 TYR 0.020 0.001 TYR C1082 PHE 0.019 0.001 PHE B 870 TRP 0.033 0.001 TRP B 102 HIS 0.005 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00375 (23757) covalent geometry : angle 0.65897 (32333) SS BOND : bond 0.00241 ( 33) SS BOND : angle 1.34924 ( 66) hydrogen bonds : bond 0.13798 ( 882) hydrogen bonds : angle 6.08061 ( 2433) link_BETA1-4 : bond 0.00648 ( 12) link_BETA1-4 : angle 1.70719 ( 36) link_NAG-ASN : bond 0.01067 ( 26) link_NAG-ASN : angle 4.92049 ( 78) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 111 average time/residue: 0.1615 time to fit residues: 29.4872 Evaluate side-chains 91 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 589 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.0030 chunk 111 optimal weight: 6.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS A1069 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.111298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.064495 restraints weight = 107115.007| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 5.24 r_work: 0.2926 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23828 Z= 0.143 Angle : 0.702 10.663 32513 Z= 0.336 Chirality : 0.049 0.514 3809 Planarity : 0.005 0.074 4123 Dihedral : 11.065 91.872 3902 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.27 % Favored : 93.62 % Rotamer: Outliers : 1.25 % Allowed : 17.96 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.16), residues: 2876 helix: 2.49 (0.22), residues: 609 sheet: 0.24 (0.21), residues: 626 loop : -2.23 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 582 TYR 0.019 0.001 TYR C1082 PHE 0.023 0.002 PHE B 580 TRP 0.040 0.002 TRP B 102 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00327 (23757) covalent geometry : angle 0.67609 (32333) SS BOND : bond 0.00289 ( 33) SS BOND : angle 1.27661 ( 66) hydrogen bonds : bond 0.05050 ( 882) hydrogen bonds : angle 5.02578 ( 2433) link_BETA1-4 : bond 0.00523 ( 12) link_BETA1-4 : angle 1.47261 ( 36) link_NAG-ASN : bond 0.00749 ( 26) link_NAG-ASN : angle 3.70097 ( 78) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: B 514 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6844 (mmm) REVERT: C 1115 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8854 (p) outliers start: 31 outliers final: 9 residues processed: 131 average time/residue: 0.1433 time to fit residues: 31.9812 Evaluate side-chains 104 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 117 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 148 optimal weight: 0.0570 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 HIS A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 GLN ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.111030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.063000 restraints weight = 110045.929| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 5.34 r_work: 0.2859 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23828 Z= 0.142 Angle : 0.662 10.749 32513 Z= 0.319 Chirality : 0.048 0.481 3809 Planarity : 0.004 0.066 4123 Dihedral : 8.555 85.046 3900 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.17 % Favored : 93.73 % Rotamer: Outliers : 1.80 % Allowed : 17.81 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.16), residues: 2876 helix: 2.68 (0.22), residues: 608 sheet: 0.25 (0.21), residues: 624 loop : -2.20 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 243 TYR 0.021 0.001 TYR C1082 PHE 0.023 0.002 PHE C 996 TRP 0.029 0.001 TRP B 102 HIS 0.011 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00330 (23757) covalent geometry : angle 0.63379 (32333) SS BOND : bond 0.00268 ( 33) SS BOND : angle 1.31833 ( 66) hydrogen bonds : bond 0.05075 ( 882) hydrogen bonds : angle 4.89623 ( 2433) link_BETA1-4 : bond 0.00424 ( 12) link_BETA1-4 : angle 1.44732 ( 36) link_NAG-ASN : bond 0.00717 ( 26) link_NAG-ASN : angle 3.68623 ( 78) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.7965 (m-10) cc_final: 0.7169 (m-10) REVERT: B 186 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: B 514 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6856 (mmm) outliers start: 45 outliers final: 23 residues processed: 138 average time/residue: 0.1421 time to fit residues: 33.5438 Evaluate side-chains 118 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 664 CYS Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 198 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 266 optimal weight: 0.0970 chunk 238 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 260 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.107559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.060493 restraints weight = 121415.351| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 5.75 r_work: 0.2758 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 23828 Z= 0.271 Angle : 0.764 10.694 32513 Z= 0.377 Chirality : 0.050 0.520 3809 Planarity : 0.005 0.067 4123 Dihedral : 8.237 86.646 3900 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.42 % Favored : 92.47 % Rotamer: Outliers : 2.23 % Allowed : 18.04 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.16), residues: 2876 helix: 2.45 (0.22), residues: 598 sheet: 0.00 (0.20), residues: 619 loop : -2.34 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 243 TYR 0.025 0.002 TYR C1082 PHE 0.026 0.002 PHE B 336 TRP 0.033 0.002 TRP B 102 HIS 0.011 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00659 (23757) covalent geometry : angle 0.73758 (32333) SS BOND : bond 0.00386 ( 33) SS BOND : angle 1.74727 ( 66) hydrogen bonds : bond 0.06678 ( 882) hydrogen bonds : angle 5.25150 ( 2433) link_BETA1-4 : bond 0.00396 ( 12) link_BETA1-4 : angle 1.19301 ( 36) link_NAG-ASN : bond 0.00566 ( 26) link_NAG-ASN : angle 3.83711 ( 78) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 98 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8080 (mm110) REVERT: A 138 PHE cc_start: 0.7480 (p90) cc_final: 0.6821 (p90) REVERT: A 628 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7267 (mp10) REVERT: B 102 TRP cc_start: 0.8340 (m-10) cc_final: 0.7644 (m-10) REVERT: B 175 GLU cc_start: 0.5185 (OUTLIER) cc_final: 0.4843 (mm-30) REVERT: B 223 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6954 (mp) REVERT: C 223 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.7054 (mp) REVERT: C 1115 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8832 (p) REVERT: C 1153 TYR cc_start: 0.8257 (t80) cc_final: 0.7985 (t80) outliers start: 56 outliers final: 27 residues processed: 147 average time/residue: 0.1487 time to fit residues: 36.7711 Evaluate side-chains 122 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 664 CYS Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 22 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN B 372 ASN ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.109478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.061114 restraints weight = 120010.722| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 5.54 r_work: 0.2813 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23828 Z= 0.146 Angle : 0.662 11.108 32513 Z= 0.321 Chirality : 0.047 0.470 3809 Planarity : 0.004 0.058 4123 Dihedral : 7.657 81.778 3900 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.34 % Favored : 93.59 % Rotamer: Outliers : 1.56 % Allowed : 18.90 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.16), residues: 2876 helix: 2.65 (0.22), residues: 604 sheet: 0.16 (0.20), residues: 635 loop : -2.25 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 243 TYR 0.022 0.001 TYR C1082 PHE 0.030 0.002 PHE B 326 TRP 0.027 0.001 TRP B 102 HIS 0.007 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00337 (23757) covalent geometry : angle 0.63488 (32333) SS BOND : bond 0.00273 ( 33) SS BOND : angle 1.25606 ( 66) hydrogen bonds : bond 0.05359 ( 882) hydrogen bonds : angle 4.95193 ( 2433) link_BETA1-4 : bond 0.00472 ( 12) link_BETA1-4 : angle 1.38674 ( 36) link_NAG-ASN : bond 0.00624 ( 26) link_NAG-ASN : angle 3.65585 ( 78) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8139 (mm110) REVERT: A 116 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6358 (mp) REVERT: A 131 PHE cc_start: 0.8496 (m-80) cc_final: 0.6843 (m-80) REVERT: A 133 PHE cc_start: 0.6932 (m-80) cc_final: 0.6428 (m-80) REVERT: B 102 TRP cc_start: 0.8246 (m-10) cc_final: 0.7519 (m-10) REVERT: B 186 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: B 384 ILE cc_start: 0.8574 (tp) cc_final: 0.8355 (mm) REVERT: C 1115 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8860 (p) REVERT: C 1153 TYR cc_start: 0.8233 (t80) cc_final: 0.7934 (t80) outliers start: 39 outliers final: 25 residues processed: 130 average time/residue: 0.1497 time to fit residues: 32.9742 Evaluate side-chains 122 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 664 CYS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 279 optimal weight: 1.9990 chunk 254 optimal weight: 0.0570 chunk 22 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 278 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 0.0270 chunk 99 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.109701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.061664 restraints weight = 131939.620| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 5.97 r_work: 0.2831 rms_B_bonded: 5.17 restraints_weight: 2.0000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23828 Z= 0.140 Angle : 0.649 10.984 32513 Z= 0.313 Chirality : 0.047 0.459 3809 Planarity : 0.004 0.056 4123 Dihedral : 7.302 77.489 3900 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.00 % Favored : 92.93 % Rotamer: Outliers : 1.56 % Allowed : 19.09 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.16), residues: 2876 helix: 2.75 (0.22), residues: 605 sheet: 0.20 (0.20), residues: 642 loop : -2.19 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 243 TYR 0.021 0.001 TYR C1082 PHE 0.021 0.001 PHE A 607 TRP 0.021 0.001 TRP B 102 HIS 0.006 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00326 (23757) covalent geometry : angle 0.62312 (32333) SS BOND : bond 0.00266 ( 33) SS BOND : angle 1.16650 ( 66) hydrogen bonds : bond 0.05009 ( 882) hydrogen bonds : angle 4.82851 ( 2433) link_BETA1-4 : bond 0.00401 ( 12) link_BETA1-4 : angle 1.38070 ( 36) link_NAG-ASN : bond 0.00590 ( 26) link_NAG-ASN : angle 3.53873 ( 78) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8050 (mm110) REVERT: A 116 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6398 (mp) REVERT: A 131 PHE cc_start: 0.8463 (m-80) cc_final: 0.6700 (m-80) REVERT: A 133 PHE cc_start: 0.7024 (m-80) cc_final: 0.6524 (m-80) REVERT: A 579 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6709 (mm110) REVERT: A 628 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7338 (mp10) REVERT: B 102 TRP cc_start: 0.8282 (m-10) cc_final: 0.7512 (m-10) REVERT: B 186 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: C 1115 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8890 (p) REVERT: C 1153 TYR cc_start: 0.8279 (t80) cc_final: 0.7919 (t80) outliers start: 39 outliers final: 27 residues processed: 128 average time/residue: 0.1491 time to fit residues: 32.4936 Evaluate side-chains 125 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 664 CYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 90 optimal weight: 30.0000 chunk 236 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 260 optimal weight: 0.8980 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.109409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.060819 restraints weight = 136906.737| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 5.89 r_work: 0.2803 rms_B_bonded: 5.14 restraints_weight: 2.0000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23828 Z= 0.152 Angle : 0.652 11.099 32513 Z= 0.314 Chirality : 0.047 0.453 3809 Planarity : 0.004 0.054 4123 Dihedral : 7.128 73.552 3900 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.66 % Favored : 93.31 % Rotamer: Outliers : 1.95 % Allowed : 18.63 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.16), residues: 2876 helix: 2.75 (0.22), residues: 605 sheet: 0.20 (0.20), residues: 640 loop : -2.17 (0.14), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.021 0.001 TYR C1082 PHE 0.022 0.002 PHE A 607 TRP 0.020 0.001 TRP B 102 HIS 0.006 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00362 (23757) covalent geometry : angle 0.62685 (32333) SS BOND : bond 0.00273 ( 33) SS BOND : angle 1.19465 ( 66) hydrogen bonds : bond 0.05098 ( 882) hydrogen bonds : angle 4.82002 ( 2433) link_BETA1-4 : bond 0.00405 ( 12) link_BETA1-4 : angle 1.37866 ( 36) link_NAG-ASN : bond 0.00542 ( 26) link_NAG-ASN : angle 3.50729 ( 78) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 97 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.8045 (mm110) REVERT: A 116 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6356 (mp) REVERT: A 131 PHE cc_start: 0.8501 (m-80) cc_final: 0.6714 (m-80) REVERT: A 138 PHE cc_start: 0.7451 (p90) cc_final: 0.6812 (p90) REVERT: A 579 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6650 (mm110) REVERT: A 628 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: B 102 TRP cc_start: 0.8194 (m-10) cc_final: 0.7423 (m-10) REVERT: B 186 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: C 1115 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8877 (p) REVERT: C 1153 TYR cc_start: 0.8298 (t80) cc_final: 0.7973 (t80) outliers start: 49 outliers final: 37 residues processed: 138 average time/residue: 0.1503 time to fit residues: 35.4229 Evaluate side-chains 136 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 93 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 664 CYS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 219 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 223 optimal weight: 0.5980 chunk 165 optimal weight: 0.0870 chunk 205 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 139 optimal weight: 30.0000 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS B 934 ASN B 972 GLN ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.110448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.062718 restraints weight = 125470.489| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 5.87 r_work: 0.2858 rms_B_bonded: 5.02 restraints_weight: 2.0000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23828 Z= 0.118 Angle : 0.629 11.239 32513 Z= 0.302 Chirality : 0.046 0.418 3809 Planarity : 0.004 0.054 4123 Dihedral : 6.819 67.370 3900 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.31 % Favored : 93.66 % Rotamer: Outliers : 1.68 % Allowed : 19.09 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.16), residues: 2876 helix: 2.89 (0.22), residues: 602 sheet: 0.24 (0.21), residues: 640 loop : -2.11 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 185 TYR 0.019 0.001 TYR C1082 PHE 0.025 0.001 PHE A 607 TRP 0.059 0.002 TRP B 504 HIS 0.006 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00266 (23757) covalent geometry : angle 0.60393 (32333) SS BOND : bond 0.00229 ( 33) SS BOND : angle 1.00365 ( 66) hydrogen bonds : bond 0.04544 ( 882) hydrogen bonds : angle 4.71005 ( 2433) link_BETA1-4 : bond 0.00446 ( 12) link_BETA1-4 : angle 1.45554 ( 36) link_NAG-ASN : bond 0.00615 ( 26) link_NAG-ASN : angle 3.41145 ( 78) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.8001 (mm110) REVERT: A 116 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6486 (mp) REVERT: A 131 PHE cc_start: 0.8464 (m-80) cc_final: 0.6768 (m-80) REVERT: A 133 PHE cc_start: 0.6911 (m-80) cc_final: 0.6455 (m-80) REVERT: A 579 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6844 (mm110) REVERT: A 628 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7975 (mp10) REVERT: B 102 TRP cc_start: 0.8148 (m-10) cc_final: 0.7336 (m-10) REVERT: B 186 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: C 1115 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8892 (p) REVERT: C 1153 TYR cc_start: 0.8342 (t80) cc_final: 0.7996 (t80) outliers start: 42 outliers final: 33 residues processed: 134 average time/residue: 0.1475 time to fit residues: 33.3789 Evaluate side-chains 133 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 664 CYS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 988 ILE Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 201 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 283 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.108803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.060458 restraints weight = 123138.787| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 5.57 r_work: 0.2810 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23828 Z= 0.187 Angle : 0.671 11.530 32513 Z= 0.325 Chirality : 0.048 0.451 3809 Planarity : 0.004 0.053 4123 Dihedral : 6.825 63.031 3900 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.14 % Favored : 92.82 % Rotamer: Outliers : 1.84 % Allowed : 19.02 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.16), residues: 2876 helix: 2.76 (0.22), residues: 600 sheet: 0.12 (0.20), residues: 644 loop : -2.14 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.022 0.001 TYR C1082 PHE 0.023 0.002 PHE A 607 TRP 0.043 0.002 TRP B 504 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00449 (23757) covalent geometry : angle 0.64672 (32333) SS BOND : bond 0.00311 ( 33) SS BOND : angle 1.30253 ( 66) hydrogen bonds : bond 0.05322 ( 882) hydrogen bonds : angle 4.87916 ( 2433) link_BETA1-4 : bond 0.00421 ( 12) link_BETA1-4 : angle 1.37669 ( 36) link_NAG-ASN : bond 0.00486 ( 26) link_NAG-ASN : angle 3.47139 ( 78) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 96 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8039 (mm110) REVERT: A 116 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6406 (mp) REVERT: A 131 PHE cc_start: 0.8489 (m-80) cc_final: 0.6867 (m-80) REVERT: A 579 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6712 (mm110) REVERT: A 628 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7329 (mp10) REVERT: B 102 TRP cc_start: 0.8144 (m-10) cc_final: 0.7380 (m-10) REVERT: B 186 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: C 562 LYS cc_start: 0.5781 (tptp) cc_final: 0.4603 (mmtt) REVERT: C 1115 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8891 (p) REVERT: C 1153 TYR cc_start: 0.8368 (t80) cc_final: 0.8032 (t80) outliers start: 45 outliers final: 37 residues processed: 136 average time/residue: 0.1487 time to fit residues: 34.3171 Evaluate side-chains 137 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 94 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 664 CYS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 988 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 54 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 160 optimal weight: 0.0040 chunk 146 optimal weight: 0.4980 chunk 198 optimal weight: 0.0060 chunk 17 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.4410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.109870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062923 restraints weight = 117646.192| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 5.94 r_work: 0.2830 rms_B_bonded: 5.16 restraints_weight: 2.0000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23828 Z= 0.111 Angle : 0.624 11.732 32513 Z= 0.300 Chirality : 0.046 0.396 3809 Planarity : 0.004 0.053 4123 Dihedral : 6.472 59.457 3900 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 1.64 % Allowed : 19.33 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.16), residues: 2876 helix: 2.91 (0.22), residues: 601 sheet: 0.24 (0.21), residues: 639 loop : -2.06 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 100 TYR 0.019 0.001 TYR C1082 PHE 0.026 0.001 PHE A 607 TRP 0.045 0.002 TRP B 504 HIS 0.006 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00244 (23757) covalent geometry : angle 0.60050 (32333) SS BOND : bond 0.00236 ( 33) SS BOND : angle 1.03019 ( 66) hydrogen bonds : bond 0.04381 ( 882) hydrogen bonds : angle 4.69495 ( 2433) link_BETA1-4 : bond 0.00466 ( 12) link_BETA1-4 : angle 1.49011 ( 36) link_NAG-ASN : bond 0.00638 ( 26) link_NAG-ASN : angle 3.33716 ( 78) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7998 (mm110) REVERT: A 116 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6551 (mp) REVERT: A 131 PHE cc_start: 0.8461 (m-80) cc_final: 0.7110 (m-80) REVERT: A 133 PHE cc_start: 0.6903 (m-80) cc_final: 0.6446 (m-80) REVERT: A 579 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6769 (mm110) REVERT: B 102 TRP cc_start: 0.8113 (m-10) cc_final: 0.7306 (m-10) REVERT: B 186 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: B 241 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6584 (pp) REVERT: C 1115 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8889 (p) REVERT: C 1153 TYR cc_start: 0.8342 (t80) cc_final: 0.7991 (t80) outliers start: 40 outliers final: 29 residues processed: 136 average time/residue: 0.1419 time to fit residues: 33.2791 Evaluate side-chains 131 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 579 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 988 ILE Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 252 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 161 optimal weight: 6.9990 chunk 256 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.106980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.058929 restraints weight = 105574.424| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 5.20 r_work: 0.2774 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 23828 Z= 0.242 Angle : 0.707 11.817 32513 Z= 0.346 Chirality : 0.049 0.467 3809 Planarity : 0.004 0.054 4123 Dihedral : 6.589 58.775 3900 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.53 % Favored : 92.44 % Rotamer: Outliers : 1.52 % Allowed : 19.48 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.16), residues: 2876 helix: 2.73 (0.22), residues: 599 sheet: 0.09 (0.21), residues: 619 loop : -2.13 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 100 TYR 0.024 0.002 TYR C1082 PHE 0.022 0.002 PHE A 607 TRP 0.041 0.002 TRP B 504 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00591 (23757) covalent geometry : angle 0.68234 (32333) SS BOND : bond 0.00337 ( 33) SS BOND : angle 1.44017 ( 66) hydrogen bonds : bond 0.05864 ( 882) hydrogen bonds : angle 4.99194 ( 2433) link_BETA1-4 : bond 0.00482 ( 12) link_BETA1-4 : angle 1.41828 ( 36) link_NAG-ASN : bond 0.00456 ( 26) link_NAG-ASN : angle 3.54812 ( 78) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7419.20 seconds wall clock time: 127 minutes 24.64 seconds (7644.64 seconds total)