Starting phenix.real_space_refine on Mon Aug 25 10:42:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmg_61601/08_2025/9jmg_61601.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmg_61601/08_2025/9jmg_61601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jmg_61601/08_2025/9jmg_61601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmg_61601/08_2025/9jmg_61601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jmg_61601/08_2025/9jmg_61601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmg_61601/08_2025/9jmg_61601.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 171 5.16 5 C 17344 2.51 5 N 4442 2.21 5 O 5383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27340 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1126, 8792 Classifications: {'peptide': 1126} Link IDs: {'PTRANS': 45, 'TRANS': 1080} Chain breaks: 7 Chain: "B" Number of atoms: 8792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1126, 8792 Classifications: {'peptide': 1126} Link IDs: {'PTRANS': 45, 'TRANS': 1080} Chain breaks: 7 Chain: "C" Number of atoms: 8792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1126, 8792 Classifications: {'peptide': 1126} Link IDs: {'PTRANS': 45, 'TRANS': 1080} Chain breaks: 7 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 234 Unusual residues: {'EIC': 1, 'FOL': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 220 Unusual residues: {'EIC': 1, 'FOL': 1, 'NAG': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 220 Unusual residues: {'EIC': 1, 'FOL': 1, 'NAG': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 6.17, per 1000 atoms: 0.23 Number of scatterers: 27340 At special positions: 0 Unit cell: (139.92, 151.8, 158.4, 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 171 16.00 O 5383 8.00 N 4442 7.00 C 17344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 187 " distance=2.04 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 337 " distance=2.02 Simple disulfide: pdb=" SG CYS A 371 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 413 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 590 " - pdb=" SG CYS A 641 " distance=2.03 Simple disulfide: pdb=" SG CYS A 607 " - pdb=" SG CYS A 637 " distance=2.03 Simple disulfide: pdb=" SG CYS A 666 " - pdb=" SG CYS A 698 " distance=2.05 Simple disulfide: pdb=" SG CYS A 712 " - pdb=" SG CYS A 721 " distance=2.03 Simple disulfide: pdb=" SG CYS A 787 " - pdb=" SG CYS A 809 " distance=2.03 Simple disulfide: pdb=" SG CYS A 792 " - pdb=" SG CYS A 798 " distance=2.04 Simple disulfide: pdb=" SG CYS A 893 " - pdb=" SG CYS A 906 " distance=2.03 Simple disulfide: pdb=" SG CYS A1087 " - pdb=" SG CYS A1098 " distance=2.02 Simple disulfide: pdb=" SG CYS A1137 " - pdb=" SG CYS A1144 " distance=2.05 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 187 " distance=2.04 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 225 " distance=2.08 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 337 " distance=2.02 Simple disulfide: pdb=" SG CYS B 371 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 413 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 571 " distance=2.03 Simple disulfide: pdb=" SG CYS B 494 " - pdb=" SG CYS B 514 " distance=2.03 Simple disulfide: pdb=" SG CYS B 590 " - pdb=" SG CYS B 641 " distance=2.03 Simple disulfide: pdb=" SG CYS B 607 " - pdb=" SG CYS B 637 " distance=2.03 Simple disulfide: pdb=" SG CYS B 666 " - pdb=" SG CYS B 698 " distance=2.02 Simple disulfide: pdb=" SG CYS B 712 " - pdb=" SG CYS B 721 " distance=2.03 Simple disulfide: pdb=" SG CYS B 787 " - pdb=" SG CYS B 809 " distance=2.03 Simple disulfide: pdb=" SG CYS B 792 " - pdb=" SG CYS B 798 " distance=2.04 Simple disulfide: pdb=" SG CYS B 893 " - pdb=" SG CYS B 906 " distance=2.05 Simple disulfide: pdb=" SG CYS B1087 " - pdb=" SG CYS B1098 " distance=2.02 Simple disulfide: pdb=" SG CYS B1137 " - pdb=" SG CYS B1144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 187 " distance=2.04 Simple disulfide: pdb=" SG CYS C 177 " - pdb=" SG CYS C 225 " distance=2.06 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 337 " distance=2.02 Simple disulfide: pdb=" SG CYS C 371 " - pdb=" SG CYS C 395 " distance=2.03 Simple disulfide: pdb=" SG CYS C 413 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 571 " distance=2.03 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 514 " distance=2.03 Simple disulfide: pdb=" SG CYS C 590 " - pdb=" SG CYS C 641 " distance=2.03 Simple disulfide: pdb=" SG CYS C 607 " - pdb=" SG CYS C 637 " distance=2.03 Simple disulfide: pdb=" SG CYS C 666 " - pdb=" SG CYS C 698 " distance=2.06 Simple disulfide: pdb=" SG CYS C 712 " - pdb=" SG CYS C 721 " distance=2.03 Simple disulfide: pdb=" SG CYS C 787 " - pdb=" SG CYS C 809 " distance=2.03 Simple disulfide: pdb=" SG CYS C 792 " - pdb=" SG CYS C 798 " distance=2.04 Simple disulfide: pdb=" SG CYS C 893 " - pdb=" SG CYS C 906 " distance=2.03 Simple disulfide: pdb=" SG CYS C1087 " - pdb=" SG CYS C1098 " distance=2.02 Simple disulfide: pdb=" SG CYS C1137 " - pdb=" SG CYS C1144 " distance=2.05 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 D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A1401 " - " ASN A 43 " " NAG A1402 " - " ASN A 60 " " NAG A1403 " - " ASN A 93 " " NAG A1404 " - " ASN A 151 " " NAG A1405 " - " ASN A 158 " " NAG A1406 " - " ASN A 232 " " NAG A1407 " - " ASN A 288 " " NAG A1408 " - " ASN A 201 " " NAG A1409 " - " ASN A 386 " " NAG A1410 " - " ASN A 704 " " NAG A1411 " - " ASN A 851 " " NAG A1412 " - " ASN A1129 " " NAG A1413 " - " ASN A1191 " " NAG B1401 " - " ASN B 43 " " NAG B1402 " - " ASN B 60 " " NAG B1403 " - " ASN B 93 " " NAG B1404 " - " ASN B 151 " " NAG B1405 " - " ASN B 158 " " NAG B1406 " - " ASN B 201 " " NAG B1407 " - " ASN B 232 " " NAG B1408 " - " ASN B 288 " " NAG B1409 " - " ASN B 704 " " NAG B1410 " - " ASN B 851 " " NAG B1411 " - " ASN B1129 " " NAG B1413 " - " ASN B1191 " " NAG C1402 " - " ASN C 43 " " NAG C1403 " - " ASN C 60 " " NAG C1404 " - " ASN C 93 " " NAG C1405 " - " ASN C 151 " " NAG C1406 " - " ASN C 158 " " NAG C1407 " - " ASN C 201 " " NAG C1408 " - " ASN C 232 " " NAG C1409 " - " ASN C 288 " " NAG C1410 " - " ASN C 704 " " NAG C1411 " - " ASN C 851 " " NAG C1412 " - " ASN C1129 " " NAG C1413 " - " ASN C1191 " " NAG D 1 " - " ASN A 114 " " NAG E 1 " - " ASN A 398 " " NAG F 1 " - " ASN B 114 " " NAG G 1 " - " ASN B 386 " " NAG H 1 " - " ASN B 398 " " NAG I 1 " - " ASN C 114 " " NAG J 1 " - " ASN C 386 " " NAG K 1 " - " ASN C 398 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 973.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB FOL A1414 " pdb=" CB FOL B1412 " pdb=" CB FOL C1414 " Number of C-beta restraints generated: 6306 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 60 sheets defined 28.4% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 30 through 35 removed outlier: 4.086A pdb=" N PHE A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 30 through 35' Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 330 through 340 Processing helix chain 'A' and resid 373 through 378 removed outlier: 3.655A pdb=" N LEU A 376 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 378 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 404 Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 437 through 444 removed outlier: 4.692A pdb=" N SER A 442 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.857A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 480 Processing helix chain 'A' and resid 511 through 521 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 665 through 673 removed outlier: 3.760A pdb=" N ILE A 669 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 670 " --> pdb=" O CYS A 666 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 671 " --> pdb=" O ASN A 667 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 672 " --> pdb=" O HIS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 793 Processing helix chain 'A' and resid 795 through 806 Processing helix chain 'A' and resid 808 through 834 removed outlier: 3.795A pdb=" N ASN A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 832 " --> pdb=" O LYS A 828 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP A 833 " --> pdb=" O SER A 829 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 834 " --> pdb=" O LEU A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 869 through 879 Processing helix chain 'A' and resid 888 through 895 removed outlier: 4.050A pdb=" N LYS A 895 " --> pdb=" O ASP A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 912 removed outlier: 4.508A pdb=" N TYR A 909 " --> pdb=" O ILE A 905 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 910 " --> pdb=" O CYS A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 934 Processing helix chain 'A' and resid 952 through 965 removed outlier: 3.692A pdb=" N GLY A 965 " --> pdb=" O MET A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 974 removed outlier: 3.659A pdb=" N ASN A 974 " --> pdb=" O VAL A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 991 removed outlier: 3.682A pdb=" N THR A 991 " --> pdb=" O GLY A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1019 Processing helix chain 'A' and resid 1020 through 1022 No H-bonds generated for 'chain 'A' and resid 1020 through 1022' Processing helix chain 'A' and resid 1031 through 1039 Processing helix chain 'A' and resid 1040 through 1088 removed outlier: 3.591A pdb=" N VAL A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 34 Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.566A pdb=" N VAL B 97 " --> pdb=" O TYR B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.554A pdb=" N PHE B 128 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 218 Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 373 through 378 removed outlier: 3.605A pdb=" N LYS B 378 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 404 removed outlier: 3.568A pdb=" N LEU B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 450 through 456 removed outlier: 3.927A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 480 Processing helix chain 'B' and resid 511 through 521 removed outlier: 3.504A pdb=" N ARG B 521 " --> pdb=" O GLY B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 665 through 673 removed outlier: 3.501A pdb=" N LYS B 670 " --> pdb=" O ASN B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 793 Processing helix chain 'B' and resid 795 through 806 Processing helix chain 'B' and resid 807 through 831 removed outlier: 4.203A pdb=" N LYS B 811 " --> pdb=" O GLN B 807 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 820 " --> pdb=" O LEU B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 856 Processing helix chain 'B' and resid 869 through 879 Processing helix chain 'B' and resid 888 through 895 Processing helix chain 'B' and resid 904 through 912 removed outlier: 4.598A pdb=" N TYR B 909 " --> pdb=" O ILE B 905 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 910 " --> pdb=" O CYS B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 934 Processing helix chain 'B' and resid 935 through 940 removed outlier: 4.555A pdb=" N GLY B 938 " --> pdb=" O SER B 935 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER B 939 " --> pdb=" O ILE B 936 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE B 940 " --> pdb=" O ALA B 937 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 935 through 940' Processing helix chain 'B' and resid 952 through 965 removed outlier: 3.560A pdb=" N GLY B 965 " --> pdb=" O MET B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 974 removed outlier: 3.550A pdb=" N ASN B 974 " --> pdb=" O VAL B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 991 removed outlier: 3.621A pdb=" N ILE B 978 " --> pdb=" O ASN B 974 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET B 989 " --> pdb=" O ALA B 985 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 990 " --> pdb=" O LEU B 986 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR B 991 " --> pdb=" O GLY B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1020 Processing helix chain 'B' and resid 1021 through 1023 No H-bonds generated for 'chain 'B' and resid 1021 through 1023' Processing helix chain 'B' and resid 1031 through 1039 Processing helix chain 'B' and resid 1040 through 1088 removed outlier: 3.642A pdb=" N VAL B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 34 Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 92 through 97 removed outlier: 4.579A pdb=" N SER C 95 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 96 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 97 " --> pdb=" O TYR C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 97' Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 330 through 340 Processing helix chain 'C' and resid 373 through 378 removed outlier: 3.525A pdb=" N LEU C 376 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 404 removed outlier: 3.708A pdb=" N LEU C 402 " --> pdb=" O ASN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 424 Processing helix chain 'C' and resid 437 through 445 removed outlier: 4.656A pdb=" N SER C 442 " --> pdb=" O SER C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 456 removed outlier: 3.866A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 480 Processing helix chain 'C' and resid 511 through 521 Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 665 through 672 removed outlier: 3.861A pdb=" N ILE C 669 " --> pdb=" O GLU C 665 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS C 670 " --> pdb=" O CYS C 666 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER C 671 " --> pdb=" O ASN C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 793 Processing helix chain 'C' and resid 795 through 806 Processing helix chain 'C' and resid 807 through 835 removed outlier: 4.116A pdb=" N LYS C 811 " --> pdb=" O GLN C 807 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 820 " --> pdb=" O LEU C 816 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP C 833 " --> pdb=" O SER C 829 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 834 " --> pdb=" O LEU C 830 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 835 " --> pdb=" O PHE C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 856 removed outlier: 3.605A pdb=" N GLU C 856 " --> pdb=" O SER C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 879 Processing helix chain 'C' and resid 888 through 895 Processing helix chain 'C' and resid 907 through 912 Processing helix chain 'C' and resid 921 through 935 Processing helix chain 'C' and resid 952 through 965 Processing helix chain 'C' and resid 967 through 974 Processing helix chain 'C' and resid 976 through 992 Processing helix chain 'C' and resid 997 through 1019 Processing helix chain 'C' and resid 1020 through 1022 No H-bonds generated for 'chain 'C' and resid 1020 through 1022' Processing helix chain 'C' and resid 1031 through 1039 removed outlier: 3.501A pdb=" N ILE C1035 " --> pdb=" O SER C1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1088 removed outlier: 3.713A pdb=" N VAL C1046 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1197 through 1201 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 6.561A pdb=" N ASP A 28 " --> pdb=" O ILE A 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 removed outlier: 6.383A pdb=" N THR A 57 " --> pdb=" O TYR C 619 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY C 627 " --> pdb=" O VAL C 618 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE C 626 " --> pdb=" O MET C 638 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 69 removed outlier: 4.062A pdb=" N GLY A 67 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 309 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.695A pdb=" N LEU A 253 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ALA A 269 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR A 255 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU A 267 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83 removed outlier: 7.333A pdb=" N SER A 82 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 286 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 99 through 100 removed outlier: 4.646A pdb=" N ALA A 137 " --> pdb=" O MET A 283 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 178 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 223 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 99 through 100 removed outlier: 4.646A pdb=" N ALA A 137 " --> pdb=" O MET A 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 116 through 117 removed outlier: 4.424A pdb=" N ALA A 297 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.178A pdb=" N ALA A 143 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.722A pdb=" N VAL A 656 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 692 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 355 removed outlier: 3.709A pdb=" N PHE A 354 " --> pdb=" O VAL A 644 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 388 through 392 removed outlier: 3.621A pdb=" N SER A 388 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A 465 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS A 413 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG A 467 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE A 411 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS A 469 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 395 through 397 removed outlier: 6.442A pdb=" N CYS A 395 " --> pdb=" O CYS A 571 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 489 through 495 removed outlier: 5.742A pdb=" N GLY A 540 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N CYS A 494 " --> pdb=" O TYR A 538 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR A 538 " --> pdb=" O CYS A 494 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ARG A 541 " --> pdb=" O ASP A 526 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASP A 526 " --> pdb=" O ARG A 541 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 590 through 594 removed outlier: 3.773A pdb=" N GLY A 600 " --> pdb=" O TYR A 593 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 639 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 605 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS A 637 " --> pdb=" O GLN A 605 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE A 617 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 702 through 709 removed outlier: 7.195A pdb=" N ARG A 703 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N HIS A 742 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N THR A 705 " --> pdb=" O HIS A 742 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 749 through 750 removed outlier: 5.504A pdb=" N LEU A 749 " --> pdb=" O SER B 839 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1162 through 1166 removed outlier: 4.430A pdb=" N PHE A1152 " --> pdb=" O ALA A1133 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A1154 " --> pdb=" O THR A1131 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR A1131 " --> pdb=" O LYS A1154 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 767 through 777 removed outlier: 5.723A pdb=" N TYR A1122 " --> pdb=" O HIS A1103 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N HIS A1103 " --> pdb=" O TYR A1122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 783 through 785 Processing sheet with id=AC3, first strand: chain 'A' and resid 838 through 839 Processing sheet with id=AC4, first strand: chain 'A' and resid 948 through 949 removed outlier: 6.541A pdb=" N THR C1131 " --> pdb=" O LYS C1154 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C1154 " --> pdb=" O THR C1131 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C1152 " --> pdb=" O ALA C1133 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1136 through 1138 removed outlier: 6.305A pdb=" N CYS A1137 " --> pdb=" O LEU A1192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AC7, first strand: chain 'B' and resid 28 through 29 removed outlier: 6.590A pdb=" N ASP B 28 " --> pdb=" O ILE B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 62 through 69 removed outlier: 3.884A pdb=" N GLY B 67 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 309 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET B 312 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG B 323 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.558A pdb=" N GLY B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 253 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA B 269 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR B 255 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU B 267 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 82 through 83 removed outlier: 7.378A pdb=" N SER B 82 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU B 198 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASN B 288 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLU B 200 " --> pdb=" O ASN B 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.753A pdb=" N VAL B 171 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.753A pdb=" N VAL B 171 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 116 through 117 removed outlier: 4.472A pdb=" N ALA B 297 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 143 through 146 removed outlier: 4.436A pdb=" N ALA B 143 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.605A pdb=" N VAL B 656 " --> pdb=" O ASP B 651 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 388 through 392 removed outlier: 3.517A pdb=" N SER B 428 " --> pdb=" O LYS B 562 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR B 465 " --> pdb=" O CYS B 413 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS B 413 " --> pdb=" O THR B 465 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG B 467 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE B 411 " --> pdb=" O ARG B 467 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N HIS B 469 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 395 through 397 removed outlier: 6.603A pdb=" N CYS B 395 " --> pdb=" O CYS B 571 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 489 through 495 removed outlier: 5.678A pdb=" N GLY B 540 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N CYS B 494 " --> pdb=" O TYR B 538 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TYR B 538 " --> pdb=" O CYS B 494 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER B 531 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR B 537 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY B 529 " --> pdb=" O TYR B 537 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B 539 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR B 527 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 590 through 594 removed outlier: 3.591A pdb=" N GLY B 600 " --> pdb=" O TYR B 593 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 605 " --> pdb=" O CYS B 637 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS B 637 " --> pdb=" O GLN B 605 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE B 626 " --> pdb=" O MET B 638 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 627 " --> pdb=" O VAL B 618 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 702 through 709 removed outlier: 7.028A pdb=" N ARG B 703 " --> pdb=" O LEU B 740 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N HIS B 742 " --> pdb=" O ARG B 703 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N THR B 705 " --> pdb=" O HIS B 742 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 741 " --> pdb=" O CYS B 721 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 749 through 750 removed outlier: 5.698A pdb=" N LEU B 749 " --> pdb=" O SER C 839 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'B' and resid 1162 through 1166 removed outlier: 4.603A pdb=" N PHE B1152 " --> pdb=" O ALA B1133 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B1154 " --> pdb=" O THR B1131 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR B1131 " --> pdb=" O LYS B1154 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 767 through 777 removed outlier: 3.523A pdb=" N VAL B1105 " --> pdb=" O VAL B1120 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR B1122 " --> pdb=" O HIS B1103 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N HIS B1103 " --> pdb=" O TYR B1122 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 783 through 785 Processing sheet with id=AE7, first strand: chain 'B' and resid 1180 through 1183 removed outlier: 4.418A pdb=" N CYS B1144 " --> pdb=" O VAL B1183 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 28 through 29 removed outlier: 6.711A pdb=" N ASP C 28 " --> pdb=" O ILE C 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 62 through 69 removed outlier: 4.048A pdb=" N GLY C 67 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 309 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG C 323 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.725A pdb=" N LEU C 253 " --> pdb=" O ALA C 269 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA C 269 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR C 255 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU C 267 " --> pdb=" O THR C 255 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 82 through 83 removed outlier: 7.263A pdb=" N SER C 82 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 286 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 99 through 100 removed outlier: 4.369A pdb=" N ALA C 137 " --> pdb=" O MET C 283 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER C 142 " --> pdb=" O HIS C 159 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N HIS C 159 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 171 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 116 through 117 removed outlier: 4.428A pdb=" N ALA C 297 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 178 through 180 removed outlier: 3.587A pdb=" N VAL C 178 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS C 223 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU C 180 " --> pdb=" O ASN C 221 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 347 through 354 removed outlier: 5.065A pdb=" N VAL C 646 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR C 353 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL C 644 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 388 through 392 removed outlier: 3.550A pdb=" N GLU C 410 " --> pdb=" O HIS C 469 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA C 471 " --> pdb=" O VAL C 408 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL C 408 " --> pdb=" O ALA C 471 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 395 through 397 removed outlier: 6.413A pdb=" N CYS C 395 " --> pdb=" O CYS C 571 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'C' and resid 489 through 495 removed outlier: 5.784A pdb=" N GLY C 540 " --> pdb=" O SER C 492 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N CYS C 494 " --> pdb=" O TYR C 538 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR C 538 " --> pdb=" O CYS C 494 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG C 541 " --> pdb=" O ASP C 526 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP C 526 " --> pdb=" O ARG C 541 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 702 through 703 removed outlier: 6.919A pdb=" N ARG C 703 " --> pdb=" O LEU C 740 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N HIS C 742 " --> pdb=" O ARG C 703 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 702 through 703 removed outlier: 6.919A pdb=" N ARG C 703 " --> pdb=" O LEU C 740 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N HIS C 742 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 741 " --> pdb=" O CYS C 721 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 767 through 776 removed outlier: 5.624A pdb=" N TYR C1122 " --> pdb=" O HIS C1103 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N HIS C1103 " --> pdb=" O TYR C1122 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 783 through 785 Processing sheet with id=AG5, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 5.892A pdb=" N CYS C1137 " --> pdb=" O LEU C1192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'C' and resid 1145 through 1147 1069 hydrogen bonds defined for protein. 2916 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.61 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4637 1.32 - 1.46: 10385 1.46 - 1.60: 12669 1.60 - 1.74: 0 1.74 - 1.87: 243 Bond restraints: 27934 Sorted by residual: bond pdb=" CA ASP A 224 " pdb=" C ASP A 224 " ideal model delta sigma weight residual 1.528 1.453 0.075 1.36e-02 5.41e+03 3.03e+01 bond pdb=" CA MET B 312 " pdb=" C MET B 312 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.24e-02 6.50e+03 2.97e+01 bond pdb=" CA ASP B 247 " pdb=" C ASP B 247 " ideal model delta sigma weight residual 1.525 1.466 0.060 1.11e-02 8.12e+03 2.90e+01 bond pdb=" CA ASP A 409 " pdb=" CB ASP A 409 " ideal model delta sigma weight residual 1.532 1.465 0.067 1.28e-02 6.10e+03 2.73e+01 bond pdb=" C ASP A 409 " pdb=" O ASP A 409 " ideal model delta sigma weight residual 1.235 1.182 0.053 1.03e-02 9.43e+03 2.61e+01 ... (remaining 27929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 36871 2.44 - 4.89: 846 4.89 - 7.33: 131 7.33 - 9.78: 34 9.78 - 12.22: 4 Bond angle restraints: 37886 Sorted by residual: angle pdb=" N SER B1140 " pdb=" CA SER B1140 " pdb=" C SER B1140 " ideal model delta sigma weight residual 111.28 119.75 -8.47 1.09e+00 8.42e-01 6.04e+01 angle pdb=" C ASP A 224 " pdb=" N CYS A 225 " pdb=" CA CYS A 225 " ideal model delta sigma weight residual 122.72 112.07 10.65 1.38e+00 5.25e-01 5.96e+01 angle pdb=" N GLY C 963 " pdb=" CA GLY C 963 " pdb=" C GLY C 963 " ideal model delta sigma weight residual 114.66 105.20 9.46 1.24e+00 6.50e-01 5.81e+01 angle pdb=" O GLY B 496 " pdb=" C GLY B 496 " pdb=" N VAL B 497 " ideal model delta sigma weight residual 122.81 116.71 6.10 8.60e-01 1.35e+00 5.03e+01 angle pdb=" N GLY A 260 " pdb=" CA GLY A 260 " pdb=" C GLY A 260 " ideal model delta sigma weight residual 111.50 123.72 -12.22 1.74e+00 3.30e-01 4.94e+01 ... (remaining 37881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.82: 16693 30.82 - 61.64: 565 61.64 - 92.47: 122 92.47 - 123.29: 24 123.29 - 154.11: 2 Dihedral angle restraints: 17406 sinusoidal: 7542 harmonic: 9864 Sorted by residual: dihedral pdb=" CB CYS B 327 " pdb=" SG CYS B 327 " pdb=" SG CYS B 337 " pdb=" CB CYS B 337 " ideal model delta sinusoidal sigma weight residual -86.00 -169.15 83.15 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS A 327 " pdb=" SG CYS A 327 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual -86.00 -162.54 76.54 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS C 327 " pdb=" SG CYS C 327 " pdb=" SG CYS C 337 " pdb=" CB CYS C 337 " ideal model delta sinusoidal sigma weight residual -86.00 -158.02 72.02 1 1.00e+01 1.00e-02 6.64e+01 ... (remaining 17403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 4281 0.146 - 0.292: 59 0.292 - 0.437: 1 0.437 - 0.583: 0 0.583 - 0.729: 1 Chirality restraints: 4342 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 398 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 NAG C1403 " pdb=" ND2 ASN C 60 " pdb=" C2 NAG C1403 " pdb=" O5 NAG C1403 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.17e+00 ... (remaining 4339 not shown) Planarity restraints: 4871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1413 " -0.177 2.00e-02 2.50e+03 1.49e-01 2.76e+02 pdb=" C7 NAG B1413 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG B1413 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B1413 " 0.237 2.00e-02 2.50e+03 pdb=" O7 NAG B1413 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 699 " -0.028 2.00e-02 2.50e+03 5.48e-02 3.00e+01 pdb=" C VAL B 699 " 0.095 2.00e-02 2.50e+03 pdb=" O VAL B 699 " -0.036 2.00e-02 2.50e+03 pdb=" N ILE B 700 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 223 " -0.022 2.00e-02 2.50e+03 4.49e-02 2.01e+01 pdb=" C LYS B 223 " 0.078 2.00e-02 2.50e+03 pdb=" O LYS B 223 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP B 224 " -0.026 2.00e-02 2.50e+03 ... (remaining 4868 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4564 2.77 - 3.30: 23993 3.30 - 3.83: 45351 3.83 - 4.37: 53582 4.37 - 4.90: 94383 Nonbonded interactions: 221873 Sorted by model distance: nonbonded pdb=" OG SER C 82 " pdb=" O PHE C 90 " model vdw 2.234 3.040 nonbonded pdb=" O SER A 118 " pdb=" NA2 FOL A1414 " model vdw 2.249 3.120 nonbonded pdb=" OG1 THR C 694 " pdb=" O GLY C 697 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR B 62 " pdb=" OD1 ASP B 314 " model vdw 2.267 3.040 nonbonded pdb=" OG SER A 82 " pdb=" O PHE A 90 " model vdw 2.270 3.040 ... (remaining 221868 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 24 through 1201 or resid 1402 through 1411 or resid 1413)) \ selection = (chain 'B' and (resid 24 through 1201 or resid 1402 through 1411 or resid 1413)) \ selection = (chain 'C' and (resid 24 through 1201 or resid 1402 through 1411 or resid 1413)) \ } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'J' } 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: 1.290 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.980 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.006 0.075 28041 Z= 0.361 Angle : 0.915 16.749 38159 Z= 0.504 Chirality : 0.054 0.729 4342 Planarity : 0.006 0.149 4826 Dihedral : 16.361 154.112 10956 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.79 % Allowed : 9.37 % Favored : 89.84 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.13), residues: 3330 helix: -0.01 (0.17), residues: 789 sheet: -0.25 (0.19), residues: 705 loop : -0.88 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 601 TYR 0.031 0.002 TYR C 176 PHE 0.026 0.002 PHE C 342 TRP 0.025 0.002 TRP C 941 HIS 0.006 0.001 HIS B 668 Details of bonding type rmsd covalent geometry : bond 0.00606 (27934) covalent geometry : angle 0.88824 (37886) SS BOND : bond 0.01130 ( 48) SS BOND : angle 2.03234 ( 96) hydrogen bonds : bond 0.20981 ( 1033) hydrogen bonds : angle 7.98329 ( 2916) link_BETA1-4 : bond 0.00689 ( 14) link_BETA1-4 : angle 2.82279 ( 42) link_NAG-ASN : bond 0.00590 ( 45) link_NAG-ASN : angle 3.13848 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 263 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8097 (mt) REVERT: B 312 MET cc_start: 0.7933 (mtm) cc_final: 0.7307 (ttm) REVERT: B 622 PHE cc_start: 0.7278 (m-10) cc_final: 0.6735 (m-80) REVERT: B 993 PHE cc_start: 0.8379 (m-10) cc_final: 0.8028 (m-80) REVERT: C 150 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.7967 (p0) REVERT: C 171 VAL cc_start: 0.7675 (p) cc_final: 0.7243 (t) REVERT: C 345 ASP cc_start: 0.7623 (m-30) cc_final: 0.7401 (m-30) REVERT: C 1142 LYS cc_start: 0.6980 (mmtt) cc_final: 0.6512 (mtmm) outliers start: 23 outliers final: 14 residues processed: 279 average time/residue: 0.5163 time to fit residues: 172.7168 Evaluate side-chains 248 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 232 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1139 SER Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 793 ASN Chi-restraints excluded: chain C residue 964 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 789 GLN B 667 ASN ** B 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1091 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.131015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.103184 restraints weight = 36314.370| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.11 r_work: 0.3046 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 28041 Z= 0.223 Angle : 0.679 13.385 38159 Z= 0.344 Chirality : 0.047 0.414 4342 Planarity : 0.005 0.063 4826 Dihedral : 9.897 151.969 4983 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.64 % Allowed : 10.23 % Favored : 87.13 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.14), residues: 3330 helix: 0.54 (0.18), residues: 786 sheet: -0.25 (0.18), residues: 783 loop : -0.71 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 389 TYR 0.023 0.002 TYR B 311 PHE 0.017 0.002 PHE B1097 TRP 0.023 0.002 TRP C 941 HIS 0.006 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00529 (27934) covalent geometry : angle 0.64715 (37886) SS BOND : bond 0.00889 ( 48) SS BOND : angle 1.80223 ( 96) hydrogen bonds : bond 0.05821 ( 1033) hydrogen bonds : angle 5.73355 ( 2916) link_BETA1-4 : bond 0.00391 ( 14) link_BETA1-4 : angle 2.92981 ( 42) link_NAG-ASN : bond 0.00416 ( 45) link_NAG-ASN : angle 2.76282 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 260 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.5805 (mmt) cc_final: 0.5323 (mmt) REVERT: A 257 ARG cc_start: 0.7294 (mmp-170) cc_final: 0.7082 (mmp-170) REVERT: B 30 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7730 (mp10) REVERT: B 109 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8736 (mt) REVERT: B 312 MET cc_start: 0.8072 (mtm) cc_final: 0.7284 (ttm) REVERT: B 463 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8123 (m-40) REVERT: B 526 ASP cc_start: 0.7876 (t0) cc_final: 0.7618 (t0) REVERT: B 669 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6845 (tt) REVERT: B 772 THR cc_start: 0.8964 (t) cc_final: 0.8626 (m) REVERT: B 856 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: B 941 TRP cc_start: 0.8702 (t60) cc_final: 0.8342 (t60) REVERT: C 156 TYR cc_start: 0.8625 (m-80) cc_final: 0.8409 (m-80) REVERT: C 217 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6658 (tp40) REVERT: C 345 ASP cc_start: 0.8021 (m-30) cc_final: 0.7738 (m-30) REVERT: C 1142 LYS cc_start: 0.7595 (mmtt) cc_final: 0.6833 (mtmm) outliers start: 77 outliers final: 31 residues processed: 309 average time/residue: 0.4706 time to fit residues: 174.5678 Evaluate side-chains 272 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 989 MET Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1139 SER Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 788 LYS Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 941 TRP Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1177 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 136 optimal weight: 0.3980 chunk 244 optimal weight: 8.9990 chunk 297 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 309 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 299 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 668 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.103921 restraints weight = 36073.428| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.09 r_work: 0.3079 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28041 Z= 0.150 Angle : 0.595 13.242 38159 Z= 0.299 Chirality : 0.044 0.351 4342 Planarity : 0.004 0.055 4826 Dihedral : 8.355 149.975 4964 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.57 % Allowed : 12.36 % Favored : 85.07 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.14), residues: 3330 helix: 0.68 (0.18), residues: 804 sheet: -0.24 (0.18), residues: 786 loop : -0.62 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 323 TYR 0.019 0.001 TYR B 311 PHE 0.024 0.001 PHE B 227 TRP 0.022 0.001 TRP C 941 HIS 0.004 0.001 HIS B 668 Details of bonding type rmsd covalent geometry : bond 0.00346 (27934) covalent geometry : angle 0.56580 (37886) SS BOND : bond 0.00533 ( 48) SS BOND : angle 1.36494 ( 96) hydrogen bonds : bond 0.05125 ( 1033) hydrogen bonds : angle 5.35168 ( 2916) link_BETA1-4 : bond 0.00449 ( 14) link_BETA1-4 : angle 2.85766 ( 42) link_NAG-ASN : bond 0.00380 ( 45) link_NAG-ASN : angle 2.53173 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 262 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5128 (mmt) REVERT: A 825 ASP cc_start: 0.8087 (t0) cc_final: 0.7867 (m-30) REVERT: B 30 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: B 109 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8767 (mt) REVERT: B 146 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7473 (ptpp) REVERT: B 312 MET cc_start: 0.8104 (mtm) cc_final: 0.7348 (ttm) REVERT: B 357 ARG cc_start: 0.6072 (ppt170) cc_final: 0.5787 (ptt90) REVERT: B 450 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6812 (mm-30) REVERT: B 463 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8118 (m-40) REVERT: B 526 ASP cc_start: 0.7804 (t0) cc_final: 0.7582 (t70) REVERT: B 856 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: B 894 MET cc_start: 0.7411 (tmm) cc_final: 0.7178 (tpp) REVERT: B 941 TRP cc_start: 0.8627 (t60) cc_final: 0.8228 (t60) REVERT: B 973 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8063 (tttt) REVERT: B 1020 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: C 345 ASP cc_start: 0.7919 (m-30) cc_final: 0.7640 (m-30) REVERT: C 655 ASP cc_start: 0.7840 (t0) cc_final: 0.7472 (t0) REVERT: C 1142 LYS cc_start: 0.7646 (mmtt) cc_final: 0.6796 (mtmm) outliers start: 75 outliers final: 38 residues processed: 310 average time/residue: 0.5132 time to fit residues: 189.9292 Evaluate side-chains 283 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 843 MET Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 989 MET Chi-restraints excluded: chain B residue 1020 GLU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 CYS Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 774 GLU Chi-restraints excluded: chain C residue 788 LYS Chi-restraints excluded: chain C residue 941 TRP Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1082 GLU Chi-restraints excluded: chain C residue 1177 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 171 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 329 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN B 71 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 456 ASN B 668 HIS B 804 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 336 GLN C 962 ASN C 975 GLN C 984 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.099994 restraints weight = 36087.571| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.08 r_work: 0.3036 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 28041 Z= 0.250 Angle : 0.681 13.019 38159 Z= 0.343 Chirality : 0.047 0.314 4342 Planarity : 0.004 0.050 4826 Dihedral : 8.170 152.567 4961 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.26 % Allowed : 13.42 % Favored : 83.32 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.14), residues: 3330 helix: 0.90 (0.19), residues: 744 sheet: -0.29 (0.18), residues: 786 loop : -0.72 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 323 TYR 0.023 0.002 TYR B 311 PHE 0.017 0.002 PHE C 101 TRP 0.025 0.002 TRP C 941 HIS 0.006 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00604 (27934) covalent geometry : angle 0.64708 (37886) SS BOND : bond 0.00674 ( 48) SS BOND : angle 2.03209 ( 96) hydrogen bonds : bond 0.05869 ( 1033) hydrogen bonds : angle 5.42601 ( 2916) link_BETA1-4 : bond 0.00434 ( 14) link_BETA1-4 : angle 2.88459 ( 42) link_NAG-ASN : bond 0.00467 ( 45) link_NAG-ASN : angle 2.80535 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 259 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6279 (OUTLIER) cc_final: 0.5191 (mmt) REVERT: A 774 GLU cc_start: 0.8663 (tt0) cc_final: 0.8360 (tt0) REVERT: A 807 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7838 (mm-40) REVERT: B 30 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: B 88 ARG cc_start: 0.7153 (ptm-80) cc_final: 0.6938 (ptm-80) REVERT: B 109 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8872 (mt) REVERT: B 146 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7540 (ptpp) REVERT: B 261 TYR cc_start: 0.7065 (m-10) cc_final: 0.6536 (m-80) REVERT: B 312 MET cc_start: 0.8124 (mtm) cc_final: 0.7302 (ttm) REVERT: B 357 ARG cc_start: 0.6549 (ppt170) cc_final: 0.6006 (ppt170) REVERT: B 450 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6925 (mm-30) REVERT: B 526 ASP cc_start: 0.7965 (t0) cc_final: 0.7658 (t70) REVERT: B 856 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: B 894 MET cc_start: 0.7470 (tmm) cc_final: 0.7250 (tpp) REVERT: B 973 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8215 (tttt) REVERT: B 1020 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: B 1065 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8132 (tm-30) REVERT: C 109 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8713 (mm) REVERT: C 217 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6968 (tp40) REVERT: C 345 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: C 526 ASP cc_start: 0.7923 (t0) cc_final: 0.7526 (t0) REVERT: C 655 ASP cc_start: 0.7872 (t0) cc_final: 0.7537 (t0) REVERT: C 856 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: C 1142 LYS cc_start: 0.7771 (mmtt) cc_final: 0.7011 (mppt) outliers start: 95 outliers final: 49 residues processed: 319 average time/residue: 0.5433 time to fit residues: 205.8366 Evaluate side-chains 304 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 242 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 989 MET Chi-restraints excluded: chain B residue 1020 GLU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 CYS Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 774 GLU Chi-restraints excluded: chain C residue 788 LYS Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 856 GLU Chi-restraints excluded: chain C residue 941 TRP Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1177 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 292 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 323 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 326 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 HIS ** C 83 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 = 0.3482 r_free = 0.3482 target = 0.129200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.101622 restraints weight = 35920.243| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.07 r_work: 0.3037 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28041 Z= 0.163 Angle : 0.603 13.389 38159 Z= 0.304 Chirality : 0.044 0.303 4342 Planarity : 0.004 0.050 4826 Dihedral : 7.632 151.867 4959 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.06 % Allowed : 14.28 % Favored : 82.66 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.14), residues: 3330 helix: 1.12 (0.19), residues: 750 sheet: -0.23 (0.18), residues: 780 loop : -0.67 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 323 TYR 0.020 0.002 TYR B 311 PHE 0.016 0.001 PHE B 759 TRP 0.023 0.002 TRP C 941 HIS 0.004 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00383 (27934) covalent geometry : angle 0.57069 (37886) SS BOND : bond 0.00648 ( 48) SS BOND : angle 1.75369 ( 96) hydrogen bonds : bond 0.05050 ( 1033) hydrogen bonds : angle 5.20474 ( 2916) link_BETA1-4 : bond 0.00435 ( 14) link_BETA1-4 : angle 2.72753 ( 42) link_NAG-ASN : bond 0.00394 ( 45) link_NAG-ASN : angle 2.61228 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 270 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.5988 (OUTLIER) cc_final: 0.5551 (mmt) REVERT: A 247 ASP cc_start: 0.7381 (t70) cc_final: 0.7091 (t0) REVERT: A 774 GLU cc_start: 0.8708 (tt0) cc_final: 0.8428 (tt0) REVERT: A 807 GLN cc_start: 0.8304 (mt0) cc_final: 0.7695 (mm-40) REVERT: A 867 TYR cc_start: 0.6886 (m-10) cc_final: 0.6629 (m-10) REVERT: A 892 GLU cc_start: 0.7668 (tt0) cc_final: 0.7348 (tp30) REVERT: B 30 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7650 (mp10) REVERT: B 146 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7547 (ptpp) REVERT: B 212 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7088 (tt) REVERT: B 261 TYR cc_start: 0.7009 (m-10) cc_final: 0.6486 (m-80) REVERT: B 312 MET cc_start: 0.8153 (mtm) cc_final: 0.7314 (ttm) REVERT: B 357 ARG cc_start: 0.6413 (ppt170) cc_final: 0.6101 (ptt90) REVERT: B 450 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6860 (mm-30) REVERT: B 526 ASP cc_start: 0.8116 (t0) cc_final: 0.7899 (p0) REVERT: B 856 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: B 894 MET cc_start: 0.7496 (tmm) cc_final: 0.7292 (tpp) REVERT: B 895 LYS cc_start: 0.5331 (ttpp) cc_final: 0.5093 (ttpp) REVERT: B 1020 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: B 1065 GLN cc_start: 0.8410 (tp-100) cc_final: 0.8127 (tm-30) REVERT: C 109 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8628 (mm) REVERT: C 131 MET cc_start: 0.5971 (OUTLIER) cc_final: 0.5066 (mtp) REVERT: C 172 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7522 (pt) REVERT: C 345 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: C 526 ASP cc_start: 0.7998 (t0) cc_final: 0.7581 (t0) REVERT: C 593 TYR cc_start: 0.8681 (p90) cc_final: 0.8460 (p90) REVERT: C 631 LYS cc_start: 0.6122 (ptmm) cc_final: 0.5915 (ptmm) REVERT: C 655 ASP cc_start: 0.7792 (t0) cc_final: 0.7502 (t0) REVERT: C 1142 LYS cc_start: 0.7718 (mmtt) cc_final: 0.6790 (mtmm) outliers start: 89 outliers final: 47 residues processed: 330 average time/residue: 0.5102 time to fit residues: 201.0990 Evaluate side-chains 306 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 248 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 989 MET Chi-restraints excluded: chain B residue 1020 GLU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 CYS Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 774 GLU Chi-restraints excluded: chain C residue 788 LYS Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 941 TRP Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 996 THR Chi-restraints excluded: chain C residue 1177 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 310 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 121 optimal weight: 0.4980 chunk 261 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 320 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 95 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103159 restraints weight = 36050.207| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.07 r_work: 0.3076 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28041 Z= 0.127 Angle : 0.564 13.067 38159 Z= 0.284 Chirality : 0.043 0.311 4342 Planarity : 0.004 0.052 4826 Dihedral : 7.036 149.655 4956 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.64 % Allowed : 15.21 % Favored : 82.15 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.14), residues: 3330 helix: 1.34 (0.19), residues: 747 sheet: -0.14 (0.18), residues: 774 loop : -0.64 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 323 TYR 0.016 0.001 TYR B 311 PHE 0.034 0.001 PHE A 702 TRP 0.021 0.001 TRP C 941 HIS 0.008 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00291 (27934) covalent geometry : angle 0.53463 (37886) SS BOND : bond 0.00562 ( 48) SS BOND : angle 1.28330 ( 96) hydrogen bonds : bond 0.04599 ( 1033) hydrogen bonds : angle 5.01780 ( 2916) link_BETA1-4 : bond 0.00413 ( 14) link_BETA1-4 : angle 2.61323 ( 42) link_NAG-ASN : bond 0.00379 ( 45) link_NAG-ASN : angle 2.55207 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 268 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6038 (OUTLIER) cc_final: 0.5400 (mmt) REVERT: A 247 ASP cc_start: 0.7314 (t70) cc_final: 0.7031 (t0) REVERT: A 359 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.5829 (mpp80) REVERT: A 774 GLU cc_start: 0.8736 (tt0) cc_final: 0.8459 (tt0) REVERT: A 807 GLN cc_start: 0.8254 (mt0) cc_final: 0.7649 (mm-40) REVERT: A 892 GLU cc_start: 0.7617 (tt0) cc_final: 0.7318 (tp30) REVERT: B 30 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7579 (mp10) REVERT: B 146 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7504 (ptpp) REVERT: B 212 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7033 (tt) REVERT: B 261 TYR cc_start: 0.6934 (m-10) cc_final: 0.6403 (m-80) REVERT: B 311 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7705 (t80) REVERT: B 312 MET cc_start: 0.8130 (mtm) cc_final: 0.7319 (ttm) REVERT: B 357 ARG cc_start: 0.6370 (ppt170) cc_final: 0.6113 (ptt90) REVERT: B 450 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6848 (mm-30) REVERT: B 526 ASP cc_start: 0.8156 (t0) cc_final: 0.7912 (p0) REVERT: B 615 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: B 856 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: B 1020 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: C 131 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5162 (mtp) REVERT: C 312 MET cc_start: 0.7647 (ttp) cc_final: 0.7437 (tmt) REVERT: C 345 ASP cc_start: 0.7803 (m-30) cc_final: 0.7594 (m-30) REVERT: C 526 ASP cc_start: 0.7928 (t0) cc_final: 0.7497 (t0) REVERT: C 593 TYR cc_start: 0.8702 (p90) cc_final: 0.8448 (p90) REVERT: C 631 LYS cc_start: 0.6069 (ptmm) cc_final: 0.5862 (ptmm) REVERT: C 655 ASP cc_start: 0.7730 (t0) cc_final: 0.7453 (t0) REVERT: C 894 MET cc_start: 0.7650 (mmm) cc_final: 0.7412 (tpt) REVERT: C 1142 LYS cc_start: 0.7651 (mmtt) cc_final: 0.7382 (mppt) outliers start: 77 outliers final: 40 residues processed: 318 average time/residue: 0.5135 time to fit residues: 193.8808 Evaluate side-chains 306 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 843 MET Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1020 GLU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 CYS Chi-restraints excluded: chain C residue 788 LYS Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 941 TRP Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 996 THR Chi-restraints excluded: chain C residue 1082 GLU Chi-restraints excluded: chain C residue 1177 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 103 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 294 optimal weight: 5.9990 chunk 284 optimal weight: 0.9980 chunk 330 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 293 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 277 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 HIS B 800 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.104028 restraints weight = 35606.493| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.04 r_work: 0.3068 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28041 Z= 0.157 Angle : 0.592 13.507 38159 Z= 0.298 Chirality : 0.044 0.299 4342 Planarity : 0.004 0.050 4826 Dihedral : 6.930 150.145 4956 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.85 % Allowed : 15.62 % Favored : 81.53 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.14), residues: 3330 helix: 1.33 (0.19), residues: 750 sheet: -0.22 (0.18), residues: 780 loop : -0.63 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 323 TYR 0.019 0.001 TYR B 311 PHE 0.030 0.002 PHE B 702 TRP 0.022 0.002 TRP C 941 HIS 0.005 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00372 (27934) covalent geometry : angle 0.56298 (37886) SS BOND : bond 0.00638 ( 48) SS BOND : angle 1.45509 ( 96) hydrogen bonds : bond 0.04863 ( 1033) hydrogen bonds : angle 5.05105 ( 2916) link_BETA1-4 : bond 0.00402 ( 14) link_BETA1-4 : angle 2.58479 ( 42) link_NAG-ASN : bond 0.00362 ( 45) link_NAG-ASN : angle 2.56529 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 263 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5435 (mmt) REVERT: A 247 ASP cc_start: 0.7267 (t70) cc_final: 0.6984 (t0) REVERT: A 312 MET cc_start: 0.8217 (pp-130) cc_final: 0.7935 (pp-130) REVERT: A 359 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.5814 (mpp80) REVERT: A 774 GLU cc_start: 0.8774 (tt0) cc_final: 0.8464 (tt0) REVERT: A 807 GLN cc_start: 0.8305 (mt0) cc_final: 0.7699 (mm-40) REVERT: A 892 GLU cc_start: 0.7632 (tt0) cc_final: 0.7330 (tp30) REVERT: B 30 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7634 (mp10) REVERT: B 146 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7519 (ptpp) REVERT: B 212 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7058 (tt) REVERT: B 240 GLU cc_start: 0.7892 (tt0) cc_final: 0.7486 (tt0) REVERT: B 261 TYR cc_start: 0.7094 (m-10) cc_final: 0.6592 (m-80) REVERT: B 311 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7742 (t80) REVERT: B 312 MET cc_start: 0.8131 (mtm) cc_final: 0.7292 (ttm) REVERT: B 357 ARG cc_start: 0.6480 (ppt170) cc_final: 0.6218 (ptt90) REVERT: B 450 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6846 (mm-30) REVERT: B 526 ASP cc_start: 0.8072 (t0) cc_final: 0.7860 (p0) REVERT: B 587 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7616 (tp) REVERT: B 615 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7112 (mp10) REVERT: B 773 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: B 856 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: B 1020 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: B 1065 GLN cc_start: 0.8375 (tp-100) cc_final: 0.8093 (tm-30) REVERT: C 131 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5091 (mtp) REVERT: C 132 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.7016 (mtpp) REVERT: C 345 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: C 526 ASP cc_start: 0.7956 (t0) cc_final: 0.7482 (t0) REVERT: C 593 TYR cc_start: 0.8696 (p90) cc_final: 0.8457 (p90) REVERT: C 631 LYS cc_start: 0.6139 (ptmm) cc_final: 0.5917 (ptmm) REVERT: C 655 ASP cc_start: 0.7740 (t0) cc_final: 0.7461 (t0) outliers start: 83 outliers final: 52 residues processed: 322 average time/residue: 0.5029 time to fit residues: 193.2670 Evaluate side-chains 319 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 252 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1070 SER Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 843 MET Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 989 MET Chi-restraints excluded: chain B residue 1020 GLU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 CYS Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 788 LYS Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 941 TRP Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 996 THR Chi-restraints excluded: chain C residue 1082 GLU Chi-restraints excluded: chain C residue 1177 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 223 optimal weight: 0.8980 chunk 256 optimal weight: 9.9990 chunk 292 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.126972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.099450 restraints weight = 36153.976| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.06 r_work: 0.3015 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 28041 Z= 0.256 Angle : 0.682 13.545 38159 Z= 0.344 Chirality : 0.047 0.298 4342 Planarity : 0.004 0.047 4826 Dihedral : 7.334 155.326 4956 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.06 % Allowed : 15.86 % Favored : 81.08 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.14), residues: 3330 helix: 1.05 (0.19), residues: 744 sheet: -0.28 (0.18), residues: 777 loop : -0.74 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 323 TYR 0.022 0.002 TYR B 311 PHE 0.023 0.002 PHE B 702 TRP 0.024 0.002 TRP C 941 HIS 0.005 0.001 HIS B 668 Details of bonding type rmsd covalent geometry : bond 0.00621 (27934) covalent geometry : angle 0.65254 (37886) SS BOND : bond 0.00738 ( 48) SS BOND : angle 1.71820 ( 96) hydrogen bonds : bond 0.05799 ( 1033) hydrogen bonds : angle 5.28738 ( 2916) link_BETA1-4 : bond 0.00449 ( 14) link_BETA1-4 : angle 2.68466 ( 42) link_NAG-ASN : bond 0.00434 ( 45) link_NAG-ASN : angle 2.78867 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 260 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 131 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.5231 (mmt) REVERT: A 247 ASP cc_start: 0.7306 (t70) cc_final: 0.6969 (t0) REVERT: A 312 MET cc_start: 0.8199 (pp-130) cc_final: 0.7950 (pp-130) REVERT: A 359 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.5739 (mpp80) REVERT: A 774 GLU cc_start: 0.8784 (tt0) cc_final: 0.8423 (tt0) REVERT: A 807 GLN cc_start: 0.8379 (mt0) cc_final: 0.7773 (mm-40) REVERT: A 892 GLU cc_start: 0.7686 (tt0) cc_final: 0.7358 (tp30) REVERT: A 1142 LYS cc_start: 0.7717 (mmpt) cc_final: 0.7336 (tppt) REVERT: B 30 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: B 146 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7547 (ptpp) REVERT: B 240 GLU cc_start: 0.7849 (tt0) cc_final: 0.7334 (tt0) REVERT: B 311 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.7632 (t80) REVERT: B 312 MET cc_start: 0.8192 (mtm) cc_final: 0.7286 (ttm) REVERT: B 357 ARG cc_start: 0.6910 (ppt170) cc_final: 0.6493 (ppt170) REVERT: B 450 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6901 (mm-30) REVERT: B 526 ASP cc_start: 0.8001 (t0) cc_final: 0.7759 (p0) REVERT: B 587 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7596 (tp) REVERT: B 615 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7181 (mp10) REVERT: B 856 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: B 1065 GLN cc_start: 0.8363 (tp-100) cc_final: 0.8083 (tm-30) REVERT: C 131 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5097 (mtp) REVERT: C 132 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6920 (mtpp) REVERT: C 345 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: C 593 TYR cc_start: 0.8710 (p90) cc_final: 0.8418 (p90) REVERT: C 655 ASP cc_start: 0.7844 (t0) cc_final: 0.7543 (t0) REVERT: C 660 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8875 (tp) REVERT: C 714 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8805 (mp) REVERT: C 856 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: C 894 MET cc_start: 0.7743 (mmm) cc_final: 0.7528 (tpt) REVERT: C 1142 LYS cc_start: 0.7199 (mppt) cc_final: 0.6296 (mtmm) outliers start: 89 outliers final: 52 residues processed: 318 average time/residue: 0.5026 time to fit residues: 189.5977 Evaluate side-chains 321 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 254 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1070 SER Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 989 MET Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 CYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 788 LYS Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 856 GLU Chi-restraints excluded: chain C residue 941 TRP Chi-restraints excluded: chain C residue 996 THR Chi-restraints excluded: chain C residue 1177 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 156 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 196 optimal weight: 0.3980 chunk 22 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 285 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 HIS B 804 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 334 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.130067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102846 restraints weight = 35766.532| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.04 r_work: 0.3039 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28041 Z= 0.150 Angle : 0.609 13.406 38159 Z= 0.306 Chirality : 0.044 0.301 4342 Planarity : 0.004 0.048 4826 Dihedral : 6.977 154.146 4954 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.68 % Allowed : 16.34 % Favored : 80.98 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.14), residues: 3330 helix: 1.24 (0.19), residues: 750 sheet: -0.26 (0.18), residues: 780 loop : -0.69 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 323 TYR 0.018 0.001 TYR B 311 PHE 0.020 0.001 PHE A 702 TRP 0.023 0.002 TRP C 941 HIS 0.007 0.001 HIS B 668 Details of bonding type rmsd covalent geometry : bond 0.00351 (27934) covalent geometry : angle 0.57718 (37886) SS BOND : bond 0.00611 ( 48) SS BOND : angle 1.79679 ( 96) hydrogen bonds : bond 0.04911 ( 1033) hydrogen bonds : angle 5.09971 ( 2916) link_BETA1-4 : bond 0.00377 ( 14) link_BETA1-4 : angle 2.53357 ( 42) link_NAG-ASN : bond 0.00372 ( 45) link_NAG-ASN : angle 2.64005 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 267 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.5633 (mmt) REVERT: A 247 ASP cc_start: 0.7311 (t0) cc_final: 0.6982 (t0) REVERT: A 312 MET cc_start: 0.8222 (pp-130) cc_final: 0.7896 (pp-130) REVERT: A 359 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.5872 (mpp80) REVERT: A 774 GLU cc_start: 0.8780 (tt0) cc_final: 0.8479 (tt0) REVERT: A 807 GLN cc_start: 0.8277 (mt0) cc_final: 0.7681 (mm-40) REVERT: A 892 GLU cc_start: 0.7681 (tt0) cc_final: 0.7346 (tp30) REVERT: A 1142 LYS cc_start: 0.7719 (mmpt) cc_final: 0.7363 (tppt) REVERT: B 30 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: B 146 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7507 (ptpp) REVERT: B 212 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7099 (tt) REVERT: B 240 GLU cc_start: 0.7898 (tt0) cc_final: 0.7411 (tt0) REVERT: B 311 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7618 (t80) REVERT: B 312 MET cc_start: 0.8210 (mtm) cc_final: 0.7377 (ttm) REVERT: B 342 PHE cc_start: 0.5249 (p90) cc_final: 0.5014 (p90) REVERT: B 357 ARG cc_start: 0.6830 (ppt170) cc_final: 0.6587 (ptt90) REVERT: B 450 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6873 (mm-30) REVERT: B 526 ASP cc_start: 0.7995 (t0) cc_final: 0.7757 (p0) REVERT: B 587 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7567 (tp) REVERT: B 615 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.7081 (mp10) REVERT: B 773 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: B 843 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8152 (tmm) REVERT: B 856 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: B 1020 GLU cc_start: 0.8570 (tt0) cc_final: 0.8368 (mt-10) REVERT: B 1065 GLN cc_start: 0.8397 (tp-100) cc_final: 0.8117 (tm-30) REVERT: C 131 MET cc_start: 0.6130 (OUTLIER) cc_final: 0.5206 (mtp) REVERT: C 217 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: C 345 ASP cc_start: 0.7904 (m-30) cc_final: 0.7695 (m-30) REVERT: C 593 TYR cc_start: 0.8690 (p90) cc_final: 0.8447 (p90) REVERT: C 655 ASP cc_start: 0.7779 (t0) cc_final: 0.7508 (t0) REVERT: C 660 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8851 (tp) REVERT: C 894 MET cc_start: 0.7765 (mmm) cc_final: 0.7464 (tpt) REVERT: C 1142 LYS cc_start: 0.7071 (mppt) cc_final: 0.6702 (mmpt) outliers start: 78 outliers final: 53 residues processed: 323 average time/residue: 0.4839 time to fit residues: 187.0095 Evaluate side-chains 322 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 254 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1070 SER Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain B residue 24 CYS Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 843 MET Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 989 MET Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1131 THR Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 CYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 788 LYS Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 941 TRP Chi-restraints excluded: chain C residue 996 THR Chi-restraints excluded: chain C residue 1177 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 223 optimal weight: 0.0970 chunk 258 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 303 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 322 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 304 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.100537 restraints weight = 36062.001| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.05 r_work: 0.3034 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 28041 Z= 0.213 Angle : 0.650 13.359 38159 Z= 0.327 Chirality : 0.046 0.303 4342 Planarity : 0.004 0.047 4826 Dihedral : 7.087 156.216 4954 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.54 % Allowed : 16.58 % Favored : 80.88 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.14), residues: 3330 helix: 1.15 (0.19), residues: 747 sheet: -0.30 (0.19), residues: 750 loop : -0.68 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 323 TYR 0.021 0.002 TYR B 311 PHE 0.018 0.002 PHE B 702 TRP 0.024 0.002 TRP C 941 HIS 0.008 0.001 HIS B 668 Details of bonding type rmsd covalent geometry : bond 0.00513 (27934) covalent geometry : angle 0.61979 (37886) SS BOND : bond 0.00687 ( 48) SS BOND : angle 1.82276 ( 96) hydrogen bonds : bond 0.05373 ( 1033) hydrogen bonds : angle 5.16912 ( 2916) link_BETA1-4 : bond 0.00413 ( 14) link_BETA1-4 : angle 2.57970 ( 42) link_NAG-ASN : bond 0.00385 ( 45) link_NAG-ASN : angle 2.71399 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6660 Ramachandran restraints generated. 3330 Oldfield, 0 Emsley, 3330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 256 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6240 (OUTLIER) cc_final: 0.5522 (mmt) REVERT: A 247 ASP cc_start: 0.7318 (t0) cc_final: 0.7008 (t0) REVERT: A 312 MET cc_start: 0.8174 (pp-130) cc_final: 0.7860 (pp-130) REVERT: A 359 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.5800 (mpp80) REVERT: A 774 GLU cc_start: 0.8785 (tt0) cc_final: 0.8419 (tt0) REVERT: A 807 GLN cc_start: 0.8345 (mt0) cc_final: 0.7734 (mm-40) REVERT: A 892 GLU cc_start: 0.7685 (tt0) cc_final: 0.7357 (tp30) REVERT: A 989 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.8014 (tmm) REVERT: A 1142 LYS cc_start: 0.7777 (mmpt) cc_final: 0.7402 (mppt) REVERT: B 30 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: B 146 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7516 (ptpp) REVERT: B 212 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.6935 (tt) REVERT: B 240 GLU cc_start: 0.7896 (tt0) cc_final: 0.7410 (tt0) REVERT: B 311 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.7734 (t80) REVERT: B 312 MET cc_start: 0.8246 (mtm) cc_final: 0.7341 (ttm) REVERT: B 357 ARG cc_start: 0.6922 (ppt170) cc_final: 0.6698 (ptt90) REVERT: B 450 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6881 (mm-30) REVERT: B 526 ASP cc_start: 0.8005 (t0) cc_final: 0.7771 (p0) REVERT: B 587 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7576 (tp) REVERT: B 615 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7146 (mp10) REVERT: B 856 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: B 1020 GLU cc_start: 0.8620 (tt0) cc_final: 0.8382 (mt-10) REVERT: B 1065 GLN cc_start: 0.8345 (tp-100) cc_final: 0.8080 (tm-30) REVERT: C 131 MET cc_start: 0.6180 (OUTLIER) cc_final: 0.5134 (mtp) REVERT: C 132 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.7020 (mtpp) REVERT: C 217 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: C 345 ASP cc_start: 0.7905 (m-30) cc_final: 0.7683 (m-30) REVERT: C 593 TYR cc_start: 0.8720 (p90) cc_final: 0.8440 (p90) REVERT: C 655 ASP cc_start: 0.7803 (t0) cc_final: 0.7517 (t0) REVERT: C 660 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8849 (tp) REVERT: C 774 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: C 894 MET cc_start: 0.7737 (mmm) cc_final: 0.7504 (tpt) REVERT: C 1142 LYS cc_start: 0.7105 (mppt) cc_final: 0.6122 (mtmm) outliers start: 74 outliers final: 52 residues processed: 305 average time/residue: 0.5315 time to fit residues: 191.9841 Evaluate side-chains 322 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 254 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1070 SER Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain B residue 24 CYS Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 989 MET Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1131 THR Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 CYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 774 GLU Chi-restraints excluded: chain C residue 788 LYS Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 941 TRP Chi-restraints excluded: chain C residue 996 THR Chi-restraints excluded: chain C residue 1177 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 8.9990 chunk 254 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 255 optimal weight: 2.9990 chunk 317 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 154 optimal weight: 0.4980 chunk 329 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN B 668 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.101116 restraints weight = 35649.030| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.04 r_work: 0.3039 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28041 Z= 0.196 Angle : 0.643 16.240 38159 Z= 0.324 Chirality : 0.045 0.297 4342 Planarity : 0.004 0.048 4826 Dihedral : 7.068 158.548 4954 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.54 % Allowed : 16.55 % Favored : 80.91 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.14), residues: 3330 helix: 1.14 (0.19), residues: 750 sheet: -0.31 (0.19), residues: 750 loop : -0.69 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 323 TYR 0.021 0.002 TYR B 311 PHE 0.020 0.002 PHE B 227 TRP 0.024 0.002 TRP C 941 HIS 0.008 0.001 HIS B 668 Details of bonding type rmsd covalent geometry : bond 0.00471 (27934) covalent geometry : angle 0.61223 (37886) SS BOND : bond 0.00635 ( 48) SS BOND : angle 1.77452 ( 96) hydrogen bonds : bond 0.05285 ( 1033) hydrogen bonds : angle 5.17026 ( 2916) link_BETA1-4 : bond 0.00379 ( 14) link_BETA1-4 : angle 2.53018 ( 42) link_NAG-ASN : bond 0.00386 ( 45) link_NAG-ASN : angle 2.70466 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7449.23 seconds wall clock time: 128 minutes 5.87 seconds (7685.87 seconds total)