Starting phenix.real_space_refine on Tue Sep 15 03:49:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dm7_27529/09_2026/8dm7_27529.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm7_27529/09_2026/8dm7_27529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm7_27529/09_2026/8dm7_27529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm7_27529/09_2026/8dm7_27529.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dm7_27529/09_2026/8dm7_27529.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dm7_27529/09_2026/8dm7_27529.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dm7_27529/09_2026/8dm7_27529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm7_27529/09_2026/8dm7_27529.cif" } resolution = 2.49 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= -0.001 sd= 0.022 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 175 5.16 5 C 22417 2.51 5 N 5791 2.21 5 O 6782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35165 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8215 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 55, 'TRANS': 992} Chain breaks: 7 Chain: "B" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8215 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 55, 'TRANS': 992} Chain breaks: 7 Chain: "C" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8215 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 55, 'TRANS': 992} Chain breaks: 7 Chain: "D" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4833 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "E" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4833 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} 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: "U" 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: "V" 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: "W" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 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 Time building chain proxies: 7.84, per 1000 atoms: 0.22 Number of scatterers: 35165 At special positions: 0 Unit cell: (136, 159, 237, 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 175 16.00 O 6782 8.00 N 5791 7.00 C 22417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 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 C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 709 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 546 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 546 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 122 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1074 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 122 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.3 seconds 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8146 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 54 sheets defined 38.0% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.679A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.279A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.038A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 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: 3.649A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.859A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.018A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.131A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.728A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.312A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.023A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 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 758 through 783 removed outlier: 3.645A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.684A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.713A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.887A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 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 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.917A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.124A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.967A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.883A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.821A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.613A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 856 removed outlier: 4.175A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.756A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.922A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 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 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.056A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.147A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 53 removed outlier: 4.081A pdb=" N GLN D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.824A pdb=" N GLU D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.685A pdb=" N SER D 106 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 128 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 5.019A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.672A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 231 removed outlier: 3.611A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.711A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.632A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.712A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.876A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.676A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.435A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.614A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.700A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.307A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 561 removed outlier: 4.036A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 560 " --> pdb=" O LYS D 556 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY D 561 " --> pdb=" O MET D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 598 Processing helix chain 'E' and resid 21 through 53 removed outlier: 3.571A pdb=" N GLN E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP E 38 " --> pdb=" O GLN E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.850A pdb=" N GLU E 87 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 88 " --> pdb=" O LEU E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 88' Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.694A pdb=" N SER E 106 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 109 through 128 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 194 removed outlier: 4.978A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.717A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 231 removed outlier: 3.660A pdb=" N LEU E 222 " --> pdb=" O ASN E 218 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU E 224 " --> pdb=" O ASN E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 252 Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.729A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.637A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.750A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.897A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 413 " --> pdb=" O SER E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.669A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.456A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.552A pdb=" N LYS E 476 " --> pdb=" O GLN E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.688A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.329A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 561 removed outlier: 4.039A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 560 " --> pdb=" O LYS E 556 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY E 561 " --> pdb=" O MET E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 575 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.716A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.557A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.040A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.793A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.837A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.822A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 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 551 through 554 removed outlier: 4.988A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.913A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.688A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.440A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.440A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.319A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.666A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 20 through 30 removed outlier: 7.984A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.011A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.676A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.819A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.631A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.853A pdb=" N ALA B 435 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.940A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.653A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.420A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.420A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.343A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 20 through 30 removed outlier: 7.870A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.002A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.779A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.203A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.002A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.002A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.999A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.471A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.471A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.402A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AF5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.906A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.312A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AF8, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.849A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.327A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1691 hydrogen bonds defined for protein. 4773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.79 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 11169 1.35 - 1.47: 9441 1.47 - 1.60: 15155 1.60 - 1.73: 0 1.73 - 1.85: 247 Bond restraints: 36012 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.94e+00 bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.335 1.370 -0.035 1.38e-02 5.25e+03 6.59e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.53e+00 ... (remaining 36007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 47581 2.28 - 4.56: 1266 4.56 - 6.84: 97 6.84 - 9.12: 19 9.12 - 11.40: 2 Bond angle restraints: 48965 Sorted by residual: angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 122.46 129.83 -7.37 1.41e+00 5.03e-01 2.73e+01 angle pdb=" N ALA B 372 " pdb=" CA ALA B 372 " pdb=" C ALA B 372 " ideal model delta sigma weight residual 109.81 121.21 -11.40 2.21e+00 2.05e-01 2.66e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 122.46 129.62 -7.16 1.41e+00 5.03e-01 2.58e+01 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.46 129.52 -7.06 1.41e+00 5.03e-01 2.51e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.28 -5.58 1.22e+00 6.72e-01 2.09e+01 ... (remaining 48960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 19153 17.73 - 35.45: 1452 35.45 - 53.18: 252 53.18 - 70.91: 57 70.91 - 88.63: 36 Dihedral angle restraints: 20950 sinusoidal: 8300 harmonic: 12650 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 54.28 38.72 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 55.15 37.85 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -50.83 -35.17 1 1.00e+01 1.00e-02 1.75e+01 ... (remaining 20947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4355 0.064 - 0.128: 1037 0.128 - 0.192: 180 0.192 - 0.256: 15 0.256 - 0.320: 1 Chirality restraints: 5588 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB ILE D 291 " pdb=" CA ILE D 291 " pdb=" CG1 ILE D 291 " pdb=" CG2 ILE D 291 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CG LEU C 858 " pdb=" CB LEU C 858 " pdb=" CD1 LEU C 858 " pdb=" CD2 LEU C 858 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 5585 not shown) Planarity restraints: 6300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 594 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C GLY A 594 " 0.060 2.00e-02 2.50e+03 pdb=" O GLY A 594 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 595 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 952 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C VAL A 952 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL A 952 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 953 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 954 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C HIS A 954 " 0.054 2.00e-02 2.50e+03 pdb=" O HIS A 954 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN A 955 " -0.018 2.00e-02 2.50e+03 ... (remaining 6297 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 9903 2.82 - 3.34: 30555 3.34 - 3.86: 60176 3.86 - 4.38: 69556 4.38 - 4.90: 119826 Nonbonded interactions: 290016 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.310 3.040 nonbonded pdb=" O ILE D 151 " pdb=" OG SER D 155 " model vdw 2.310 3.040 nonbonded pdb=" O ILE E 151 " pdb=" OG SER E 155 " model vdw 2.313 3.040 ... (remaining 290011 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.730 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: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 34.760 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.200 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:10.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 : 0.005 0.069 36119 Z= 0.242 Angle : 0.851 11.403 49240 Z= 0.473 Chirality : 0.056 0.320 5588 Planarity : 0.007 0.070 6257 Dihedral : 13.309 88.635 12666 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.58 % Allowed : 3.51 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.44 (0.12), residues: 4278 helix: 1.26 (0.12), residues: 1424 sheet: 0.80 (0.18), residues: 703 loop : -0.51 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 273 TYR 0.035 0.002 TYR D 385 PHE 0.027 0.002 PHE A 377 TRP 0.036 0.002 TRP B 886 HIS 0.019 0.002 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.24 (36012) covalent geometry : angle 0.83790 / 0.47 (48965) SS BOND : bond 0.00492 / 0.28 ( 46) SS BOND : angle 1.62823 / 1.11 ( 92) hydrogen bonds : bond 0.12744 / 8.51 ( 1600) hydrogen bonds : angle 6.87295 / 4.77 ( 4773) link_BETA1-4 : bond 0.00747 / 0.48 ( 18) link_BETA1-4 : angle 1.60426 / 1.09 ( 54) link_NAG-ASN : bond 0.00413 / 0.25 ( 43) link_NAG-ASN : angle 2.66946 / 1.76 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 469 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7737 (tm130) REVERT: A 342 PHE cc_start: 0.7970 (m-80) cc_final: 0.7770 (m-80) REVERT: A 371 PHE cc_start: 0.4326 (OUTLIER) cc_final: 0.4057 (m-80) REVERT: A 448 ASN cc_start: 0.6341 (t0) cc_final: 0.6133 (t0) REVERT: B 740 MET cc_start: 0.8329 (ttt) cc_final: 0.8116 (ttm) REVERT: C 54 LEU cc_start: 0.8902 (mt) cc_final: 0.8621 (mp) REVERT: C 177 MET cc_start: 0.6643 (pmm) cc_final: 0.6182 (ppp) REVERT: C 245 HIS cc_start: 0.6681 (m90) cc_final: 0.6137 (m90) REVERT: D 157 ASP cc_start: 0.0229 (t0) cc_final: 0.0029 (t0) REVERT: D 216 ASN cc_start: 0.4784 (m-40) cc_final: 0.4444 (m-40) REVERT: D 249 MET cc_start: 0.0422 (ttm) cc_final: 0.0081 (tmt) REVERT: D 298 MET cc_start: 0.2317 (mmm) cc_final: 0.1920 (ptt) REVERT: D 322 HIS cc_start: 0.6514 (m-70) cc_final: 0.5915 (m-70) REVERT: D 323 MET cc_start: 0.0222 (mmm) cc_final: -0.1300 (mmm) REVERT: D 332 MET cc_start: 0.2830 (ptm) cc_final: 0.2564 (ppp) REVERT: D 341 LYS cc_start: 0.7357 (mmmm) cc_final: 0.6774 (mppt) REVERT: D 360 MET cc_start: 0.1996 (ttm) cc_final: 0.1331 (ttm) REVERT: D 535 TYR cc_start: 0.0060 (t80) cc_final: -0.0532 (p90) REVERT: E 26 LYS cc_start: 0.6760 (mtpt) cc_final: 0.6510 (mmtt) REVERT: E 62 MET cc_start: 0.3354 (ttp) cc_final: 0.2852 (tpt) REVERT: E 98 GLN cc_start: 0.5556 (mt0) cc_final: 0.5228 (mm110) REVERT: E 135 PRO cc_start: 0.2066 (Cg_endo) cc_final: 0.1335 (Cg_exo) REVERT: E 165 TRP cc_start: 0.0369 (t60) cc_final: -0.0735 (m-90) REVERT: E 246 ARG cc_start: 0.1689 (ttp-110) cc_final: 0.1097 (tmm-80) REVERT: E 249 MET cc_start: 0.2490 (ttm) cc_final: 0.2060 (tpp) REVERT: E 270 MET cc_start: -0.1758 (tpt) cc_final: -0.2184 (tpt) REVERT: E 298 MET cc_start: 0.1731 (mmm) cc_final: 0.0648 (tmm) REVERT: E 328 TRP cc_start: 0.4405 (m100) cc_final: 0.3592 (t-100) REVERT: E 418 LEU cc_start: 0.1073 (mt) cc_final: 0.0815 (mt) REVERT: E 435 GLU cc_start: -0.0319 (mm-30) cc_final: -0.0694 (pt0) REVERT: E 546 ASN cc_start: 0.2596 (m110) cc_final: 0.1242 (t0) outliers start: 22 outliers final: 1 residues processed: 485 average time/residue: 0.6752 time to fit residues: 393.9847 Evaluate side-chains 215 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain B residue 371 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.5980 chunk 401 optimal weight: 0.6980 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN A 66 HIS A 115 GLN A 360 ASN A 613 GLN A 824 ASN A 957 GLN B 23 GLN B 613 GLN B 755 GLN B 824 ASN C 134 GLN C 856 ASN C 926 GLN D 113 ASN D 117 ASN D 239 HIS D 345 HIS ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN E 98 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.181143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.112222 restraints weight = 75257.310| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.34 r_work: 0.3325 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36119 Z= 0.149 Angle : 0.605 16.265 49240 Z= 0.308 Chirality : 0.044 0.254 5588 Planarity : 0.004 0.044 6257 Dihedral : 4.508 54.271 4665 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.79 % Allowed : 9.10 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.12), residues: 4278 helix: 1.71 (0.13), residues: 1444 sheet: 0.73 (0.17), residues: 718 loop : -0.30 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 95 TYR 0.024 0.001 TYR B1067 PHE 0.033 0.001 PHE D 369 TRP 0.020 0.002 TRP C 258 HIS 0.009 0.001 HIS D 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (36012) covalent geometry : angle 0.58348 / 0.30 (48965) SS BOND : bond 0.00297 / 0.18 ( 46) SS BOND : angle 1.40165 / 0.95 ( 92) hydrogen bonds : bond 0.04508 / 2.95 ( 1600) hydrogen bonds : angle 5.41987 / 3.78 ( 4773) link_BETA1-4 : bond 0.00251 / 0.18 ( 18) link_BETA1-4 : angle 1.14850 / 0.80 ( 54) link_NAG-ASN : bond 0.00380 / 0.25 ( 43) link_NAG-ASN : angle 2.90093 / 1.83 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 237 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7937 (tm130) REVERT: A 258 TRP cc_start: 0.5058 (m-90) cc_final: 0.4745 (m-90) REVERT: A 448 ASN cc_start: 0.6177 (t0) cc_final: 0.5880 (t0) REVERT: A 740 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7831 (ttp) REVERT: A 1050 MET cc_start: 0.9503 (ptm) cc_final: 0.9243 (ptp) REVERT: B 214 ARG cc_start: 0.7096 (mtp85) cc_final: 0.6504 (tpm170) REVERT: B 394 ASN cc_start: 0.6920 (m-40) cc_final: 0.6708 (t0) REVERT: B 740 MET cc_start: 0.8645 (ttt) cc_final: 0.8284 (ttm) REVERT: C 177 MET cc_start: 0.7428 (pmm) cc_final: 0.5687 (mmm) REVERT: C 200 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6920 (t80) REVERT: C 245 HIS cc_start: 0.6632 (m90) cc_final: 0.5736 (m-70) REVERT: C 246 ARG cc_start: 0.4542 (OUTLIER) cc_final: 0.1794 (pmt170) REVERT: C 258 TRP cc_start: 0.6551 (m-90) cc_final: 0.6001 (m100) REVERT: C 355 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.7025 (tpp-160) REVERT: C 517 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5210 (tm) REVERT: C 969 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8800 (mtpp) REVERT: D 249 MET cc_start: 0.0788 (ttm) cc_final: 0.0415 (tmt) REVERT: D 270 MET cc_start: 0.1107 (OUTLIER) cc_final: 0.0863 (tmt) REVERT: D 298 MET cc_start: 0.2364 (mmm) cc_final: 0.1968 (ptt) REVERT: D 341 LYS cc_start: 0.7443 (mmmm) cc_final: 0.6851 (mppt) REVERT: D 360 MET cc_start: 0.1780 (ttm) cc_final: 0.1145 (ttm) REVERT: D 483 GLU cc_start: 0.5638 (tp30) cc_final: 0.5286 (pt0) REVERT: D 535 TYR cc_start: 0.0425 (t80) cc_final: -0.0343 (p90) REVERT: E 28 PHE cc_start: 0.4702 (t80) cc_final: 0.4459 (t80) REVERT: E 62 MET cc_start: 0.3240 (ttp) cc_final: 0.2786 (tpt) REVERT: E 95 ARG cc_start: 0.2048 (ptp-110) cc_final: 0.1676 (tpp-160) REVERT: E 163 TRP cc_start: 0.3070 (m-90) cc_final: 0.2643 (m-90) REVERT: E 165 TRP cc_start: 0.0012 (t60) cc_final: -0.0744 (m-90) REVERT: E 246 ARG cc_start: 0.1675 (ttp-110) cc_final: 0.1039 (tmm-80) REVERT: E 249 MET cc_start: 0.2773 (ttm) cc_final: 0.2333 (tpp) REVERT: E 271 TRP cc_start: 0.1224 (OUTLIER) cc_final: 0.0938 (m-90) REVERT: E 298 MET cc_start: 0.1468 (mmm) cc_final: 0.0589 (tmm) REVERT: E 328 TRP cc_start: 0.4550 (m100) cc_final: 0.3686 (t-100) REVERT: E 462 MET cc_start: 0.1568 (OUTLIER) cc_final: 0.0622 (ttt) REVERT: E 546 ASN cc_start: 0.1899 (m110) cc_final: 0.1340 (p0) outliers start: 68 outliers final: 14 residues processed: 284 average time/residue: 0.6014 time to fit residues: 210.4033 Evaluate side-chains 209 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 462 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 292 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 347 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 chunk 417 optimal weight: 20.0000 chunk 217 optimal weight: 10.0000 chunk 363 optimal weight: 4.9990 chunk 419 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN C 317 ASN C 394 ASN C 824 ASN D 239 HIS D 330 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.185526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.117507 restraints weight = 73297.688| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.66 r_work: 0.3176 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 36119 Z= 0.315 Angle : 0.717 15.195 49240 Z= 0.365 Chirality : 0.050 0.247 5588 Planarity : 0.005 0.043 6257 Dihedral : 4.911 54.535 4665 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.08 % Allowed : 11.19 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.12), residues: 4278 helix: 1.51 (0.13), residues: 1432 sheet: 0.58 (0.18), residues: 734 loop : -0.38 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 387 TYR 0.030 0.002 TYR B1067 PHE 0.037 0.002 PHE D 369 TRP 0.026 0.002 TRP A 886 HIS 0.016 0.002 HIS E 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.32 (36012) covalent geometry : angle 0.69895 / 0.36 (48965) SS BOND : bond 0.00389 / 0.24 ( 46) SS BOND : angle 1.35797 / 0.97 ( 92) hydrogen bonds : bond 0.05242 / 3.45 ( 1600) hydrogen bonds : angle 5.58385 / 3.92 ( 4773) link_BETA1-4 : bond 0.00534 / 0.38 ( 18) link_BETA1-4 : angle 1.54446 / 1.06 ( 54) link_NAG-ASN : bond 0.00676 / 0.44 ( 43) link_NAG-ASN : angle 2.93752 / 1.95 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 207 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7917 (tm-30) REVERT: A 258 TRP cc_start: 0.5238 (m-90) cc_final: 0.4931 (m-90) REVERT: A 371 PHE cc_start: 0.5026 (OUTLIER) cc_final: 0.4806 (t80) REVERT: A 448 ASN cc_start: 0.6536 (t0) cc_final: 0.6318 (t0) REVERT: A 740 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.7867 (ttp) REVERT: A 780 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8942 (mm-30) REVERT: B 214 ARG cc_start: 0.7321 (mtp85) cc_final: 0.6685 (tpm170) REVERT: B 740 MET cc_start: 0.8676 (ttt) cc_final: 0.8427 (ttm) REVERT: C 177 MET cc_start: 0.7296 (pmm) cc_final: 0.6682 (ppp) REVERT: C 200 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.7024 (t80) REVERT: C 220 PHE cc_start: 0.7889 (t80) cc_final: 0.7666 (t80) REVERT: C 245 HIS cc_start: 0.7001 (m90) cc_final: 0.5868 (m90) REVERT: C 355 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6853 (tpp-160) REVERT: C 987 PRO cc_start: 0.8452 (Cg_exo) cc_final: 0.8219 (Cg_endo) REVERT: D 249 MET cc_start: 0.0464 (ttm) cc_final: 0.0249 (tmt) REVERT: D 270 MET cc_start: 0.0866 (OUTLIER) cc_final: 0.0628 (tmt) REVERT: D 298 MET cc_start: 0.1954 (mmm) cc_final: 0.1574 (ptt) REVERT: D 332 MET cc_start: 0.4014 (ppp) cc_final: 0.3495 (ppp) REVERT: D 340 ARG cc_start: 0.3885 (OUTLIER) cc_final: 0.0899 (mmm160) REVERT: D 341 LYS cc_start: 0.7306 (mmmm) cc_final: 0.6621 (mmpt) REVERT: D 408 MET cc_start: 0.3838 (mmp) cc_final: 0.3267 (tpt) REVERT: D 535 TYR cc_start: 0.1437 (t80) cc_final: 0.0409 (p90) REVERT: E 62 MET cc_start: 0.3156 (ttp) cc_final: 0.2845 (tpt) REVERT: E 95 ARG cc_start: 0.2290 (ptp-110) cc_final: 0.2021 (ttm110) REVERT: E 144 LEU cc_start: 0.0837 (tm) cc_final: 0.0119 (pt) REVERT: E 246 ARG cc_start: 0.1608 (ttp-110) cc_final: 0.1039 (tmm-80) REVERT: E 249 MET cc_start: 0.2961 (ttm) cc_final: 0.2602 (tpp) REVERT: E 275 TRP cc_start: 0.4059 (m-10) cc_final: 0.3833 (m-10) REVERT: E 298 MET cc_start: 0.1601 (mmm) cc_final: 0.0785 (tmm) REVERT: E 328 TRP cc_start: 0.3987 (m100) cc_final: 0.3575 (t-100) REVERT: E 366 MET cc_start: -0.0049 (tpt) cc_final: -0.0499 (tpt) REVERT: E 482 ARG cc_start: 0.4833 (ptt90) cc_final: 0.4575 (mtt180) REVERT: E 546 ASN cc_start: 0.2033 (m110) cc_final: 0.1236 (t0) outliers start: 79 outliers final: 25 residues processed: 266 average time/residue: 0.6380 time to fit residues: 207.9212 Evaluate side-chains 213 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 94 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 174 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 240 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 425 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN D 239 HIS D 345 HIS E 30 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.175552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.103959 restraints weight = 75292.419| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.73 r_work: 0.3229 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36119 Z= 0.181 Angle : 0.590 13.911 49240 Z= 0.299 Chirality : 0.045 0.213 5588 Planarity : 0.004 0.065 6257 Dihedral : 4.638 54.827 4665 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.56 % Allowed : 12.64 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.12), residues: 4278 helix: 1.72 (0.14), residues: 1432 sheet: 0.44 (0.17), residues: 730 loop : -0.27 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 237 TYR 0.023 0.001 TYR A1067 PHE 0.026 0.001 PHE D 369 TRP 0.019 0.001 TRP D 165 HIS 0.011 0.001 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (36012) covalent geometry : angle 0.57461 / 0.30 (48965) SS BOND : bond 0.00301 / 0.18 ( 46) SS BOND : angle 1.05193 / 0.74 ( 92) hydrogen bonds : bond 0.04326 / 2.84 ( 1600) hydrogen bonds : angle 5.34282 / 3.76 ( 4773) link_BETA1-4 : bond 0.00258 / 0.15 ( 18) link_BETA1-4 : angle 1.06921 / 0.74 ( 54) link_NAG-ASN : bond 0.00375 / 0.23 ( 43) link_NAG-ASN : angle 2.52670 / 1.66 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 199 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8337 (tm-30) cc_final: 0.7868 (tm-30) REVERT: A 158 ARG cc_start: 0.5867 (mtt-85) cc_final: 0.5622 (mtt-85) REVERT: A 168 PHE cc_start: 0.7239 (t80) cc_final: 0.6916 (t80) REVERT: A 177 MET cc_start: 0.7077 (pmm) cc_final: 0.5549 (mtt) REVERT: A 258 TRP cc_start: 0.4978 (m-90) cc_final: 0.4685 (m-90) REVERT: A 371 PHE cc_start: 0.5073 (OUTLIER) cc_final: 0.4764 (t80) REVERT: A 448 ASN cc_start: 0.6527 (t0) cc_final: 0.6305 (t0) REVERT: A 740 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7853 (ttp) REVERT: A 820 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8427 (m-30) REVERT: B 214 ARG cc_start: 0.7349 (mtp85) cc_final: 0.6719 (tpm170) REVERT: B 697 MET cc_start: 0.9396 (ptt) cc_final: 0.9109 (ptt) REVERT: B 740 MET cc_start: 0.8640 (ttt) cc_final: 0.8379 (ttm) REVERT: C 177 MET cc_start: 0.7336 (pmm) cc_final: 0.6800 (ppp) REVERT: C 188 ASN cc_start: 0.5629 (t0) cc_final: 0.5403 (t0) REVERT: C 200 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.7066 (t80) REVERT: C 228 ASP cc_start: 0.8252 (m-30) cc_final: 0.8014 (m-30) REVERT: C 245 HIS cc_start: 0.7154 (m90) cc_final: 0.6011 (m90) REVERT: C 987 PRO cc_start: 0.8506 (Cg_exo) cc_final: 0.8297 (Cg_endo) REVERT: D 89 GLN cc_start: 0.3887 (mp10) cc_final: 0.3369 (tp40) REVERT: D 132 VAL cc_start: -0.3317 (OUTLIER) cc_final: -0.3564 (t) REVERT: D 249 MET cc_start: 0.0563 (ttm) cc_final: 0.0320 (tmt) REVERT: D 298 MET cc_start: 0.2318 (mmm) cc_final: 0.1966 (ptt) REVERT: D 340 ARG cc_start: 0.3765 (OUTLIER) cc_final: 0.3258 (ptt-90) REVERT: D 341 LYS cc_start: 0.7305 (mmmm) cc_final: 0.6865 (mppt) REVERT: D 408 MET cc_start: 0.3969 (mmp) cc_final: 0.3324 (tpt) REVERT: D 535 TYR cc_start: 0.1323 (t80) cc_final: 0.0028 (p90) REVERT: E 22 GLU cc_start: 0.3046 (tt0) cc_final: 0.2760 (mm-30) REVERT: E 62 MET cc_start: 0.3100 (ttp) cc_final: 0.2752 (tpt) REVERT: E 95 ARG cc_start: 0.2348 (ptp-110) cc_final: 0.1977 (tpp-160) REVERT: E 144 LEU cc_start: 0.0869 (tm) cc_final: 0.0178 (pp) REVERT: E 210 GLU cc_start: 0.4450 (tp30) cc_final: 0.4240 (mm-30) REVERT: E 249 MET cc_start: 0.2903 (ttm) cc_final: 0.2638 (tpp) REVERT: E 275 TRP cc_start: 0.4017 (m-10) cc_final: 0.3806 (m-10) REVERT: E 298 MET cc_start: 0.1574 (mmm) cc_final: 0.0802 (tmm) REVERT: E 328 TRP cc_start: 0.3935 (m100) cc_final: 0.3583 (t-100) REVERT: E 366 MET cc_start: -0.0133 (tpt) cc_final: -0.0593 (tpt) REVERT: E 482 ARG cc_start: 0.4678 (ptt90) cc_final: 0.4444 (mtt180) REVERT: E 546 ASN cc_start: 0.1886 (m110) cc_final: 0.1133 (t0) outliers start: 59 outliers final: 21 residues processed: 243 average time/residue: 0.6264 time to fit residues: 187.9657 Evaluate side-chains 204 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 128 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 389 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 351 optimal weight: 0.0570 chunk 335 optimal weight: 20.0000 chunk 367 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 320 optimal weight: 30.0000 chunk 246 optimal weight: 2.9990 chunk 399 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN B 115 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 115 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 872 GLN D 239 HIS D 345 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.183376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.115996 restraints weight = 72893.430| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.51 r_work: 0.3167 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 36119 Z= 0.312 Angle : 0.700 14.643 49240 Z= 0.355 Chirality : 0.049 0.293 5588 Planarity : 0.005 0.050 6257 Dihedral : 4.924 52.896 4665 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.37 % Allowed : 12.56 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.12), residues: 4278 helix: 1.43 (0.13), residues: 1430 sheet: 0.35 (0.18), residues: 726 loop : -0.48 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 466 TYR 0.027 0.002 TYR B1067 PHE 0.031 0.002 PHE D 369 TRP 0.026 0.002 TRP A 353 HIS 0.010 0.002 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.31 (36012) covalent geometry : angle 0.68194 / 0.35 (48965) SS BOND : bond 0.00639 / 0.43 ( 46) SS BOND : angle 1.44536 / 1.01 ( 92) hydrogen bonds : bond 0.05043 / 3.30 ( 1600) hydrogen bonds : angle 5.60338 / 3.94 ( 4773) link_BETA1-4 : bond 0.00443 / 0.29 ( 18) link_BETA1-4 : angle 1.33822 / 0.92 ( 54) link_NAG-ASN : bond 0.00634 / 0.41 ( 43) link_NAG-ASN : angle 2.87854 / 1.94 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 189 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7788 (tm-30) REVERT: A 125 ASN cc_start: 0.6128 (p0) cc_final: 0.5854 (m-40) REVERT: A 177 MET cc_start: 0.7247 (pmm) cc_final: 0.5478 (mtt) REVERT: A 207 HIS cc_start: 0.7491 (m170) cc_final: 0.7264 (m-70) REVERT: A 258 TRP cc_start: 0.4970 (m-90) cc_final: 0.4499 (m-90) REVERT: A 371 PHE cc_start: 0.5265 (OUTLIER) cc_final: 0.4986 (t80) REVERT: A 448 ASN cc_start: 0.6506 (t0) cc_final: 0.6288 (t0) REVERT: A 524 VAL cc_start: 0.5589 (OUTLIER) cc_final: 0.5334 (m) REVERT: A 740 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7778 (ttp) REVERT: A 820 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8572 (m-30) REVERT: A 994 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8098 (t70) REVERT: B 214 ARG cc_start: 0.7463 (mtp85) cc_final: 0.6800 (tpm170) REVERT: B 697 MET cc_start: 0.9400 (ptt) cc_final: 0.9122 (ptt) REVERT: B 740 MET cc_start: 0.8654 (ttt) cc_final: 0.8378 (ttm) REVERT: C 188 ASN cc_start: 0.5679 (t0) cc_final: 0.5441 (t0) REVERT: C 200 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.7337 (t80) REVERT: C 237 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7620 (ttp-110) REVERT: C 740 MET cc_start: 0.8705 (ttp) cc_final: 0.8226 (ttp) REVERT: C 987 PRO cc_start: 0.8501 (Cg_exo) cc_final: 0.8284 (Cg_endo) REVERT: D 89 GLN cc_start: 0.3901 (mp10) cc_final: 0.3305 (tp40) REVERT: D 249 MET cc_start: 0.0269 (ttm) cc_final: 0.0033 (tmt) REVERT: D 298 MET cc_start: 0.2286 (mmm) cc_final: 0.1871 (ptt) REVERT: D 408 MET cc_start: 0.3631 (mmp) cc_final: 0.2984 (tpt) REVERT: D 483 GLU cc_start: 0.5505 (tp30) cc_final: 0.5263 (pt0) REVERT: D 535 TYR cc_start: 0.1170 (t80) cc_final: -0.0184 (p90) REVERT: E 20 LEU cc_start: 0.3440 (OUTLIER) cc_final: 0.3132 (tt) REVERT: E 22 GLU cc_start: 0.3094 (tt0) cc_final: 0.2565 (mm-30) REVERT: E 62 MET cc_start: 0.3126 (ttp) cc_final: 0.2818 (tpt) REVERT: E 78 LYS cc_start: 0.4581 (OUTLIER) cc_final: 0.4253 (tptp) REVERT: E 144 LEU cc_start: 0.0474 (tm) cc_final: -0.0124 (pp) REVERT: E 246 ARG cc_start: 0.1947 (ptp-110) cc_final: 0.0411 (tmm-80) REVERT: E 249 MET cc_start: 0.2813 (ttm) cc_final: 0.2377 (tpp) REVERT: E 275 TRP cc_start: 0.4085 (m-10) cc_final: 0.3878 (m-10) REVERT: E 298 MET cc_start: 0.1414 (mmm) cc_final: 0.0676 (tmm) REVERT: E 366 MET cc_start: -0.0152 (tpt) cc_final: -0.0454 (tpt) REVERT: E 482 ARG cc_start: 0.4491 (ptt90) cc_final: 0.4256 (mtt180) REVERT: E 546 ASN cc_start: 0.1937 (m110) cc_final: 0.1228 (t0) outliers start: 90 outliers final: 36 residues processed: 262 average time/residue: 0.6187 time to fit residues: 199.5440 Evaluate side-chains 211 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 163 TRP Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 203 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 110 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 401 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 chunk 306 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 393 optimal weight: 20.0000 chunk 352 optimal weight: 0.6980 chunk 380 optimal weight: 20.0000 chunk 231 optimal weight: 3.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.178058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.105319 restraints weight = 71795.187| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.99 r_work: 0.3210 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36119 Z= 0.153 Angle : 0.586 13.557 49240 Z= 0.295 Chirality : 0.044 0.228 5588 Planarity : 0.004 0.042 6257 Dihedral : 4.631 52.303 4665 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.79 % Allowed : 13.93 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.63 (0.12), residues: 4278 helix: 1.66 (0.14), residues: 1429 sheet: 0.35 (0.18), residues: 705 loop : -0.38 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 237 TYR 0.022 0.001 TYR E 381 PHE 0.025 0.001 PHE E 28 TRP 0.026 0.001 TRP A 353 HIS 0.007 0.001 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (36012) covalent geometry : angle 0.57248 / 0.29 (48965) SS BOND : bond 0.00428 / 0.28 ( 46) SS BOND : angle 1.04084 / 0.72 ( 92) hydrogen bonds : bond 0.04136 / 2.69 ( 1600) hydrogen bonds : angle 5.31307 / 3.75 ( 4773) link_BETA1-4 : bond 0.00346 / 0.22 ( 18) link_BETA1-4 : angle 0.98054 / 0.66 ( 54) link_NAG-ASN : bond 0.00331 / 0.20 ( 43) link_NAG-ASN : angle 2.35498 / 1.55 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 179 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5453 (mtt-85) cc_final: 0.5204 (mtt-85) REVERT: A 177 MET cc_start: 0.7353 (pmm) cc_final: 0.6525 (ppp) REVERT: A 258 TRP cc_start: 0.4485 (m-90) cc_final: 0.4181 (m-90) REVERT: A 359 SER cc_start: 0.5268 (p) cc_final: 0.4952 (t) REVERT: A 371 PHE cc_start: 0.5453 (OUTLIER) cc_final: 0.5054 (t80) REVERT: A 448 ASN cc_start: 0.6198 (t0) cc_final: 0.5995 (t0) REVERT: A 740 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7845 (ttp) REVERT: A 820 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8384 (m-30) REVERT: A 994 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8027 (t70) REVERT: B 214 ARG cc_start: 0.7473 (mtp85) cc_final: 0.6781 (tpm170) REVERT: B 697 MET cc_start: 0.9385 (ptt) cc_final: 0.9069 (ptt) REVERT: B 740 MET cc_start: 0.8661 (ttt) cc_final: 0.8379 (ttm) REVERT: C 188 ASN cc_start: 0.5634 (t0) cc_final: 0.5377 (t0) REVERT: C 200 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7401 (t80) REVERT: C 237 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7518 (ttp-110) REVERT: C 987 PRO cc_start: 0.8547 (Cg_exo) cc_final: 0.8336 (Cg_endo) REVERT: D 45 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6918 (pp) REVERT: D 89 GLN cc_start: 0.4201 (mp10) cc_final: 0.3514 (tp40) REVERT: D 249 MET cc_start: 0.0303 (ttm) cc_final: 0.0051 (tmt) REVERT: D 298 MET cc_start: 0.2527 (mmm) cc_final: 0.2115 (ptt) REVERT: D 408 MET cc_start: 0.3916 (mmp) cc_final: 0.3175 (tpt) REVERT: D 483 GLU cc_start: 0.5415 (tp30) cc_final: 0.5180 (pt0) REVERT: D 535 TYR cc_start: 0.1223 (t80) cc_final: -0.0197 (p90) REVERT: E 22 GLU cc_start: 0.3378 (tt0) cc_final: 0.3037 (mm-30) REVERT: E 57 GLU cc_start: 0.2311 (OUTLIER) cc_final: 0.1708 (tp30) REVERT: E 62 MET cc_start: 0.3117 (ttp) cc_final: 0.2663 (tpt) REVERT: E 144 LEU cc_start: 0.1282 (tm) cc_final: 0.0692 (pp) REVERT: E 246 ARG cc_start: 0.1606 (ptp-110) cc_final: -0.0097 (tmm-80) REVERT: E 249 MET cc_start: 0.2737 (ttm) cc_final: 0.2266 (tpp) REVERT: E 281 LEU cc_start: 0.1700 (OUTLIER) cc_final: 0.1473 (mm) REVERT: E 298 MET cc_start: 0.1303 (mmm) cc_final: 0.0517 (tmm) REVERT: E 323 MET cc_start: 0.2888 (tpt) cc_final: 0.2307 (tpp) REVERT: E 366 MET cc_start: -0.0142 (tpt) cc_final: -0.0671 (tpt) REVERT: E 388 GLN cc_start: 0.4179 (mm-40) cc_final: 0.3925 (mm-40) REVERT: E 482 ARG cc_start: 0.4580 (ptt90) cc_final: 0.4259 (mtt180) REVERT: E 546 ASN cc_start: 0.1973 (m110) cc_final: 0.1127 (t0) outliers start: 68 outliers final: 29 residues processed: 233 average time/residue: 0.6211 time to fit residues: 179.0343 Evaluate side-chains 203 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 281 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 215 optimal weight: 8.9990 chunk 236 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 362 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 397 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 241 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.175463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.105662 restraints weight = 73020.276| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.30 r_work: 0.3182 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 36119 Z= 0.196 Angle : 0.605 13.493 49240 Z= 0.304 Chirality : 0.045 0.238 5588 Planarity : 0.004 0.038 6257 Dihedral : 4.600 52.778 4665 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.90 % Allowed : 14.38 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.13), residues: 4278 helix: 1.67 (0.14), residues: 1417 sheet: 0.30 (0.18), residues: 709 loop : -0.38 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 577 TYR 0.023 0.002 TYR B1067 PHE 0.022 0.002 PHE E 28 TRP 0.029 0.001 TRP A 353 HIS 0.006 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (36012) covalent geometry : angle 0.59034 / 0.30 (48965) SS BOND : bond 0.00306 / 0.18 ( 46) SS BOND : angle 1.23214 / 0.86 ( 92) hydrogen bonds : bond 0.04283 / 2.79 ( 1600) hydrogen bonds : angle 5.30182 / 3.74 ( 4773) link_BETA1-4 : bond 0.00336 / 0.19 ( 18) link_BETA1-4 : angle 1.06835 / 0.72 ( 54) link_NAG-ASN : bond 0.00390 / 0.25 ( 43) link_NAG-ASN : angle 2.38104 / 1.58 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 177 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5973 (mtt-85) cc_final: 0.5592 (mtt-85) REVERT: A 258 TRP cc_start: 0.4942 (m-90) cc_final: 0.4610 (m-90) REVERT: A 359 SER cc_start: 0.5762 (p) cc_final: 0.5511 (t) REVERT: A 371 PHE cc_start: 0.5512 (OUTLIER) cc_final: 0.5221 (t80) REVERT: A 448 ASN cc_start: 0.6263 (t0) cc_final: 0.6042 (t0) REVERT: A 524 VAL cc_start: 0.5749 (OUTLIER) cc_final: 0.5489 (m) REVERT: A 740 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7695 (ttp) REVERT: A 820 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8345 (m-30) REVERT: A 994 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8052 (t70) REVERT: B 214 ARG cc_start: 0.7495 (mtp85) cc_final: 0.6797 (tpm170) REVERT: B 697 MET cc_start: 0.9382 (ptt) cc_final: 0.9057 (ptt) REVERT: B 740 MET cc_start: 0.8591 (ttt) cc_final: 0.8308 (ttm) REVERT: C 200 TYR cc_start: 0.7703 (OUTLIER) cc_final: 0.7418 (t80) REVERT: C 237 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7625 (ttp-110) REVERT: C 580 GLN cc_start: 0.8058 (tt0) cc_final: 0.7737 (mm-40) REVERT: C 987 PRO cc_start: 0.8532 (Cg_exo) cc_final: 0.8309 (Cg_endo) REVERT: D 45 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6937 (pp) REVERT: D 89 GLN cc_start: 0.4025 (mp10) cc_final: 0.3325 (tp40) REVERT: D 249 MET cc_start: 0.0257 (ttm) cc_final: 0.0051 (tmt) REVERT: D 298 MET cc_start: 0.2448 (mmm) cc_final: 0.2070 (ptt) REVERT: D 408 MET cc_start: 0.3855 (mmp) cc_final: 0.3147 (tpt) REVERT: D 483 GLU cc_start: 0.5412 (tp30) cc_final: 0.5186 (pt0) REVERT: D 535 TYR cc_start: 0.1313 (t80) cc_final: -0.0226 (p90) REVERT: E 22 GLU cc_start: 0.2820 (tt0) cc_final: 0.2463 (mm-30) REVERT: E 62 MET cc_start: 0.3201 (ttp) cc_final: 0.2822 (tpt) REVERT: E 97 LEU cc_start: 0.3087 (OUTLIER) cc_final: 0.2725 (tt) REVERT: E 144 LEU cc_start: 0.1268 (tm) cc_final: 0.0650 (pp) REVERT: E 246 ARG cc_start: 0.1868 (ptp-110) cc_final: 0.1531 (pmm-80) REVERT: E 249 MET cc_start: 0.2808 (ttm) cc_final: 0.2445 (tpp) REVERT: E 281 LEU cc_start: 0.1998 (OUTLIER) cc_final: 0.1771 (mm) REVERT: E 298 MET cc_start: 0.1291 (mmm) cc_final: 0.0556 (tmm) REVERT: E 482 ARG cc_start: 0.4630 (ptt90) cc_final: 0.4291 (mtt180) REVERT: E 546 ASN cc_start: 0.1834 (m110) cc_final: 0.1090 (t0) outliers start: 72 outliers final: 36 residues processed: 237 average time/residue: 0.5800 time to fit residues: 170.7400 Evaluate side-chains 210 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 163 TRP Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 281 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 176 optimal weight: 0.6980 chunk 382 optimal weight: 0.9980 chunk 314 optimal weight: 30.0000 chunk 235 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 340 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 399 optimal weight: 10.0000 chunk 391 optimal weight: 20.0000 chunk 337 optimal weight: 20.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.174959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.105453 restraints weight = 72972.201| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.15 r_work: 0.3202 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 36119 Z= 0.205 Angle : 0.610 13.024 49240 Z= 0.306 Chirality : 0.045 0.274 5588 Planarity : 0.004 0.040 6257 Dihedral : 4.618 52.534 4665 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.01 % Allowed : 14.41 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.13), residues: 4278 helix: 1.58 (0.13), residues: 1430 sheet: 0.31 (0.18), residues: 708 loop : -0.39 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 466 TYR 0.023 0.002 TYR B1067 PHE 0.031 0.002 PHE C 855 TRP 0.036 0.002 TRP B 353 HIS 0.005 0.001 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (36012) covalent geometry : angle 0.59622 / 0.30 (48965) SS BOND : bond 0.00302 / 0.18 ( 46) SS BOND : angle 1.15901 / 0.81 ( 92) hydrogen bonds : bond 0.04265 / 2.78 ( 1600) hydrogen bonds : angle 5.30249 / 3.74 ( 4773) link_BETA1-4 : bond 0.00285 / 0.17 ( 18) link_BETA1-4 : angle 0.99327 / 0.66 ( 54) link_NAG-ASN : bond 0.00376 / 0.24 ( 43) link_NAG-ASN : angle 2.38912 / 1.59 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 174 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5491 (mtt-85) cc_final: 0.5111 (mtt-85) REVERT: A 371 PHE cc_start: 0.5470 (OUTLIER) cc_final: 0.5218 (t80) REVERT: A 448 ASN cc_start: 0.6159 (t0) cc_final: 0.5927 (t0) REVERT: A 524 VAL cc_start: 0.5767 (OUTLIER) cc_final: 0.5498 (m) REVERT: A 740 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7681 (ttp) REVERT: A 820 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: A 994 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8018 (t70) REVERT: B 214 ARG cc_start: 0.7509 (mtp85) cc_final: 0.6737 (tpm170) REVERT: B 697 MET cc_start: 0.9381 (ptt) cc_final: 0.9035 (ptt) REVERT: B 740 MET cc_start: 0.8583 (ttt) cc_final: 0.8293 (ttm) REVERT: C 200 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7542 (t80) REVERT: C 355 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6800 (tpp-160) REVERT: C 580 GLN cc_start: 0.8062 (tt0) cc_final: 0.7741 (mm-40) REVERT: C 987 PRO cc_start: 0.8625 (Cg_exo) cc_final: 0.8408 (Cg_endo) REVERT: D 45 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6906 (pp) REVERT: D 249 MET cc_start: 0.0205 (ttm) cc_final: -0.0013 (tmt) REVERT: D 298 MET cc_start: 0.2463 (mmm) cc_final: 0.2089 (ptt) REVERT: D 408 MET cc_start: 0.3955 (mmp) cc_final: 0.3252 (tpt) REVERT: D 483 GLU cc_start: 0.5524 (tp30) cc_final: 0.5282 (pt0) REVERT: D 535 TYR cc_start: 0.1366 (t80) cc_final: -0.0262 (p90) REVERT: E 22 GLU cc_start: 0.2804 (tt0) cc_final: 0.2411 (mm-30) REVERT: E 62 MET cc_start: 0.3131 (ttp) cc_final: 0.2750 (tpt) REVERT: E 144 LEU cc_start: 0.1388 (tm) cc_final: 0.0692 (pp) REVERT: E 246 ARG cc_start: 0.1785 (ptp-110) cc_final: 0.0213 (tmm-80) REVERT: E 249 MET cc_start: 0.2901 (ttm) cc_final: 0.2510 (tpp) REVERT: E 298 MET cc_start: 0.1214 (mmm) cc_final: 0.0535 (tmm) REVERT: E 323 MET cc_start: 0.3922 (tpt) cc_final: 0.3523 (tpp) REVERT: E 366 MET cc_start: -0.0166 (tpt) cc_final: -0.0571 (tpt) REVERT: E 482 ARG cc_start: 0.4709 (ptt90) cc_final: 0.4327 (mtt180) REVERT: E 546 ASN cc_start: 0.1936 (m110) cc_final: 0.1246 (t0) outliers start: 76 outliers final: 40 residues processed: 237 average time/residue: 0.5545 time to fit residues: 163.9463 Evaluate side-chains 208 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 203 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 58 optimal weight: 0.8980 chunk 311 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 chunk 396 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 176 optimal weight: 0.4980 chunk 335 optimal weight: 0.5980 chunk 263 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN D 188 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 HIS E 536 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.175199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.107230 restraints weight = 73550.433| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.14 r_work: 0.3222 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36119 Z= 0.121 Angle : 0.569 12.825 49240 Z= 0.286 Chirality : 0.043 0.194 5588 Planarity : 0.004 0.039 6257 Dihedral : 4.404 51.696 4665 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.40 % Allowed : 15.07 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.13), residues: 4278 helix: 1.72 (0.14), residues: 1424 sheet: 0.26 (0.18), residues: 709 loop : -0.28 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 237 TYR 0.026 0.001 TYR B 170 PHE 0.029 0.001 PHE C 855 TRP 0.027 0.001 TRP A 353 HIS 0.006 0.001 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (36012) covalent geometry : angle 0.55815 / 0.28 (48965) SS BOND : bond 0.00252 / 0.15 ( 46) SS BOND : angle 1.11906 / 0.77 ( 92) hydrogen bonds : bond 0.03782 / 2.45 ( 1600) hydrogen bonds : angle 5.12079 / 3.62 ( 4773) link_BETA1-4 : bond 0.00344 / 0.21 ( 18) link_BETA1-4 : angle 0.91131 / 0.60 ( 54) link_NAG-ASN : bond 0.00265 / 0.16 ( 43) link_NAG-ASN : angle 2.05084 / 1.34 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 158 ARG cc_start: 0.5677 (mtt-85) cc_final: 0.5250 (tpp80) REVERT: A 177 MET cc_start: 0.6873 (pmm) cc_final: 0.5968 (ppp) REVERT: A 448 ASN cc_start: 0.6020 (t0) cc_final: 0.5803 (t0) REVERT: A 524 VAL cc_start: 0.5794 (OUTLIER) cc_final: 0.5535 (m) REVERT: A 740 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7756 (ttp) REVERT: A 994 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8048 (t70) REVERT: B 214 ARG cc_start: 0.7450 (mtp85) cc_final: 0.6702 (tpm170) REVERT: B 697 MET cc_start: 0.9385 (ptt) cc_final: 0.9092 (ptt) REVERT: B 740 MET cc_start: 0.8645 (ttt) cc_final: 0.8389 (ttm) REVERT: C 200 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7452 (t80) REVERT: C 355 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6940 (tpp-160) REVERT: C 580 GLN cc_start: 0.8115 (tt0) cc_final: 0.7867 (mt0) REVERT: C 987 PRO cc_start: 0.8547 (Cg_exo) cc_final: 0.8318 (Cg_endo) REVERT: C 1142 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7822 (tm-30) REVERT: D 45 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6913 (pp) REVERT: D 249 MET cc_start: 0.0234 (ttm) cc_final: -0.0033 (tmt) REVERT: D 298 MET cc_start: 0.2655 (mmm) cc_final: 0.2208 (ptt) REVERT: D 325 GLN cc_start: 0.6330 (pm20) cc_final: 0.5415 (pp30) REVERT: D 483 GLU cc_start: 0.5442 (tp30) cc_final: 0.5188 (pt0) REVERT: D 518 ARG cc_start: 0.4060 (ttp80) cc_final: 0.3705 (tmt170) REVERT: D 535 TYR cc_start: 0.1373 (t80) cc_final: -0.0264 (p90) REVERT: E 22 GLU cc_start: 0.2763 (tt0) cc_final: 0.2359 (mm-30) REVERT: E 62 MET cc_start: 0.3166 (ttp) cc_final: 0.2709 (tpt) REVERT: E 144 LEU cc_start: 0.1349 (tm) cc_final: 0.0793 (pp) REVERT: E 246 ARG cc_start: 0.1833 (ptp-110) cc_final: 0.0167 (tmm-80) REVERT: E 249 MET cc_start: 0.2980 (ttm) cc_final: 0.2592 (tpp) REVERT: E 298 MET cc_start: 0.1307 (mmm) cc_final: 0.0540 (tmm) REVERT: E 323 MET cc_start: 0.2621 (tpt) cc_final: 0.2123 (tpp) REVERT: E 366 MET cc_start: 0.0100 (tpt) cc_final: -0.0196 (tpt) REVERT: E 482 ARG cc_start: 0.4573 (ptt90) cc_final: 0.4154 (mtt180) REVERT: E 546 ASN cc_start: 0.2041 (m110) cc_final: 0.1199 (t0) outliers start: 53 outliers final: 30 residues processed: 221 average time/residue: 0.5989 time to fit residues: 163.3280 Evaluate side-chains 197 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 128 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 29 optimal weight: 8.9990 chunk 160 optimal weight: 0.5980 chunk 281 optimal weight: 2.9990 chunk 414 optimal weight: 20.0000 chunk 234 optimal weight: 0.0270 chunk 57 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 335 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 307 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.176595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.108987 restraints weight = 73117.002| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.20 r_work: 0.3235 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36119 Z= 0.117 Angle : 0.568 13.825 49240 Z= 0.284 Chirality : 0.043 0.179 5588 Planarity : 0.004 0.041 6257 Dihedral : 4.227 52.084 4663 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.19 % Allowed : 15.57 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.13), residues: 4278 helix: 1.78 (0.14), residues: 1425 sheet: 0.36 (0.18), residues: 707 loop : -0.25 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 357 TYR 0.026 0.001 TYR A 421 PHE 0.029 0.001 PHE C 855 TRP 0.034 0.001 TRP D 165 HIS 0.005 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (36012) covalent geometry : angle 0.55768 / 0.28 (48965) SS BOND : bond 0.00247 / 0.14 ( 46) SS BOND : angle 1.10538 / 0.75 ( 92) hydrogen bonds : bond 0.03669 / 2.38 ( 1600) hydrogen bonds : angle 5.04169 / 3.57 ( 4773) link_BETA1-4 : bond 0.00325 / 0.20 ( 18) link_BETA1-4 : angle 0.90416 / 0.60 ( 54) link_NAG-ASN : bond 0.00248 / 0.15 ( 43) link_NAG-ASN : angle 1.94913 / 1.27 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 144 TYR cc_start: 0.3943 (p90) cc_final: 0.3690 (p90) REVERT: A 158 ARG cc_start: 0.5891 (mtt-85) cc_final: 0.5521 (tpp80) REVERT: A 168 PHE cc_start: 0.7251 (t80) cc_final: 0.6837 (t80) REVERT: A 170 TYR cc_start: 0.7794 (t80) cc_final: 0.7572 (t80) REVERT: A 177 MET cc_start: 0.6798 (pmm) cc_final: 0.5861 (ppp) REVERT: A 229 LEU cc_start: 0.7160 (mt) cc_final: 0.6633 (mm) REVERT: A 448 ASN cc_start: 0.6050 (t0) cc_final: 0.5836 (t0) REVERT: A 524 VAL cc_start: 0.5753 (OUTLIER) cc_final: 0.5516 (m) REVERT: A 740 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7659 (ttp) REVERT: A 994 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8036 (t70) REVERT: B 214 ARG cc_start: 0.7422 (mtp85) cc_final: 0.6639 (tpm170) REVERT: B 697 MET cc_start: 0.9386 (ptt) cc_final: 0.9045 (ptt) REVERT: B 740 MET cc_start: 0.8567 (ttt) cc_final: 0.8308 (ttm) REVERT: C 200 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7510 (t80) REVERT: C 355 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6938 (tpp-160) REVERT: C 580 GLN cc_start: 0.8128 (tt0) cc_final: 0.7875 (mm-40) REVERT: C 987 PRO cc_start: 0.8556 (Cg_exo) cc_final: 0.8326 (Cg_endo) REVERT: C 1142 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7855 (tm-30) REVERT: D 45 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6883 (pp) REVERT: D 249 MET cc_start: 0.0339 (ttm) cc_final: 0.0086 (tmt) REVERT: D 298 MET cc_start: 0.2680 (mmm) cc_final: 0.2297 (ptt) REVERT: D 325 GLN cc_start: 0.6232 (pm20) cc_final: 0.5387 (pp30) REVERT: D 518 ARG cc_start: 0.4021 (ttp80) cc_final: 0.3723 (tmt170) REVERT: D 535 TYR cc_start: 0.1816 (t80) cc_final: 0.0128 (p90) REVERT: E 22 GLU cc_start: 0.2735 (tt0) cc_final: 0.2389 (mm-30) REVERT: E 62 MET cc_start: 0.3192 (ttp) cc_final: 0.2811 (tpt) REVERT: E 144 LEU cc_start: 0.1821 (tm) cc_final: 0.1314 (pp) REVERT: E 246 ARG cc_start: 0.1912 (ptp-110) cc_final: 0.0348 (tmm-80) REVERT: E 249 MET cc_start: 0.3148 (ttm) cc_final: 0.2789 (tpp) REVERT: E 298 MET cc_start: 0.1313 (mmm) cc_final: 0.0625 (tmm) REVERT: E 323 MET cc_start: 0.4249 (tpt) cc_final: 0.3697 (tpp) REVERT: E 333 LEU cc_start: 0.3504 (mp) cc_final: 0.2523 (pt) REVERT: E 366 MET cc_start: 0.0242 (tpt) cc_final: -0.0196 (tpt) REVERT: E 482 ARG cc_start: 0.4886 (ptt90) cc_final: 0.4540 (mtt180) REVERT: E 546 ASN cc_start: 0.1827 (m110) cc_final: 0.1182 (t0) REVERT: E 564 GLU cc_start: 0.4231 (mp0) cc_final: 0.3897 (mt-10) outliers start: 45 outliers final: 30 residues processed: 212 average time/residue: 0.5627 time to fit residues: 148.7651 Evaluate side-chains 203 residues out of total 3790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 128 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 226 optimal weight: 0.9990 chunk 405 optimal weight: 20.0000 chunk 337 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 164 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 276 optimal weight: 0.6980 chunk 234 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.174075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.108290 restraints weight = 73612.303| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.96 r_work: 0.3185 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 36119 Z= 0.175 Angle : 0.598 13.113 49240 Z= 0.298 Chirality : 0.044 0.304 5588 Planarity : 0.004 0.042 6257 Dihedral : 4.358 51.897 4663 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.37 % Allowed : 15.41 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.13), residues: 4278 helix: 1.69 (0.14), residues: 1431 sheet: 0.41 (0.18), residues: 718 loop : -0.29 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 237 TYR 0.022 0.001 TYR B1067 PHE 0.026 0.001 PHE E 28 TRP 0.031 0.002 TRP B 353 HIS 0.011 0.001 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (36012) covalent geometry : angle 0.58692 / 0.30 (48965) SS BOND : bond 0.00278 / 0.17 ( 46) SS BOND : angle 1.12368 / 0.78 ( 92) hydrogen bonds : bond 0.04040 / 2.63 ( 1600) hydrogen bonds : angle 5.15207 / 3.64 ( 4773) link_BETA1-4 : bond 0.00290 / 0.19 ( 18) link_BETA1-4 : angle 0.97420 / 0.65 ( 54) link_NAG-ASN : bond 0.00309 / 0.20 ( 43) link_NAG-ASN : angle 2.12178 / 1.40 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27657.12 seconds wall clock time: 467 minutes 35.58 seconds (28055.58 seconds total)