Starting phenix.real_space_refine on Sun Sep 29 18:58:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upx_42456/09_2024/8upx_42456.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upx_42456/09_2024/8upx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upx_42456/09_2024/8upx_42456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upx_42456/09_2024/8upx_42456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upx_42456/09_2024/8upx_42456.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upx_42456/09_2024/8upx_42456.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 23.38, per 1000 atoms: 1.01 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: 5.91 Conformation dependent library (CDL) restraints added in 5.7 seconds 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: 3.31 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: 9.76 Time building geometry restraints manager: 6.85 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 1161 or resid 1301 throug \ h 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 1161 or resid 1301 throug \ h 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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 67.280 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.940 ------------------------------------------------------------------------------- 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 23757 Z= 0.248 Angle : 0.659 12.866 32333 Z= 0.334 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 : 7.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (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 TRP 0.033 0.001 TRP B 102 HIS 0.005 0.001 HIS C 202 PHE 0.019 0.001 PHE B 870 TYR 0.020 0.001 TYR C1082 ARG 0.004 0.000 ARG C 44 *********************** 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 fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 111 average time/residue: 0.3536 time to fit residues: 64.6453 Evaluate side-chains 91 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 2.860 ------------------------------------------------------------------------------- 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 244 optimal weight: 4.9990 chunk 219 optimal weight: 0.0370 chunk 121 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 226 optimal weight: 0.0470 chunk 87 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 168 optimal weight: 0.1980 chunk 262 optimal weight: 1.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23757 Z= 0.173 Angle : 0.659 10.902 32333 Z= 0.320 Chirality : 0.048 0.510 3809 Planarity : 0.005 0.075 4123 Dihedral : 11.162 91.097 3902 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.68 % Favored : 94.22 % Rotamer: Outliers : 1.05 % Allowed : 18.04 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2876 helix: 2.57 (0.22), residues: 608 sheet: 0.30 (0.21), residues: 601 loop : -2.18 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 102 HIS 0.006 0.001 HIS A 141 PHE 0.025 0.001 PHE B 580 TYR 0.017 0.001 TYR C1082 ARG 0.004 0.000 ARG C 582 *********************** 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 131 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 172 MET cc_start: 0.2966 (ppp) cc_final: 0.2564 (pmm) REVERT: B 514 MET cc_start: 0.5887 (OUTLIER) cc_final: 0.5278 (mmm) outliers start: 26 outliers final: 9 residues processed: 127 average time/residue: 0.2982 time to fit residues: 64.6910 Evaluate side-chains 103 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 2.795 ------------------------------------------------------------------------------- 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 1107 GLU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 587 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 145 optimal weight: 0.0770 chunk 81 optimal weight: 0.6980 chunk 218 optimal weight: 0.3980 chunk 178 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 262 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 260 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 210 optimal weight: 9.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23757 Z= 0.218 Angle : 0.633 10.826 32333 Z= 0.311 Chirality : 0.047 0.482 3809 Planarity : 0.004 0.066 4123 Dihedral : 8.606 84.727 3900 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.20 % Favored : 93.69 % Rotamer: Outliers : 1.56 % Allowed : 17.96 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.16), residues: 2876 helix: 2.71 (0.22), residues: 608 sheet: 0.22 (0.21), residues: 624 loop : -2.16 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 102 HIS 0.011 0.001 HIS A 141 PHE 0.023 0.001 PHE C 996 TYR 0.020 0.001 TYR C1082 ARG 0.004 0.000 ARG A 243 *********************** 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 140 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 101 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.7231 (m-10) cc_final: 0.6955 (m-10) REVERT: B 514 MET cc_start: 0.5922 (OUTLIER) cc_final: 0.5264 (mmm) outliers start: 39 outliers final: 17 residues processed: 134 average time/residue: 0.2955 time to fit residues: 67.7259 Evaluate side-chains 110 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 2.459 ------------------------------------------------------------------------------- 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 626 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 866 CYS 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 323 ILE Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 949 ILE 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 1119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 259 optimal weight: 4.9990 chunk 197 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 263 optimal weight: 0.8980 chunk 279 optimal weight: 0.8980 chunk 137 optimal weight: 40.0000 chunk 250 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23757 Z= 0.226 Angle : 0.628 11.013 32333 Z= 0.310 Chirality : 0.047 0.468 3809 Planarity : 0.004 0.061 4123 Dihedral : 7.752 79.832 3900 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.24 % Favored : 93.66 % Rotamer: Outliers : 1.80 % Allowed : 17.65 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2876 helix: 2.76 (0.22), residues: 608 sheet: 0.24 (0.20), residues: 633 loop : -2.17 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 102 HIS 0.009 0.001 HIS A 141 PHE 0.024 0.002 PHE B 336 TYR 0.020 0.001 TYR C1082 ARG 0.004 0.000 ARG A 243 *********************** 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 142 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 97 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7908 (mm110) REVERT: B 172 MET cc_start: 0.3143 (ppp) cc_final: 0.2267 (ptt) outliers start: 45 outliers final: 26 residues processed: 135 average time/residue: 0.3226 time to fit residues: 72.8881 Evaluate side-chains 117 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 2.569 ------------------------------------------------------------------------------- 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 551 ASN Chi-restraints excluded: chain A residue 558 PHE 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 866 CYS 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 A residue 1115 THR Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 323 ILE 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 924 ILE Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 760 ASP 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 232 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 238 optimal weight: 3.9990 chunk 193 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 142 optimal weight: 0.9980 chunk 250 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23757 Z= 0.254 Angle : 0.629 11.009 32333 Z= 0.312 Chirality : 0.047 0.471 3809 Planarity : 0.004 0.057 4123 Dihedral : 7.377 76.489 3900 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 1.84 % Allowed : 18.08 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2876 helix: 2.78 (0.22), residues: 601 sheet: 0.18 (0.20), residues: 639 loop : -2.17 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP B 102 HIS 0.007 0.001 HIS A 141 PHE 0.027 0.002 PHE A 152 TYR 0.022 0.001 TYR C1082 ARG 0.004 0.000 ARG A 243 *********************** 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 139 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 93 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7896 (mm110) REVERT: A 116 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6654 (mp) REVERT: A 133 PHE cc_start: 0.7278 (m-80) cc_final: 0.7004 (m-80) REVERT: A 628 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: B 172 MET cc_start: 0.3285 (ppp) cc_final: 0.2802 (ptm) outliers start: 46 outliers final: 28 residues processed: 134 average time/residue: 0.3089 time to fit residues: 70.7871 Evaluate side-chains 120 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 2.770 ------------------------------------------------------------------------------- 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 303 PHE Chi-restraints excluded: chain A residue 558 PHE 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 767 LEU Chi-restraints excluded: chain A residue 866 CYS 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 A residue 1115 THR Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 564 THR 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 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 549 VAL 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 1119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 93 optimal weight: 6.9990 chunk 251 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 164 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 279 optimal weight: 0.0870 chunk 232 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN B 934 ASN ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23757 Z= 0.170 Angle : 0.597 11.281 32333 Z= 0.294 Chirality : 0.046 0.428 3809 Planarity : 0.004 0.055 4123 Dihedral : 6.952 70.487 3900 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.10 % Favored : 93.83 % Rotamer: Outliers : 1.29 % Allowed : 18.90 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2876 helix: 2.89 (0.22), residues: 601 sheet: 0.24 (0.20), residues: 638 loop : -2.07 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 102 HIS 0.006 0.001 HIS A 141 PHE 0.022 0.001 PHE B 336 TYR 0.019 0.001 TYR C1082 ARG 0.004 0.000 ARG C1106 *********************** 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 130 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 98 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7822 (mm110) REVERT: A 116 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.6735 (mp) REVERT: A 131 PHE cc_start: 0.8234 (m-80) cc_final: 0.6853 (m-80) REVERT: A 133 PHE cc_start: 0.7330 (m-80) cc_final: 0.7021 (m-80) REVERT: B 102 TRP cc_start: 0.7287 (m-10) cc_final: 0.7060 (m-10) REVERT: B 172 MET cc_start: 0.3290 (ppp) cc_final: 0.2941 (ptm) outliers start: 32 outliers final: 26 residues processed: 126 average time/residue: 0.3123 time to fit residues: 67.6542 Evaluate side-chains 122 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 2.741 ------------------------------------------------------------------------------- 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 303 PHE 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 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 976 THR Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 242 HIS 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 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 992 LEU 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 269 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 204 optimal weight: 0.2980 chunk 158 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23757 Z= 0.272 Angle : 0.627 10.989 32333 Z= 0.311 Chirality : 0.047 0.459 3809 Planarity : 0.004 0.054 4123 Dihedral : 6.892 66.406 3900 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.04 % Favored : 92.93 % Rotamer: Outliers : 1.52 % Allowed : 18.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 2876 helix: 2.75 (0.22), residues: 607 sheet: 0.18 (0.20), residues: 634 loop : -2.12 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 102 HIS 0.006 0.001 HIS A 141 PHE 0.020 0.002 PHE B 235 TYR 0.022 0.001 TYR B 399 ARG 0.003 0.000 ARG A 243 *********************** 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 135 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 97 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7804 (mm110) REVERT: A 116 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.6866 (mp) REVERT: A 131 PHE cc_start: 0.8278 (m-80) cc_final: 0.6875 (m-80) REVERT: A 138 PHE cc_start: 0.7138 (p90) cc_final: 0.6390 (p90) REVERT: A 628 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7722 (mp10) REVERT: B 172 MET cc_start: 0.3304 (ppp) cc_final: 0.3042 (ptm) outliers start: 38 outliers final: 28 residues processed: 130 average time/residue: 0.2999 time to fit residues: 66.2069 Evaluate side-chains 125 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 2.450 ------------------------------------------------------------------------------- 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 303 PHE 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 767 LEU Chi-restraints excluded: chain A residue 866 CYS 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 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 664 CYS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 1151 THR 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 992 LEU 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 172 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 137 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 972 GLN ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23757 Z= 0.182 Angle : 0.602 11.299 32333 Z= 0.296 Chirality : 0.046 0.421 3809 Planarity : 0.004 0.054 4123 Dihedral : 6.621 60.709 3900 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.34 % Favored : 93.62 % Rotamer: Outliers : 1.29 % Allowed : 18.94 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.16), residues: 2876 helix: 2.91 (0.22), residues: 601 sheet: 0.26 (0.21), residues: 633 loop : -2.06 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP B 102 HIS 0.006 0.001 HIS A 141 PHE 0.028 0.001 PHE B 181 TYR 0.020 0.001 TYR C1082 ARG 0.006 0.000 ARG B 493 *********************** 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 128 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7732 (mm110) REVERT: A 116 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.6861 (mp) REVERT: A 131 PHE cc_start: 0.8274 (m-80) cc_final: 0.6962 (m-80) REVERT: A 133 PHE cc_start: 0.7194 (m-80) cc_final: 0.6933 (m-80) REVERT: B 172 MET cc_start: 0.3225 (ppp) cc_final: 0.2919 (ptm) outliers start: 32 outliers final: 28 residues processed: 124 average time/residue: 0.3332 time to fit residues: 69.5496 Evaluate side-chains 124 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 2.974 ------------------------------------------------------------------------------- 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 303 PHE 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 866 CYS 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 235 PHE Chi-restraints excluded: chain B residue 242 HIS 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 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 1119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 253 optimal weight: 1.9990 chunk 266 optimal weight: 0.0570 chunk 243 optimal weight: 0.0870 chunk 259 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 chunk 113 optimal weight: 0.0970 chunk 203 optimal weight: 0.0770 chunk 79 optimal weight: 2.9990 chunk 234 optimal weight: 8.9990 chunk 245 optimal weight: 0.1980 chunk 258 optimal weight: 7.9990 overall best weight: 0.1032 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 23757 Z= 0.144 Angle : 0.580 11.319 32333 Z= 0.284 Chirality : 0.046 0.362 3809 Planarity : 0.004 0.055 4123 Dihedral : 6.063 59.518 3900 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.78 % Favored : 94.18 % Rotamer: Outliers : 1.09 % Allowed : 19.06 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2876 helix: 3.00 (0.22), residues: 605 sheet: 0.45 (0.21), residues: 603 loop : -1.93 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 504 HIS 0.006 0.001 HIS A 141 PHE 0.031 0.001 PHE B 181 TYR 0.027 0.001 TYR B 399 ARG 0.004 0.000 ARG C1106 *********************** 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 131 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7689 (mm110) REVERT: A 85 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.6650 (t0) REVERT: A 116 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.6773 (mp) REVERT: A 131 PHE cc_start: 0.8228 (m-80) cc_final: 0.6989 (m-80) REVERT: A 133 PHE cc_start: 0.7206 (m-80) cc_final: 0.6946 (m-80) outliers start: 27 outliers final: 18 residues processed: 129 average time/residue: 0.3206 time to fit residues: 69.4265 Evaluate side-chains 115 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 2.593 ------------------------------------------------------------------------------- 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 303 PHE 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 639 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 558 PHE 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 1119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 0.8980 chunk 274 optimal weight: 0.6980 chunk 167 optimal weight: 0.7980 chunk 130 optimal weight: 0.0030 chunk 190 optimal weight: 0.9980 chunk 287 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS A 819 GLN ** B 113 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23757 Z= 0.171 Angle : 0.584 11.897 32333 Z= 0.286 Chirality : 0.046 0.379 3809 Planarity : 0.004 0.055 4123 Dihedral : 6.006 58.728 3900 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.11 % Rotamer: Outliers : 0.94 % Allowed : 19.37 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2876 helix: 2.96 (0.22), residues: 604 sheet: 0.41 (0.21), residues: 616 loop : -1.94 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 102 HIS 0.006 0.001 HIS A 141 PHE 0.034 0.001 PHE A 870 TYR 0.018 0.001 TYR C1082 ARG 0.003 0.000 ARG C 185 ********************** 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 124 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7661 (mm110) REVERT: A 85 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.6581 (t0) REVERT: A 116 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.6899 (mp) REVERT: A 131 PHE cc_start: 0.8230 (m-80) cc_final: 0.7132 (m-80) REVERT: A 133 PHE cc_start: 0.7130 (m-80) cc_final: 0.6858 (m-80) outliers start: 23 outliers final: 20 residues processed: 121 average time/residue: 0.3027 time to fit residues: 62.8543 Evaluate side-chains 120 residues out of total 2549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 2.582 ------------------------------------------------------------------------------- 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 303 PHE 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 767 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 558 PHE 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 992 LEU 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 182 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 211 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 235 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.108861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.060595 restraints weight = 110803.575| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 5.37 r_work: 0.2807 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23757 Z= 0.323 Angle : 0.652 11.462 32333 Z= 0.326 Chirality : 0.048 0.430 3809 Planarity : 0.004 0.055 4123 Dihedral : 6.214 58.496 3900 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.04 % Favored : 92.93 % Rotamer: Outliers : 1.05 % Allowed : 19.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2876 helix: 2.81 (0.22), residues: 601 sheet: 0.19 (0.21), residues: 633 loop : -2.02 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 102 HIS 0.005 0.001 HIS A 141 PHE 0.029 0.002 PHE B 181 TYR 0.025 0.001 TYR C1082 ARG 0.003 0.000 ARG B1015 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4387.30 seconds wall clock time: 79 minutes 35.33 seconds (4775.33 seconds total)