Starting phenix.real_space_refine on Tue Oct 27 17:05:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xm3_22254/10_2026/6xm3_22254.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xm3_22254/10_2026/6xm3_22254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xm3_22254/10_2026/6xm3_22254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xm3_22254/10_2026/6xm3_22254.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xm3_22254/10_2026/6xm3_22254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xm3_22254/10_2026/6xm3_22254.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xm3_22254/10_2026/6xm3_22254.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xm3_22254/10_2026/6xm3_22254.cif" } resolution = 2.9 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= 0.965 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 110 5.16 5 C 16148 2.51 5 N 4142 2.21 5 O 4984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25384 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8111 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 51, 'TRANS': 986} Chain breaks: 7 Chain: "B" Number of atoms: 8259 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1058, 8253 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 52, 'TRANS': 1005} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1058, 8253 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 52, 'TRANS': 1005} Chain breaks: 5 bond proxies already assigned to first conformer: 8435 Chain: "C" Number of atoms: 8174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8174 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 52, 'TRANS': 994} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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 chiralities: 2 Chain: "R" 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 chiralities: 2 Chain: "S" 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 chiralities: 2 Chain: "T" 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 chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.01, per 1000 atoms: 0.28 Number of scatterers: 25384 At special positions: 0 Unit cell: (140.25, 136, 199.75, 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 110 16.00 O 4984 8.00 N 4142 7.00 C 16148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 234 " " NAG K 1 " - " ASN B 331 " " NAG L 1 " - " ASN B 343 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.2 seconds 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5898 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 44 sheets defined 24.2% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.503A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.613A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.686A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.698A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.569A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 443' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.741A pdb=" N LEU A 629 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.896A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.557A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.559A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 removed outlier: 3.560A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 removed outlier: 3.979A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.603A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.511A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.605A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.733A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 935 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.605A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.684A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.747A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.565A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 749 through 754 removed outlier: 3.632A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.509A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 806 Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 832 through 839 removed outlier: 3.554A pdb=" N GLY B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.636A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.762A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.655A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 935 removed outlier: 3.513A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.037A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.605A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.135A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.598A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.553A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.124A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.891A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.522A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 629 removed outlier: 4.018A pdb=" N LEU C 629 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.610A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.636A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 782 removed outlier: 3.637A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 824 removed outlier: 3.545A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.531A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.803A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.691A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.611A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.037A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 989 Processing helix chain 'C' and resid 992 through 1032 removed outlier: 3.754A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.014A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.866A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.439A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.256A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.671A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 3.978A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.585A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.581A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.834A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.665A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.665A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.652A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.012A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.391A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.572A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.470A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.210A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.860A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.295A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.001A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.657A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.025A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.744A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.684A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.021A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.617A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.790A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.535A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.669A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.679A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.066A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.795A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.545A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.640A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.544A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.609A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.609A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.677A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 836 hydrogen bonds defined for protein. 2250 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.77 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7554 1.33 - 1.46: 7080 1.46 - 1.60: 11176 1.60 - 1.73: 1 1.73 - 1.86: 134 Bond restraints: 25945 Sorted by residual: bond pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 1.336 1.381 -0.045 1.20e-02 6.94e+03 1.39e+01 bond pdb=" C PRO B 986 " pdb=" O PRO B 986 " ideal model delta sigma weight residual 1.240 1.201 0.040 1.12e-02 7.97e+03 1.26e+01 bond pdb=" N VAL B 615 " pdb=" CA VAL B 615 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.06e-02 8.90e+03 1.18e+01 bond pdb=" C LYS B 790 " pdb=" N THR B 791 " ideal model delta sigma weight residual 1.331 1.265 0.066 2.07e-02 2.33e+03 1.03e+01 bond pdb=" C ASP B 808 " pdb=" N PRO B 809 " ideal model delta sigma weight residual 1.337 1.370 -0.033 1.06e-02 8.90e+03 9.79e+00 ... (remaining 25940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 34462 2.80 - 5.59: 762 5.59 - 8.39: 73 8.39 - 11.18: 19 11.18 - 13.98: 5 Bond angle restraints: 35321 Sorted by residual: angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 113.30 99.46 13.84 1.34e+00 5.57e-01 1.07e+02 angle pdb=" C ASN B 616 " pdb=" CA ASN B 616 " pdb=" CB ASN B 616 " ideal model delta sigma weight residual 109.83 119.71 -9.88 9.90e-01 1.02e+00 9.95e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.38 104.21 9.17 1.23e+00 6.61e-01 5.56e+01 angle pdb=" C SER C 31 " pdb=" N PHE C 32 " pdb=" CA PHE C 32 " ideal model delta sigma weight residual 121.54 133.10 -11.56 1.91e+00 2.74e-01 3.66e+01 angle pdb=" CA VAL B 620 " pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 120.83 124.32 -3.49 6.10e-01 2.69e+00 3.28e+01 ... (remaining 35316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 13384 17.50 - 35.00: 1260 35.00 - 52.50: 258 52.50 - 70.00: 42 70.00 - 87.49: 31 Dihedral angle restraints: 14975 sinusoidal: 5814 harmonic: 9161 Sorted by residual: dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 176.60 -83.60 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 161.11 -68.11 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -30.58 -55.42 1 1.00e+01 1.00e-02 4.15e+01 ... (remaining 14972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3527 0.095 - 0.189: 614 0.189 - 0.284: 49 0.284 - 0.378: 4 0.378 - 0.473: 6 Chirality restraints: 4200 Sorted by residual: chirality pdb=" CA ASN B 616 " pdb=" N ASN B 616 " pdb=" C ASN B 616 " pdb=" CB ASN B 616 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CA CYS C 617 " pdb=" N CYS C 617 " pdb=" C CYS C 617 " pdb=" CB CYS C 617 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.56e+00 ... (remaining 4197 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 987 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 393 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C THR A 393 " 0.056 2.00e-02 2.50e+03 pdb=" O THR A 393 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN A 394 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " 0.020 2.00e-02 2.50e+03 2.38e-02 9.94e+00 pdb=" CG PHE C 906 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " 0.002 2.00e-02 2.50e+03 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5127 2.77 - 3.30: 20566 3.30 - 3.83: 39415 3.83 - 4.37: 46372 4.37 - 4.90: 82677 Nonbonded interactions: 194157 Sorted by model distance: nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.233 3.040 nonbonded pdb=" O GLN A 134 " pdb=" OH TYR A 160 " model vdw 2.252 3.040 nonbonded pdb=" O LEU B 293 " pdb=" OG1 THR B 632 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.265 3.040 nonbonded pdb=" O GLN C 134 " pdb=" OH TYR C 160 " model vdw 2.266 3.040 ... (remaining 194152 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 27 through 172 or resid 186 through 250 or resid 265 throu \ gh 492 or resid 494 through 848 or resid 850 through 1308)) selection = (chain 'B' and (resid 27 through 250 or resid 265 through 444 or resid 447 throu \ gh 492 or resid 494 through 828 or resid 848 or resid 850 through 1308)) selection = (chain 'C' and (resid 27 through 250 or resid 265 through 492 or resid 494 throu \ gh 828 or resid 830 or resid 834 or resid 851 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.570 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: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 26.160 Find NCS groups from input model: 0.940 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: 0.000 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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 : 0.012 0.137 26046 Z= 0.537 Angle : 1.061 13.975 35583 Z= 0.577 Chirality : 0.071 0.473 4200 Planarity : 0.008 0.104 4493 Dihedral : 14.511 87.494 8954 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.36 % Favored : 92.48 % Rotamer: Outliers : 0.66 % Allowed : 6.37 % Favored : 92.97 % 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 are not related in a simple way. whole: -4.38 (0.12), residues: 3100 helix: -4.55 (0.08), residues: 672 sheet: -1.28 (0.19), residues: 705 loop : -3.00 (0.12), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 403 TYR 0.034 0.003 TYR B 904 PHE 0.054 0.003 PHE C 906 TRP 0.043 0.003 TRP A 886 HIS 0.011 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01251 / 0.54 (25945) covalent geometry : angle 1.03475 / 0.57 (35321) SS BOND : bond 0.00782 / 0.47 ( 41) SS BOND : angle 2.90747 / 1.73 ( 82) hydrogen bonds : bond 0.31068 / 20.75 ( 810) hydrogen bonds : angle 9.95275 / 6.84 ( 2250) link_BETA1-4 : bond 0.00875 / 0.48 ( 17) link_BETA1-4 : angle 2.16118 / 1.33 ( 51) link_NAG-ASN : bond 0.00732 / 0.50 ( 43) link_NAG-ASN : angle 3.21469 / 2.14 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 254 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7273 (mtpp) cc_final: 0.6850 (mtmm) REVERT: A 351 TYR cc_start: 0.8090 (p90) cc_final: 0.7682 (p90) REVERT: A 365 TYR cc_start: 0.8053 (m-80) cc_final: 0.7734 (m-80) REVERT: A 378 LYS cc_start: 0.7585 (tttm) cc_final: 0.6897 (tmtt) REVERT: A 385 THR cc_start: 0.8488 (m) cc_final: 0.8245 (p) REVERT: A 403 ARG cc_start: 0.7635 (ttp-170) cc_final: 0.7292 (ttm-80) REVERT: A 417 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7343 (mtpt) REVERT: A 420 ASP cc_start: 0.7937 (m-30) cc_final: 0.7542 (m-30) REVERT: A 505 TYR cc_start: 0.7701 (m-80) cc_final: 0.7478 (m-80) REVERT: A 773 GLU cc_start: 0.8145 (tt0) cc_final: 0.7767 (tt0) REVERT: A 904 TYR cc_start: 0.7612 (m-80) cc_final: 0.7233 (m-80) REVERT: A 1086 LYS cc_start: 0.8406 (mmpt) cc_final: 0.8136 (mtpt) REVERT: B 218 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8170 (mm-40) REVERT: B 396 TYR cc_start: 0.7445 (m-80) cc_final: 0.7039 (m-80) REVERT: B 613 GLN cc_start: 0.7621 (mt0) cc_final: 0.6962 (pt0) REVERT: B 635 VAL cc_start: 0.8125 (t) cc_final: 0.7832 (m) REVERT: B 850 ILE cc_start: 0.8167 (mp) cc_final: 0.7796 (mm) REVERT: B 1125 ASN cc_start: 0.7939 (m-40) cc_final: 0.7585 (t0) REVERT: B 1138 TYR cc_start: 0.7816 (t80) cc_final: 0.7516 (t80) REVERT: C 190 ARG cc_start: 0.5823 (mtt-85) cc_final: 0.4879 (ttp-170) REVERT: C 273 ARG cc_start: 0.7415 (mmt90) cc_final: 0.7208 (mmt-90) REVERT: C 319 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7658 (ttm110) REVERT: C 357 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7648 (ttt-90) REVERT: C 430 THR cc_start: 0.8416 (t) cc_final: 0.8210 (m) REVERT: C 603 ASN cc_start: 0.8640 (t0) cc_final: 0.8364 (t0) REVERT: C 1092 GLU cc_start: 0.7289 (mp0) cc_final: 0.6869 (pp20) outliers start: 16 outliers final: 6 residues processed: 267 average time/residue: 0.5766 time to fit residues: 179.9840 Evaluate side-chains 181 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 439 ASN A 787 GLN A 901 GLN A 954 GLN B 30 ASN B 134 GLN B 137 ASN B 211 ASN B 321 GLN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 556 ASN B 675 GLN B 901 GLN C 87 ASN C 211 ASN C 314 GLN C 564 GLN C 613 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.171457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.108291 restraints weight = 34277.587| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.62 r_work: 0.3030 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 26046 Z= 0.126 Angle : 0.670 24.330 35583 Z= 0.341 Chirality : 0.047 0.289 4200 Planarity : 0.005 0.077 4493 Dihedral : 5.846 44.981 3373 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.78 % Allowed : 9.91 % Favored : 88.31 % Cbeta Deviations : 0.00 % 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 are not related in a simple way. whole: -2.84 (0.13), residues: 3100 helix: -2.05 (0.17), residues: 671 sheet: -0.48 (0.20), residues: 655 loop : -2.46 (0.12), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1107 TYR 0.028 0.001 TYR B 904 PHE 0.023 0.001 PHE B 377 TRP 0.016 0.001 TRP B 886 HIS 0.004 0.000 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (25945) covalent geometry : angle 0.65187 / 0.34 (35321) SS BOND : bond 0.00277 / 0.15 ( 41) SS BOND : angle 1.73791 / 1.12 ( 82) hydrogen bonds : bond 0.06004 / 3.98 ( 810) hydrogen bonds : angle 5.88603 / 4.00 ( 2250) link_BETA1-4 : bond 0.00341 / 0.19 ( 17) link_BETA1-4 : angle 1.12218 / 0.68 ( 51) link_NAG-ASN : bond 0.00335 / 0.23 ( 43) link_NAG-ASN : angle 2.24824 / 1.49 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.6878 (pt0) cc_final: 0.6642 (pp20) REVERT: A 129 LYS cc_start: 0.7399 (mtpp) cc_final: 0.7036 (mtmm) REVERT: A 351 TYR cc_start: 0.8232 (p90) cc_final: 0.7899 (p90) REVERT: A 385 THR cc_start: 0.8501 (m) cc_final: 0.8297 (p) REVERT: A 403 ARG cc_start: 0.7889 (ttp-170) cc_final: 0.7626 (ttm-80) REVERT: A 417 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7426 (mtpt) REVERT: A 420 ASP cc_start: 0.8291 (m-30) cc_final: 0.7966 (m-30) REVERT: A 462 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7887 (mppt) REVERT: A 505 TYR cc_start: 0.7720 (m-80) cc_final: 0.7514 (m-80) REVERT: A 563 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.4838 (mp10) REVERT: A 773 GLU cc_start: 0.8793 (tt0) cc_final: 0.8398 (tt0) REVERT: A 904 TYR cc_start: 0.8491 (m-80) cc_final: 0.8242 (m-80) REVERT: A 1086 LYS cc_start: 0.8460 (mmpt) cc_final: 0.8112 (mtpt) REVERT: B 237 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7644 (mtm110) REVERT: B 396 TYR cc_start: 0.7447 (m-80) cc_final: 0.7022 (m-80) REVERT: B 613 GLN cc_start: 0.8028 (mt0) cc_final: 0.7448 (pt0) REVERT: B 635 VAL cc_start: 0.8266 (t) cc_final: 0.7981 (m) REVERT: B 826 VAL cc_start: 0.9073 (p) cc_final: 0.8617 (t) REVERT: B 850 ILE cc_start: 0.7896 (mp) cc_final: 0.7589 (mm) REVERT: B 988 GLU cc_start: 0.7953 (mp0) cc_final: 0.7290 (mp0) REVERT: B 1125 ASN cc_start: 0.8183 (m-40) cc_final: 0.7602 (t0) REVERT: B 1138 TYR cc_start: 0.8057 (t80) cc_final: 0.7810 (t80) REVERT: C 205 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8972 (t) REVERT: C 314 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8232 (tp-100) REVERT: C 505 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.6046 (m-80) REVERT: C 603 ASN cc_start: 0.8823 (t0) cc_final: 0.8585 (t0) REVERT: C 646 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7977 (mtp180) outliers start: 47 outliers final: 12 residues processed: 237 average time/residue: 0.5475 time to fit residues: 153.4960 Evaluate side-chains 193 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: [126, 261, 106, 279, 29, 301, 217, 230, 118, 168, 297] chunk 126 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 29 optimal weight: 0.0030 chunk 301 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 168 optimal weight: 0.3980 chunk 297 optimal weight: 0.9980 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN B 321 GLN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.171160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.108439 restraints weight = 36767.982| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.88 r_work: 0.2997 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26046 Z= 0.131 Angle : 0.629 21.261 35583 Z= 0.317 Chirality : 0.046 0.268 4200 Planarity : 0.005 0.066 4493 Dihedral : 5.310 42.751 3369 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.86 % Allowed : 11.40 % Favored : 86.74 % Cbeta Deviations : 0.00 % 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 are not related in a simple way. whole: -2.16 (0.14), residues: 3100 helix: -0.87 (0.20), residues: 677 sheet: -0.18 (0.21), residues: 658 loop : -2.25 (0.13), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1107 TYR 0.030 0.001 TYR B 904 PHE 0.016 0.001 PHE C 32 TRP 0.014 0.001 TRP B 436 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (25945) covalent geometry : angle 0.61269 / 0.31 (35321) SS BOND : bond 0.00298 / 0.17 ( 41) SS BOND : angle 1.71212 / 1.09 ( 82) hydrogen bonds : bond 0.05463 / 3.64 ( 810) hydrogen bonds : angle 5.40903 / 3.67 ( 2250) link_BETA1-4 : bond 0.00376 / 0.22 ( 17) link_BETA1-4 : angle 1.13198 / 0.69 ( 51) link_NAG-ASN : bond 0.00284 / 0.19 ( 43) link_NAG-ASN : angle 1.98227 / 1.32 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.6931 (pt0) cc_final: 0.6642 (pp20) REVERT: A 129 LYS cc_start: 0.7300 (mtpp) cc_final: 0.6962 (mtmm) REVERT: A 351 TYR cc_start: 0.8280 (p90) cc_final: 0.7983 (p90) REVERT: A 385 THR cc_start: 0.8552 (m) cc_final: 0.8328 (p) REVERT: A 417 LYS cc_start: 0.7992 (mtmt) cc_final: 0.7497 (mtpt) REVERT: A 420 ASP cc_start: 0.8306 (m-30) cc_final: 0.7924 (m-30) REVERT: A 462 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7773 (mppt) REVERT: A 563 GLN cc_start: 0.6622 (OUTLIER) cc_final: 0.4844 (mp10) REVERT: A 773 GLU cc_start: 0.8840 (tt0) cc_final: 0.8462 (tt0) REVERT: A 1086 LYS cc_start: 0.8473 (mmpt) cc_final: 0.8085 (mtpt) REVERT: B 396 TYR cc_start: 0.7482 (m-80) cc_final: 0.7089 (m-80) REVERT: B 613 GLN cc_start: 0.8088 (mt0) cc_final: 0.7490 (pt0) REVERT: B 635 VAL cc_start: 0.8234 (t) cc_final: 0.7983 (m) REVERT: B 826 VAL cc_start: 0.9080 (p) cc_final: 0.8618 (t) REVERT: B 850 ILE cc_start: 0.7798 (mp) cc_final: 0.7476 (mm) REVERT: B 988 GLU cc_start: 0.7970 (mp0) cc_final: 0.7312 (mp0) REVERT: B 1118 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8035 (t70) REVERT: B 1125 ASN cc_start: 0.8177 (m-40) cc_final: 0.7598 (t0) REVERT: B 1138 TYR cc_start: 0.8108 (t80) cc_final: 0.7880 (t80) REVERT: C 505 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.6072 (m-80) REVERT: C 561 PRO cc_start: 0.8482 (Cg_exo) cc_final: 0.8205 (Cg_endo) REVERT: C 603 ASN cc_start: 0.8803 (t0) cc_final: 0.8587 (t0) REVERT: C 748 GLU cc_start: 0.8413 (tp30) cc_final: 0.8122 (tp30) REVERT: C 1092 GLU cc_start: 0.7950 (mp0) cc_final: 0.7727 (pm20) outliers start: 49 outliers final: 22 residues processed: 220 average time/residue: 0.5268 time to fit residues: 138.2514 Evaluate side-chains 205 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 974 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: [116, 51, 106, 290, 188, 203, 138, 91, 253, 145, 96] chunk 116 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 145 optimal weight: 30.0000 chunk 96 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN B 321 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN C 314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.169004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.105556 restraints weight = 36033.822| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.84 r_work: 0.2954 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26046 Z= 0.178 Angle : 0.661 19.585 35583 Z= 0.333 Chirality : 0.049 0.265 4200 Planarity : 0.005 0.062 4493 Dihedral : 5.318 40.910 3367 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.59 % Allowed : 11.94 % Favored : 85.47 % Cbeta Deviations : 0.00 % 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 are not related in a simple way. whole: -1.92 (0.14), residues: 3100 helix: -0.47 (0.20), residues: 677 sheet: -0.07 (0.20), residues: 665 loop : -2.19 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.026 0.002 TYR B 904 PHE 0.021 0.002 PHE A 592 TRP 0.013 0.002 TRP C 436 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (25945) covalent geometry : angle 0.64556 / 0.33 (35321) SS BOND : bond 0.00345 / 0.21 ( 41) SS BOND : angle 1.72712 / 1.10 ( 82) hydrogen bonds : bond 0.05975 / 3.98 ( 810) hydrogen bonds : angle 5.36349 / 3.64 ( 2250) link_BETA1-4 : bond 0.00370 / 0.22 ( 17) link_BETA1-4 : angle 1.24794 / 0.76 ( 51) link_NAG-ASN : bond 0.00310 / 0.21 ( 43) link_NAG-ASN : angle 1.99021 / 1.33 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 182 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7620 (mtpt) REVERT: A 420 ASP cc_start: 0.8348 (m-30) cc_final: 0.7897 (m-30) REVERT: A 466 ARG cc_start: 0.7916 (mtp180) cc_final: 0.7647 (ttt-90) REVERT: A 563 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.4917 (mp10) REVERT: A 773 GLU cc_start: 0.8924 (tt0) cc_final: 0.8530 (tt0) REVERT: B 53 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: B 237 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7839 (mtm110) REVERT: B 396 TYR cc_start: 0.7522 (m-80) cc_final: 0.7290 (m-80) REVERT: B 613 GLN cc_start: 0.8198 (mt0) cc_final: 0.7583 (pt0) REVERT: B 635 VAL cc_start: 0.8344 (t) cc_final: 0.8070 (m) REVERT: B 675 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7517 (pp30) REVERT: B 826 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8649 (t) REVERT: B 850 ILE cc_start: 0.7842 (mp) cc_final: 0.7504 (mm) REVERT: B 1118 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8140 (t70) REVERT: B 1125 ASN cc_start: 0.8276 (m-40) cc_final: 0.7752 (t0) REVERT: B 1138 TYR cc_start: 0.8162 (t80) cc_final: 0.7955 (t80) REVERT: C 505 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6050 (m-80) REVERT: C 561 PRO cc_start: 0.8511 (Cg_exo) cc_final: 0.8228 (Cg_endo) REVERT: C 603 ASN cc_start: 0.8847 (t0) cc_final: 0.8639 (t0) REVERT: C 748 GLU cc_start: 0.8569 (tp30) cc_final: 0.8230 (tp30) REVERT: C 1092 GLU cc_start: 0.8066 (mp0) cc_final: 0.7849 (mp0) outliers start: 69 outliers final: 29 residues processed: 226 average time/residue: 0.5161 time to fit residues: 138.9540 Evaluate side-chains 208 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 974 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: [3, 121, 226, 129, 181, 37, 143, 158, 43, 104, 268] chunk 3 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1101 HIS B 321 GLN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN C 564 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.167274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.104268 restraints weight = 40778.790| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.76 r_work: 0.2938 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 26046 Z= 0.286 Angle : 0.770 20.240 35583 Z= 0.386 Chirality : 0.054 0.280 4200 Planarity : 0.005 0.060 4493 Dihedral : 5.668 42.289 3367 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.59 % Allowed : 13.04 % Favored : 84.38 % Cbeta Deviations : 0.00 % 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 are not related in a simple way. whole: -2.03 (0.14), residues: 3100 helix: -0.62 (0.20), residues: 692 sheet: -0.09 (0.20), residues: 667 loop : -2.27 (0.13), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1107 TYR 0.024 0.002 TYR C1067 PHE 0.028 0.002 PHE A 592 TRP 0.031 0.002 TRP B 436 HIS 0.011 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.29 (25945) covalent geometry : angle 0.74983 / 0.38 (35321) SS BOND : bond 0.00511 / 0.32 ( 41) SS BOND : angle 2.48601 / 1.47 ( 82) hydrogen bonds : bond 0.07053 / 4.71 ( 810) hydrogen bonds : angle 5.54601 / 3.75 ( 2250) link_BETA1-4 : bond 0.00469 / 0.27 ( 17) link_BETA1-4 : angle 1.48555 / 0.89 ( 51) link_NAG-ASN : bond 0.00372 / 0.26 ( 43) link_NAG-ASN : angle 2.19953 / 1.47 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 171 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8039 (mtmt) cc_final: 0.7691 (mtpt) REVERT: A 420 ASP cc_start: 0.8303 (m-30) cc_final: 0.7907 (m-30) REVERT: A 563 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.5055 (mp10) REVERT: A 773 GLU cc_start: 0.8946 (tt0) cc_final: 0.8565 (tt0) REVERT: A 1139 ASP cc_start: 0.7936 (t0) cc_final: 0.7701 (t70) REVERT: B 53 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: B 237 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7901 (mtm110) REVERT: B 396 TYR cc_start: 0.7522 (m-80) cc_final: 0.7278 (m-80) REVERT: B 613 GLN cc_start: 0.8280 (mt0) cc_final: 0.7637 (pt0) REVERT: B 635 VAL cc_start: 0.8347 (t) cc_final: 0.8052 (m) REVERT: B 826 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8692 (t) REVERT: B 850 ILE cc_start: 0.7802 (mp) cc_final: 0.7436 (mm) REVERT: B 1118 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8160 (t70) REVERT: B 1125 ASN cc_start: 0.8257 (m-40) cc_final: 0.7786 (t0) REVERT: B 1138 TYR cc_start: 0.8167 (t80) cc_final: 0.7946 (t80) REVERT: C 129 LYS cc_start: 0.6395 (OUTLIER) cc_final: 0.5845 (mttt) REVERT: C 505 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.5943 (m-80) REVERT: C 748 GLU cc_start: 0.8570 (tp30) cc_final: 0.8225 (tp30) REVERT: C 1092 GLU cc_start: 0.8084 (mp0) cc_final: 0.7848 (mp0) outliers start: 69 outliers final: 36 residues processed: 221 average time/residue: 0.5236 time to fit residues: 137.7750 Evaluate side-chains 207 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: [275, 286, 224, 213, 302, 109, 169, 112, 63, 143, 97] chunk 275 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 224 optimal weight: 0.3980 chunk 213 optimal weight: 9.9990 chunk 302 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1101 HIS B 321 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.170730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.110078 restraints weight = 47933.142| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.08 r_work: 0.2989 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26046 Z= 0.129 Angle : 0.625 18.179 35583 Z= 0.315 Chirality : 0.047 0.276 4200 Planarity : 0.004 0.057 4493 Dihedral : 5.140 40.881 3367 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.26 % Allowed : 14.02 % Favored : 83.72 % Cbeta Deviations : 0.00 % 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 are not related in a simple way. whole: -1.65 (0.14), residues: 3100 helix: -0.02 (0.20), residues: 678 sheet: 0.09 (0.20), residues: 672 loop : -2.12 (0.13), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1107 TYR 0.023 0.001 TYR A 170 PHE 0.028 0.001 PHE B 392 TRP 0.028 0.001 TRP B 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (25945) covalent geometry : angle 0.60790 / 0.31 (35321) SS BOND : bond 0.00270 / 0.16 ( 41) SS BOND : angle 1.95473 / 1.15 ( 82) hydrogen bonds : bond 0.04989 / 3.32 ( 810) hydrogen bonds : angle 5.17497 / 3.50 ( 2250) link_BETA1-4 : bond 0.00375 / 0.22 ( 17) link_BETA1-4 : angle 1.11362 / 0.68 ( 51) link_NAG-ASN : bond 0.00252 / 0.17 ( 43) link_NAG-ASN : angle 1.93500 / 1.29 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 179 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7775 (mtpt) REVERT: A 420 ASP cc_start: 0.8293 (m-30) cc_final: 0.7947 (m-30) REVERT: A 462 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7786 (mppt) REVERT: A 558 LYS cc_start: 0.6488 (mmtm) cc_final: 0.6125 (mmtt) REVERT: A 563 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.5065 (mp10) REVERT: A 773 GLU cc_start: 0.8889 (tt0) cc_final: 0.8463 (tt0) REVERT: B 191 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8229 (pt0) REVERT: B 396 TYR cc_start: 0.7521 (m-80) cc_final: 0.7250 (m-80) REVERT: B 581 THR cc_start: 0.6944 (OUTLIER) cc_final: 0.6733 (p) REVERT: B 613 GLN cc_start: 0.8209 (mt0) cc_final: 0.7633 (pt0) REVERT: B 635 VAL cc_start: 0.8382 (t) cc_final: 0.8179 (m) REVERT: B 826 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8628 (t) REVERT: B 850 ILE cc_start: 0.7864 (mp) cc_final: 0.7534 (mm) REVERT: B 1118 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8205 (t70) REVERT: B 1125 ASN cc_start: 0.8248 (m-40) cc_final: 0.7795 (t0) REVERT: C 239 GLN cc_start: 0.8390 (pt0) cc_final: 0.8042 (pt0) REVERT: C 281 GLU cc_start: 0.8578 (pt0) cc_final: 0.8203 (pm20) REVERT: C 505 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.5987 (m-80) REVERT: C 554 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: C 748 GLU cc_start: 0.8595 (tp30) cc_final: 0.8251 (tp30) REVERT: C 1092 GLU cc_start: 0.8079 (mp0) cc_final: 0.7819 (mp0) outliers start: 60 outliers final: 31 residues processed: 225 average time/residue: 0.5014 time to fit residues: 134.9603 Evaluate side-chains 205 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: [275, 52, 4, 90, 7, 248, 168, 101, 263, 289, 94] chunk 275 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 4 optimal weight: 0.0040 chunk 90 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 263 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 94 optimal weight: 0.2980 overall best weight: 2.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN A 787 GLN B 321 GLN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 703 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.169519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.108739 restraints weight = 33961.298| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.50 r_work: 0.2992 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26046 Z= 0.183 Angle : 0.664 17.952 35583 Z= 0.334 Chirality : 0.049 0.264 4200 Planarity : 0.005 0.056 4493 Dihedral : 5.226 40.255 3367 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.84 % Allowed : 14.13 % Favored : 83.03 % Cbeta Deviations : 0.00 % 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 are not related in a simple way. whole: -1.66 (0.14), residues: 3100 helix: -0.05 (0.20), residues: 686 sheet: 0.05 (0.20), residues: 679 loop : -2.12 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 319 TYR 0.020 0.002 TYR C1067 PHE 0.027 0.002 PHE B 392 TRP 0.026 0.002 TRP B 436 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.18 (25945) covalent geometry : angle 0.64620 / 0.33 (35321) SS BOND : bond 0.00349 / 0.21 ( 41) SS BOND : angle 2.00890 / 1.20 ( 82) hydrogen bonds : bond 0.05743 / 3.83 ( 810) hydrogen bonds : angle 5.24049 / 3.55 ( 2250) link_BETA1-4 : bond 0.00399 / 0.24 ( 17) link_BETA1-4 : angle 1.23946 / 0.75 ( 51) link_NAG-ASN : bond 0.00258 / 0.17 ( 43) link_NAG-ASN : angle 1.98942 / 1.32 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 166 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8019 (mtmt) cc_final: 0.7767 (mtpt) REVERT: A 420 ASP cc_start: 0.8249 (m-30) cc_final: 0.7872 (m-30) REVERT: A 462 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7782 (mppt) REVERT: A 563 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.5071 (mp10) REVERT: A 773 GLU cc_start: 0.8881 (tt0) cc_final: 0.8438 (tt0) REVERT: B 53 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: B 396 TYR cc_start: 0.7549 (m-80) cc_final: 0.7299 (m-80) REVERT: B 581 THR cc_start: 0.6924 (OUTLIER) cc_final: 0.6717 (p) REVERT: B 613 GLN cc_start: 0.8237 (mt0) cc_final: 0.7610 (pt0) REVERT: B 635 VAL cc_start: 0.8431 (t) cc_final: 0.8201 (m) REVERT: B 826 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8663 (t) REVERT: B 850 ILE cc_start: 0.7898 (mp) cc_final: 0.7542 (mm) REVERT: B 1118 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8198 (t70) REVERT: B 1125 ASN cc_start: 0.8226 (m-40) cc_final: 0.7794 (t0) REVERT: C 202 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8270 (mmtp) REVERT: C 239 GLN cc_start: 0.8430 (pt0) cc_final: 0.8122 (pt0) REVERT: C 281 GLU cc_start: 0.8554 (pt0) cc_final: 0.8130 (pm20) REVERT: C 505 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.5973 (m-80) REVERT: C 554 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: C 748 GLU cc_start: 0.8555 (tp30) cc_final: 0.8206 (tp30) REVERT: C 1092 GLU cc_start: 0.8064 (mp0) cc_final: 0.7782 (mp0) outliers start: 76 outliers final: 43 residues processed: 219 average time/residue: 0.5040 time to fit residues: 131.8726 Evaluate side-chains 217 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 165 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: [119, 201, 239, 183, 3, 221, 202, 27, 70, 250, 98] chunk 119 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 221 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN A 787 GLN B 321 GLN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.170578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107997 restraints weight = 36028.331| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.67 r_work: 0.3001 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26046 Z= 0.145 Angle : 0.626 16.665 35583 Z= 0.315 Chirality : 0.047 0.261 4200 Planarity : 0.004 0.055 4493 Dihedral : 5.054 38.398 3367 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.66 % Allowed : 14.57 % Favored : 82.77 % Cbeta Deviations : 0.00 % 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 are not related in a simple way. whole: -1.49 (0.14), residues: 3100 helix: 0.13 (0.20), residues: 685 sheet: 0.20 (0.20), residues: 669 loop : -2.04 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 319 TYR 0.027 0.001 TYR A 170 PHE 0.024 0.001 PHE B 392 TRP 0.025 0.002 TRP B 436 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (25945) covalent geometry : angle 0.61052 / 0.31 (35321) SS BOND : bond 0.00303 / 0.18 ( 41) SS BOND : angle 1.82074 / 1.09 ( 82) hydrogen bonds : bond 0.05166 / 3.44 ( 810) hydrogen bonds : angle 5.12684 / 3.47 ( 2250) link_BETA1-4 : bond 0.00378 / 0.23 ( 17) link_BETA1-4 : angle 1.15169 / 0.70 ( 51) link_NAG-ASN : bond 0.00257 / 0.18 ( 43) link_NAG-ASN : angle 1.86020 / 1.24 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 175 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7726 (mmtt) REVERT: A 420 ASP cc_start: 0.8198 (m-30) cc_final: 0.7848 (m-30) REVERT: A 462 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7734 (mppt) REVERT: A 558 LYS cc_start: 0.6503 (mmtm) cc_final: 0.6111 (mmtt) REVERT: A 563 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.5069 (mp10) REVERT: A 773 GLU cc_start: 0.8873 (tt0) cc_final: 0.8439 (tt0) REVERT: B 53 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7655 (m-30) REVERT: B 396 TYR cc_start: 0.7460 (m-80) cc_final: 0.7199 (m-80) REVERT: B 613 GLN cc_start: 0.8227 (mt0) cc_final: 0.7614 (pt0) REVERT: B 826 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8624 (t) REVERT: B 850 ILE cc_start: 0.7915 (mp) cc_final: 0.7569 (mm) REVERT: B 1118 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8209 (t70) REVERT: B 1125 ASN cc_start: 0.8205 (m-40) cc_final: 0.7778 (t0) REVERT: C 102 ARG cc_start: 0.6696 (mmt90) cc_final: 0.4904 (mtp180) REVERT: C 202 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8230 (mmtp) REVERT: C 239 GLN cc_start: 0.8407 (pt0) cc_final: 0.8063 (pt0) REVERT: C 281 GLU cc_start: 0.8558 (pt0) cc_final: 0.8167 (pm20) REVERT: C 360 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7560 (m-40) REVERT: C 505 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.5934 (m-80) REVERT: C 554 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: C 748 GLU cc_start: 0.8584 (tp30) cc_final: 0.8238 (tp30) REVERT: C 1092 GLU cc_start: 0.8035 (mp0) cc_final: 0.7743 (mp0) outliers start: 71 outliers final: 43 residues processed: 226 average time/residue: 0.5230 time to fit residues: 141.4286 Evaluate side-chains 220 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: [247, 298, 229, 224, 120, 49, 119, 86, 95, 3, 6] chunk 247 optimal weight: 0.0670 chunk 298 optimal weight: 0.9980 chunk 229 optimal weight: 0.0000 chunk 224 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 overall best weight: 0.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN B 321 GLN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.174425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.112179 restraints weight = 40771.100| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.90 r_work: 0.3057 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26046 Z= 0.096 Angle : 0.560 13.797 35583 Z= 0.283 Chirality : 0.045 0.258 4200 Planarity : 0.004 0.054 4493 Dihedral : 4.570 33.563 3367 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.49 % Allowed : 15.95 % Favored : 82.56 % Cbeta Deviations : 0.00 % 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 are not related in a simple way. whole: -1.07 (0.15), residues: 3100 helix: 0.64 (0.21), residues: 680 sheet: 0.39 (0.21), residues: 646 loop : -1.77 (0.13), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 319 TYR 0.025 0.001 TYR A 170 PHE 0.023 0.001 PHE A 855 TRP 0.022 0.001 TRP B 436 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (25945) covalent geometry : angle 0.54805 / 0.28 (35321) SS BOND : bond 0.00226 / 0.13 ( 41) SS BOND : angle 1.47639 / 0.86 ( 82) hydrogen bonds : bond 0.03725 / 2.46 ( 810) hydrogen bonds : angle 4.81803 / 3.26 ( 2250) link_BETA1-4 : bond 0.00385 / 0.24 ( 17) link_BETA1-4 : angle 0.97109 / 0.60 ( 51) link_NAG-ASN : bond 0.00237 / 0.16 ( 43) link_NAG-ASN : angle 1.62501 / 1.09 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.7210 (pt) cc_final: 0.6983 (pt) REVERT: A 417 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7734 (mmtt) REVERT: A 420 ASP cc_start: 0.8249 (m-30) cc_final: 0.7903 (m-30) REVERT: A 773 GLU cc_start: 0.8795 (tt0) cc_final: 0.8367 (tt0) REVERT: A 1002 GLN cc_start: 0.8929 (tt0) cc_final: 0.8497 (mt0) REVERT: A 1125 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.8018 (m-40) REVERT: B 45 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7354 (m) REVERT: B 53 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: B 396 TYR cc_start: 0.7401 (m-80) cc_final: 0.7157 (m-80) REVERT: B 613 GLN cc_start: 0.8112 (mt0) cc_final: 0.7549 (pt0) REVERT: B 826 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8520 (t) REVERT: B 850 ILE cc_start: 0.7754 (mp) cc_final: 0.7429 (mm) REVERT: B 1118 ASP cc_start: 0.8419 (m-30) cc_final: 0.8166 (t70) REVERT: B 1125 ASN cc_start: 0.8048 (m-40) cc_final: 0.7564 (t0) REVERT: C 202 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8116 (mmtp) REVERT: C 281 GLU cc_start: 0.8564 (pt0) cc_final: 0.8195 (pm20) REVERT: C 505 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.5924 (m-80) REVERT: C 561 PRO cc_start: 0.8438 (Cg_exo) cc_final: 0.8174 (Cg_endo) REVERT: C 748 GLU cc_start: 0.8610 (tp30) cc_final: 0.8272 (tp30) outliers start: 39 outliers final: 24 residues processed: 226 average time/residue: 0.5099 time to fit residues: 138.1978 Evaluate side-chains 203 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: [115, 232, 285, 274, 183, 146, 119, 46, 151, 162, 210] chunk 115 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 183 optimal weight: 0.0970 chunk 146 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.168854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.107520 restraints weight = 34324.585| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.53 r_work: 0.2975 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 26046 Z= 0.235 Angle : 0.709 17.033 35583 Z= 0.357 Chirality : 0.051 0.267 4200 Planarity : 0.005 0.065 4493 Dihedral : 5.195 36.172 3367 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.60 % Allowed : 16.53 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -1.47 (0.14), residues: 3100 helix: 0.12 (0.20), residues: 686 sheet: 0.11 (0.20), residues: 679 loop : -1.97 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 319 TYR 0.023 0.002 TYR C1067 PHE 0.023 0.002 PHE B 541 TRP 0.022 0.002 TRP B 436 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.24 (25945) covalent geometry : angle 0.69018 / 0.35 (35321) SS BOND : bond 0.00460 / 0.30 ( 41) SS BOND : angle 2.27059 / 1.38 ( 82) hydrogen bonds : bond 0.06373 / 4.25 ( 810) hydrogen bonds : angle 5.26610 / 3.56 ( 2250) link_BETA1-4 : bond 0.00469 / 0.26 ( 17) link_BETA1-4 : angle 1.33639 / 0.81 ( 51) link_NAG-ASN : bond 0.00354 / 0.25 ( 43) link_NAG-ASN : angle 2.09033 / 1.36 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7836 (mmtt) REVERT: A 420 ASP cc_start: 0.8162 (m-30) cc_final: 0.7781 (m-30) REVERT: A 773 GLU cc_start: 0.8936 (tt0) cc_final: 0.8527 (tt0) REVERT: B 53 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7787 (m-30) REVERT: B 396 TYR cc_start: 0.7511 (m-80) cc_final: 0.7252 (m-80) REVERT: B 613 GLN cc_start: 0.8277 (mt0) cc_final: 0.7652 (pt0) REVERT: B 826 VAL cc_start: 0.9114 (OUTLIER) cc_final: 0.8659 (t) REVERT: B 850 ILE cc_start: 0.7912 (mp) cc_final: 0.7542 (mm) REVERT: B 1118 ASP cc_start: 0.8495 (m-30) cc_final: 0.8241 (t70) REVERT: B 1125 ASN cc_start: 0.8198 (m-40) cc_final: 0.7776 (t0) REVERT: C 102 ARG cc_start: 0.6501 (mmt-90) cc_final: 0.4334 (mtp180) REVERT: C 202 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8247 (mmtp) REVERT: C 239 GLN cc_start: 0.8458 (pt0) cc_final: 0.8149 (pt0) REVERT: C 281 GLU cc_start: 0.8561 (pt0) cc_final: 0.8134 (pm20) REVERT: C 360 ASN cc_start: 0.7792 (m110) cc_final: 0.7514 (m-40) REVERT: C 505 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.5991 (m-80) REVERT: C 619 GLU cc_start: 0.7437 (pt0) cc_final: 0.7204 (pt0) REVERT: C 748 GLU cc_start: 0.8593 (tp30) cc_final: 0.8230 (tp30) REVERT: C 1092 GLU cc_start: 0.8122 (mp0) cc_final: 0.7828 (mp0) outliers start: 42 outliers final: 30 residues processed: 199 average time/residue: 0.5302 time to fit residues: 125.7420 Evaluate side-chains 197 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: [149, 40, 293, 78, 203, 271, 228, 213, 226, 307, 163] chunk 149 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 203 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 226 optimal weight: 20.0000 chunk 307 optimal weight: 3.9990 chunk 163 optimal weight: 0.0010 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN B 321 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN C 564 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.171190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109111 restraints weight = 31677.835| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.31 r_work: 0.3044 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26046 Z= 0.131 Angle : 0.613 15.499 35583 Z= 0.309 Chirality : 0.047 0.258 4200 Planarity : 0.004 0.062 4493 Dihedral : 4.928 34.291 3367 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.60 % Allowed : 16.68 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -1.30 (0.14), residues: 3100 helix: 0.34 (0.21), residues: 685 sheet: 0.28 (0.21), residues: 660 loop : -1.91 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 319 TYR 0.025 0.001 TYR A 170 PHE 0.024 0.001 PHE B 392 TRP 0.022 0.001 TRP B 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (25945) covalent geometry : angle 0.59706 / 0.30 (35321) SS BOND : bond 0.00257 / 0.15 ( 41) SS BOND : angle 1.86739 / 1.12 ( 82) hydrogen bonds : bond 0.04920 / 3.28 ( 810) hydrogen bonds : angle 5.05961 / 3.43 ( 2250) link_BETA1-4 : bond 0.00409 / 0.24 ( 17) link_BETA1-4 : angle 1.12411 / 0.68 ( 51) link_NAG-ASN : bond 0.00278 / 0.20 ( 43) link_NAG-ASN : angle 1.84143 / 1.21 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10801.54 seconds wall clock time: 183 minutes 46.77 seconds (11026.77 seconds total)