Starting phenix.real_space_refine on Tue Aug 26 09:31:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm5_27527/08_2025/8dm5_27527.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm5_27527/08_2025/8dm5_27527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm5_27527/08_2025/8dm5_27527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm5_27527/08_2025/8dm5_27527.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm5_27527/08_2025/8dm5_27527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm5_27527/08_2025/8dm5_27527.cif" } resolution = 2.51 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 22511 2.51 5 N 5769 2.21 5 O 6824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35279 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 8192 Classifications: {'peptide': 1045} Link IDs: {'PTRANS': 55, 'TRANS': 989} Chain breaks: 8 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: 8192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 8192 Classifications: {'peptide': 1045} Link IDs: {'PTRANS': 55, 'TRANS': 989} Chain breaks: 8 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 21 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 dihedrals: 21 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 9.05, per 1000 atoms: 0.26 Number of scatterers: 35279 At special positions: 0 Unit cell: (137, 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 6824 8.00 N 5769 7.00 C 22511 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=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.02 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=2.03 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=2.03 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 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " 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: 3.57 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8142 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 52 sheets defined 38.1% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.866A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.713A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) 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: 4.052A 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: 3.644A 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: 3.881A 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: 4.020A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.099A 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: 3.725A 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 384 through 388 removed outlier: 3.514A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.298A 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: 4.001A 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: 3.633A 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: 3.653A 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: 3.709A 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: 3.890A 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: 3.935A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.121A 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: 4.017A 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: 3.888A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.575A 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: 3.829A 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: 3.624A 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: 4.059A 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: 3.745A 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: 3.927A 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: 4.044A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.138A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.217A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.622A pdb=" N SER D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 Proline residue: D 178 - end of helix removed outlier: 3.785A 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 221 through 252 removed outlier: 4.004A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.863A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.525A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.811A 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 397 through 413 removed outlier: 4.346A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.516A 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: 3.580A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.391A 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 Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.734A 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: 4.366A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.665A 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 559 removed outlier: 3.510A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (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 599 Processing helix chain 'E' and resid 20 through 53 Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.291A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.605A pdb=" N SER E 155 " --> pdb=" O ILE E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.788A 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 221 through 252 removed outlier: 3.990A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.875A 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: 3.514A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.821A 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 397 through 413 removed outlier: 4.336A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.555A 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: 3.564A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.421A 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 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.746A 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: 4.423A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.644A 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 559 removed outlier: 3.922A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (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 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.842A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.053A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.687A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.820A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.746A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.932A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.915A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.715A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.463A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.854A 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: 6.775A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.689A 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: 4.351A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.463A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.854A 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: 6.775A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.287A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.625A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 20 through 30 removed outlier: 7.874A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.002A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.669A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.759A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.874A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.721A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.604A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.467A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.467A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.324A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 20 through 30 removed outlier: 7.903A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.035A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.721A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.946A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.058A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.916A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.859A 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: 3.916A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.361A 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: 5.970A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.416A 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: 6.435A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.907A 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: 6.435A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.530A 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: 4.416A 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 262 through 263 removed outlier: 5.930A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.249A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.924A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.248A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1706 hydrogen bonds defined for protein. 4806 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: 10.86 Time building geometry restraints manager: 4.67 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: 11168 1.35 - 1.47: 9488 1.47 - 1.60: 15227 1.60 - 1.73: 0 1.73 - 1.85: 247 Bond restraints: 36130 Sorted by residual: bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.69e+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 6.53e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.44e+00 bond pdb=" C1 NAG D 706 " pdb=" O5 NAG D 706 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.25e+00 ... (remaining 36125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 47847 2.35 - 4.70: 1163 4.70 - 7.05: 98 7.05 - 9.39: 19 9.39 - 11.74: 8 Bond angle restraints: 49135 Sorted by residual: angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 122.46 129.81 -7.35 1.41e+00 5.03e-01 2.72e+01 angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 122.46 129.63 -7.17 1.41e+00 5.03e-01 2.58e+01 angle pdb=" N ALA B 372 " pdb=" CA ALA B 372 " pdb=" C ALA B 372 " ideal model delta sigma weight residual 109.81 120.54 -10.73 2.21e+00 2.05e-01 2.36e+01 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.46 129.21 -6.75 1.41e+00 5.03e-01 2.29e+01 angle pdb=" N ALA A 372 " pdb=" CA ALA A 372 " pdb=" C ALA A 372 " ideal model delta sigma weight residual 109.81 119.79 -9.98 2.21e+00 2.05e-01 2.04e+01 ... (remaining 49130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 20418 17.73 - 35.45: 1521 35.45 - 53.18: 317 53.18 - 70.90: 83 70.90 - 88.63: 36 Dihedral angle restraints: 22375 sinusoidal: 9733 harmonic: 12642 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 38.17 54.83 1 1.00e+01 1.00e-02 4.07e+01 dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual 93.00 38.98 54.02 1 1.00e+01 1.00e-02 3.96e+01 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 55.36 37.64 1 1.00e+01 1.00e-02 2.00e+01 ... (remaining 22372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4520 0.069 - 0.139: 1007 0.139 - 0.208: 106 0.208 - 0.277: 6 0.277 - 0.346: 1 Chirality restraints: 5640 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 -2.05 -0.35 2.00e-01 2.50e+01 3.00e+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 -2.34 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ASP B 198 " pdb=" N ASP B 198 " pdb=" C ASP B 198 " pdb=" CB ASP B 198 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 5637 not shown) Planarity restraints: 6312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 594 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C GLY A 594 " 0.059 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 GLY B 550 " 0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLY B 550 " -0.057 2.00e-02 2.50e+03 pdb=" O GLY B 550 " 0.022 2.00e-02 2.50e+03 pdb=" N VAL B 551 " 0.019 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 3.23e-02 1.05e+01 pdb=" C HIS A 954 " 0.056 2.00e-02 2.50e+03 pdb=" O HIS A 954 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN A 955 " -0.019 2.00e-02 2.50e+03 ... (remaining 6309 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9563 2.81 - 3.33: 30599 3.33 - 3.85: 60457 3.85 - 4.38: 69342 4.38 - 4.90: 120216 Nonbonded interactions: 290177 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.311 3.040 ... (remaining 290172 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 211 or resid 215 through 1307)) 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: 6.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 38.880 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.130 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:9.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 0.076 36245 Z= 0.246 Angle : 0.864 11.743 49434 Z= 0.475 Chirality : 0.056 0.346 5640 Planarity : 0.007 0.067 6261 Dihedral : 13.485 88.628 14095 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.50 % Allowed : 3.95 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.12), residues: 4272 helix: 1.10 (0.12), residues: 1429 sheet: 0.86 (0.18), residues: 691 loop : -0.66 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 273 TYR 0.038 0.002 TYR D 385 PHE 0.026 0.002 PHE C 371 TRP 0.035 0.002 TRP A 886 HIS 0.020 0.002 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00500 (36130) covalent geometry : angle 0.84991 (49135) SS BOND : bond 0.00463 ( 46) SS BOND : angle 1.53476 ( 92) hydrogen bonds : bond 0.12653 ( 1615) hydrogen bonds : angle 6.93364 ( 4806) link_BETA1-4 : bond 0.00716 ( 18) link_BETA1-4 : angle 1.68336 ( 54) link_NAG-ASN : bond 0.00405 ( 51) link_NAG-ASN : angle 2.62519 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 413 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6262 (p0) cc_final: 0.5695 (m110) REVERT: A 170 TYR cc_start: 0.7237 (t80) cc_final: 0.6904 (t80) REVERT: C 189 LEU cc_start: 0.8061 (tp) cc_final: 0.7516 (tt) REVERT: C 1141 LEU cc_start: 0.8583 (tt) cc_final: 0.8252 (tm) REVERT: D 94 LYS cc_start: 0.5515 (tttt) cc_final: 0.5093 (mmmm) REVERT: D 98 GLN cc_start: 0.6354 (mt0) cc_final: 0.5511 (tm-30) REVERT: D 121 ASN cc_start: 0.4828 (m-40) cc_final: 0.4447 (t0) REVERT: D 249 MET cc_start: 0.3229 (ttm) cc_final: 0.2480 (tmm) REVERT: D 309 LYS cc_start: 0.6333 (mmtt) cc_final: 0.6071 (tmmm) REVERT: D 323 MET cc_start: 0.0334 (mmm) cc_final: -0.1171 (mpm) REVERT: D 462 MET cc_start: 0.3618 (mtm) cc_final: 0.3316 (mmt) REVERT: D 484 ILE cc_start: -0.0187 (mt) cc_final: -0.1204 (mt) REVERT: D 526 GLN cc_start: 0.1938 (tp40) cc_final: 0.1585 (tp40) REVERT: D 579 MET cc_start: -0.1629 (mtm) cc_final: -0.2477 (mmm) REVERT: E 31 LYS cc_start: -0.0353 (tttt) cc_final: -0.1229 (pttp) REVERT: E 62 MET cc_start: 0.1151 (ttp) cc_final: 0.0095 (tmm) REVERT: E 183 TYR cc_start: -0.0526 (t80) cc_final: -0.0768 (t80) REVERT: E 199 TYR cc_start: -0.0849 (t80) cc_final: -0.1308 (t80) REVERT: E 249 MET cc_start: 0.3545 (ttm) cc_final: 0.3338 (mtm) REVERT: E 332 MET cc_start: -0.0793 (ttp) cc_final: -0.1905 (mpp) REVERT: E 364 VAL cc_start: 0.2758 (t) cc_final: 0.2428 (m) REVERT: E 515 TYR cc_start: 0.0593 (m-80) cc_final: 0.0007 (m-10) REVERT: E 557 MET cc_start: 0.1401 (tmm) cc_final: -0.0418 (mmp) REVERT: E 579 MET cc_start: -0.2542 (mtm) cc_final: -0.2935 (ptp) outliers start: 19 outliers final: 0 residues processed: 427 average time/residue: 0.7156 time to fit residues: 369.2394 Evaluate side-chains 199 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 30.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 755 GLN A 824 ASN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 30 ASN B 115 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 439 ASN B 613 GLN B 824 ASN C 23 GLN C 115 GLN C 321 GLN C 824 ASN C 926 GLN ** C 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 42 GLN D 61 ASN D 96 GLN D 374 HIS D 442 GLN D 522 GLN D 524 GLN D 599 ASN E 24 GLN E 42 GLN E 63 ASN E 96 GLN E 137 ASN E 175 GLN E 442 GLN E 522 GLN E 535 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.204841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.135845 restraints weight = 67877.116| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 4.44 r_work: 0.3180 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 36245 Z= 0.359 Angle : 0.766 24.455 49434 Z= 0.385 Chirality : 0.053 0.833 5640 Planarity : 0.005 0.048 6261 Dihedral : 6.831 58.455 6094 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.63 % Allowed : 9.07 % Favored : 89.30 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.12), residues: 4272 helix: 1.32 (0.13), residues: 1437 sheet: 0.66 (0.18), residues: 699 loop : -0.54 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 905 TYR 0.033 0.002 TYR A1067 PHE 0.032 0.003 PHE D 438 TRP 0.030 0.003 TRP B 886 HIS 0.009 0.002 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00830 (36130) covalent geometry : angle 0.73544 (49135) SS BOND : bond 0.00461 ( 46) SS BOND : angle 1.33820 ( 92) hydrogen bonds : bond 0.05463 ( 1615) hydrogen bonds : angle 5.66072 ( 4806) link_BETA1-4 : bond 0.00349 ( 18) link_BETA1-4 : angle 1.56442 ( 54) link_NAG-ASN : bond 0.00670 ( 51) link_NAG-ASN : angle 3.76103 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 216 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6597 (p0) cc_final: 0.6216 (m110) REVERT: A 170 TYR cc_start: 0.7538 (t80) cc_final: 0.7203 (t80) REVERT: A 342 PHE cc_start: 0.7623 (m-80) cc_final: 0.7337 (m-80) REVERT: A 1010 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: B 360 ASN cc_start: 0.6132 (OUTLIER) cc_final: 0.5362 (m-40) REVERT: B 697 MET cc_start: 0.9411 (ptt) cc_final: 0.9199 (ptt) REVERT: C 88 ASP cc_start: 0.7983 (m-30) cc_final: 0.7771 (p0) REVERT: C 205 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8063 (m) REVERT: C 564 GLN cc_start: 0.7281 (mm-40) cc_final: 0.7071 (mm-40) REVERT: C 740 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8616 (ttp) REVERT: D 98 GLN cc_start: 0.6535 (mt0) cc_final: 0.6035 (tm-30) REVERT: D 121 ASN cc_start: 0.4724 (m-40) cc_final: 0.4507 (t0) REVERT: D 249 MET cc_start: 0.2744 (ttm) cc_final: 0.2195 (tmm) REVERT: D 309 LYS cc_start: 0.5954 (mmtt) cc_final: 0.5690 (tmmm) REVERT: D 312 GLU cc_start: 0.4614 (tt0) cc_final: 0.4334 (mm-30) REVERT: D 581 VAL cc_start: 0.1568 (OUTLIER) cc_final: 0.1097 (t) REVERT: E 62 MET cc_start: 0.1168 (ttp) cc_final: 0.0424 (tmm) REVERT: E 165 TRP cc_start: 0.1060 (t60) cc_final: 0.0367 (t-100) REVERT: E 270 MET cc_start: 0.0439 (OUTLIER) cc_final: -0.1228 (tpp) REVERT: E 332 MET cc_start: -0.1491 (ttp) cc_final: -0.2087 (mmt) REVERT: E 376 MET cc_start: 0.0629 (tpt) cc_final: 0.0198 (tpt) REVERT: E 480 MET cc_start: 0.0874 (ppp) cc_final: -0.0698 (mpp) REVERT: E 557 MET cc_start: 0.1535 (tmm) cc_final: -0.0030 (mpp) REVERT: E 579 MET cc_start: -0.1283 (mtm) cc_final: -0.2491 (ptp) outliers start: 62 outliers final: 19 residues processed: 258 average time/residue: 0.6180 time to fit residues: 195.6489 Evaluate side-chains 182 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 270 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 120 optimal weight: 2.9990 chunk 232 optimal weight: 0.9990 chunk 324 optimal weight: 0.0470 chunk 373 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 285 optimal weight: 0.6980 chunk 313 optimal weight: 20.0000 chunk 288 optimal weight: 0.6980 chunk 186 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 856 ASN A 957 GLN B 125 ASN B 188 ASN B 360 ASN C 30 ASN C 321 GLN D 194 ASN D 374 HIS E 175 GLN E 374 HIS E 437 ASN E 442 GLN E 524 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.196172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.119438 restraints weight = 71823.659| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 4.00 r_work: 0.3252 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 36245 Z= 0.117 Angle : 0.577 12.560 49434 Z= 0.289 Chirality : 0.043 0.276 5640 Planarity : 0.004 0.062 6261 Dihedral : 6.123 59.949 6094 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.26 % Allowed : 10.86 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.12), residues: 4272 helix: 1.76 (0.13), residues: 1435 sheet: 0.67 (0.18), residues: 679 loop : -0.36 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 357 TYR 0.025 0.001 TYR B 170 PHE 0.033 0.001 PHE D 314 TRP 0.033 0.002 TRP D 328 HIS 0.006 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00244 (36130) covalent geometry : angle 0.55626 (49135) SS BOND : bond 0.00276 ( 46) SS BOND : angle 0.99406 ( 92) hydrogen bonds : bond 0.04285 ( 1615) hydrogen bonds : angle 5.25411 ( 4806) link_BETA1-4 : bond 0.00319 ( 18) link_BETA1-4 : angle 1.16673 ( 54) link_NAG-ASN : bond 0.00580 ( 51) link_NAG-ASN : angle 2.69008 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6542 (p0) cc_final: 0.6213 (m110) REVERT: A 170 TYR cc_start: 0.7597 (t80) cc_final: 0.7082 (t80) REVERT: A 1010 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: B 697 MET cc_start: 0.9430 (ptt) cc_final: 0.9183 (ptt) REVERT: B 1142 GLN cc_start: 0.8105 (tp40) cc_final: 0.7674 (tm-30) REVERT: C 88 ASP cc_start: 0.8074 (m-30) cc_final: 0.7746 (p0) REVERT: D 98 GLN cc_start: 0.6508 (mt0) cc_final: 0.5890 (tm-30) REVERT: D 121 ASN cc_start: 0.4725 (m-40) cc_final: 0.4476 (t0) REVERT: D 224 GLU cc_start: 0.1859 (OUTLIER) cc_final: 0.1404 (mp0) REVERT: D 309 LYS cc_start: 0.6180 (mmtt) cc_final: 0.5807 (tmmm) REVERT: D 360 MET cc_start: -0.0009 (tpt) cc_final: -0.0316 (tpp) REVERT: E 31 LYS cc_start: -0.1230 (tptp) cc_final: -0.1902 (tptp) REVERT: E 62 MET cc_start: 0.0936 (ttp) cc_final: 0.0112 (tmm) REVERT: E 82 MET cc_start: 0.3669 (ptt) cc_final: 0.2364 (mmt) REVERT: E 165 TRP cc_start: 0.0791 (t60) cc_final: 0.0383 (t-100) REVERT: E 270 MET cc_start: -0.0474 (OUTLIER) cc_final: -0.1765 (tpp) REVERT: E 332 MET cc_start: -0.1560 (ttp) cc_final: -0.2105 (mmt) REVERT: E 480 MET cc_start: 0.0594 (ppp) cc_final: -0.0782 (mpp) REVERT: E 512 PHE cc_start: 0.1384 (t80) cc_final: 0.0995 (t80) REVERT: E 521 TYR cc_start: 0.2712 (m-80) cc_final: 0.2185 (m-80) REVERT: E 557 MET cc_start: 0.1506 (tmm) cc_final: -0.0230 (mmp) REVERT: E 579 MET cc_start: -0.1699 (mtm) cc_final: -0.3258 (ptp) outliers start: 48 outliers final: 10 residues processed: 218 average time/residue: 0.5413 time to fit residues: 147.1256 Evaluate side-chains 174 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain E residue 270 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 306 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 274 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 393 optimal weight: 40.0000 chunk 15 optimal weight: 9.9990 chunk 368 optimal weight: 0.7980 chunk 282 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 173 GLN A 360 ASN A 755 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN D 374 HIS D 535 HIS E 442 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.198410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.124374 restraints weight = 70724.383| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 4.85 r_work: 0.3192 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 36245 Z= 0.180 Angle : 0.583 12.240 49434 Z= 0.293 Chirality : 0.044 0.198 5640 Planarity : 0.004 0.050 6261 Dihedral : 5.842 59.302 6094 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.63 % Allowed : 11.73 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.12), residues: 4272 helix: 1.74 (0.13), residues: 1434 sheet: 0.60 (0.18), residues: 687 loop : -0.30 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 357 TYR 0.023 0.001 TYR C1067 PHE 0.018 0.001 PHE C 565 TRP 0.022 0.002 TRP D 606 HIS 0.013 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00404 (36130) covalent geometry : angle 0.56378 (49135) SS BOND : bond 0.00289 ( 46) SS BOND : angle 0.99502 ( 92) hydrogen bonds : bond 0.04375 ( 1615) hydrogen bonds : angle 5.20001 ( 4806) link_BETA1-4 : bond 0.00210 ( 18) link_BETA1-4 : angle 1.26419 ( 54) link_NAG-ASN : bond 0.00450 ( 51) link_NAG-ASN : angle 2.57567 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 174 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6628 (p0) cc_final: 0.6344 (m110) REVERT: A 170 TYR cc_start: 0.7434 (t80) cc_final: 0.7166 (t80) REVERT: A 1010 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.7785 (mp10) REVERT: B 144 TYR cc_start: 0.3582 (p90) cc_final: 0.3292 (p90) REVERT: B 153 MET cc_start: 0.5111 (OUTLIER) cc_final: 0.4731 (pmm) REVERT: B 697 MET cc_start: 0.9411 (ptt) cc_final: 0.9206 (ptt) REVERT: B 869 MET cc_start: 0.9344 (mtm) cc_final: 0.8991 (mtp) REVERT: B 1141 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8011 (tm) REVERT: C 88 ASP cc_start: 0.7997 (m-30) cc_final: 0.7727 (p0) REVERT: C 200 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: C 205 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.7958 (m) REVERT: C 851 CYS cc_start: 0.6067 (m) cc_final: 0.5691 (p) REVERT: D 98 GLN cc_start: 0.6437 (mt0) cc_final: 0.5866 (tm-30) REVERT: D 121 ASN cc_start: 0.4645 (m-40) cc_final: 0.4396 (t0) REVERT: D 224 GLU cc_start: 0.1929 (OUTLIER) cc_final: 0.1485 (mp0) REVERT: D 309 LYS cc_start: 0.6080 (mmtt) cc_final: 0.5831 (tmmm) REVERT: D 312 GLU cc_start: 0.5208 (OUTLIER) cc_final: 0.4994 (mm-30) REVERT: D 323 MET cc_start: 0.1020 (OUTLIER) cc_final: -0.0318 (tpt) REVERT: D 360 MET cc_start: 0.0077 (tpt) cc_final: -0.0136 (tpp) REVERT: E 62 MET cc_start: 0.0960 (ttp) cc_final: 0.0226 (tmm) REVERT: E 82 MET cc_start: 0.3941 (OUTLIER) cc_final: 0.2748 (mmt) REVERT: E 165 TRP cc_start: 0.0819 (t60) cc_final: 0.0366 (t-100) REVERT: E 270 MET cc_start: -0.0333 (OUTLIER) cc_final: -0.1676 (tpp) REVERT: E 332 MET cc_start: -0.1227 (ttp) cc_final: -0.1717 (mmt) REVERT: E 480 MET cc_start: 0.0541 (ppp) cc_final: -0.0067 (mtp) REVERT: E 557 MET cc_start: 0.1551 (tmm) cc_final: -0.0242 (mmp) REVERT: E 579 MET cc_start: -0.1119 (mtm) cc_final: -0.2658 (ptp) outliers start: 62 outliers final: 17 residues processed: 217 average time/residue: 0.5974 time to fit residues: 165.0300 Evaluate side-chains 180 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 168 optimal weight: 1.9990 chunk 259 optimal weight: 0.4980 chunk 129 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 300 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 383 optimal weight: 1.9990 chunk 307 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 316 optimal weight: 30.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 907 ASN B 125 ASN B 907 ASN C 125 ASN E 442 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.195699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.122646 restraints weight = 71458.469| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 4.84 r_work: 0.3246 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 36245 Z= 0.118 Angle : 0.537 10.623 49434 Z= 0.269 Chirality : 0.043 0.210 5640 Planarity : 0.004 0.043 6261 Dihedral : 5.483 56.498 6094 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.47 % Allowed : 12.68 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.12), residues: 4272 helix: 1.85 (0.14), residues: 1430 sheet: 0.61 (0.18), residues: 682 loop : -0.23 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.027 0.001 TYR B 170 PHE 0.022 0.001 PHE A 855 TRP 0.024 0.001 TRP D 349 HIS 0.004 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00253 (36130) covalent geometry : angle 0.52033 (49135) SS BOND : bond 0.00278 ( 46) SS BOND : angle 0.89727 ( 92) hydrogen bonds : bond 0.03923 ( 1615) hydrogen bonds : angle 5.01423 ( 4806) link_BETA1-4 : bond 0.00311 ( 18) link_BETA1-4 : angle 1.16206 ( 54) link_NAG-ASN : bond 0.00318 ( 51) link_NAG-ASN : angle 2.27451 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 176 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7624 (t80) cc_final: 0.7241 (t80) REVERT: A 177 MET cc_start: 0.6739 (pmm) cc_final: 0.5520 (mmt) REVERT: B 533 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7609 (tt) REVERT: B 697 MET cc_start: 0.9389 (ptt) cc_final: 0.9172 (ptt) REVERT: B 869 MET cc_start: 0.9273 (mtm) cc_final: 0.9027 (mtp) REVERT: C 88 ASP cc_start: 0.7934 (m-30) cc_final: 0.7702 (p0) REVERT: C 851 CYS cc_start: 0.6120 (m) cc_final: 0.5715 (p) REVERT: C 983 ARG cc_start: 0.8267 (mtm110) cc_final: 0.8062 (tmm-80) REVERT: D 121 ASN cc_start: 0.4601 (m-40) cc_final: 0.4343 (t0) REVERT: D 224 GLU cc_start: 0.2070 (OUTLIER) cc_final: 0.1599 (mp0) REVERT: D 262 LEU cc_start: 0.0488 (OUTLIER) cc_final: 0.0272 (mm) REVERT: D 309 LYS cc_start: 0.6077 (mmtt) cc_final: 0.5823 (tmmm) REVERT: D 323 MET cc_start: 0.0773 (OUTLIER) cc_final: -0.1085 (tpt) REVERT: D 360 MET cc_start: -0.0118 (tpt) cc_final: -0.0381 (tpp) REVERT: D 383 MET cc_start: 0.5155 (ptm) cc_final: 0.4030 (ppp) REVERT: D 526 GLN cc_start: 0.2241 (tp40) cc_final: 0.2015 (pt0) REVERT: E 62 MET cc_start: 0.1135 (ttp) cc_final: 0.0273 (tmm) REVERT: E 82 MET cc_start: 0.3754 (OUTLIER) cc_final: 0.2468 (mmt) REVERT: E 332 MET cc_start: -0.1363 (ttp) cc_final: -0.1723 (mmt) REVERT: E 557 MET cc_start: 0.1385 (tmm) cc_final: -0.0252 (mmp) outliers start: 56 outliers final: 17 residues processed: 219 average time/residue: 0.6191 time to fit residues: 169.8571 Evaluate side-chains 177 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 300 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 291 optimal weight: 2.9990 chunk 322 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 401 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1010 GLN B 125 ASN C 314 GLN ** C 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN D 552 GLN E 442 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.201477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.136566 restraints weight = 67479.009| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 4.05 r_work: 0.3229 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 36245 Z= 0.224 Angle : 0.602 10.346 49434 Z= 0.303 Chirality : 0.045 0.223 5640 Planarity : 0.004 0.046 6261 Dihedral : 5.758 58.256 6094 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.71 % Allowed : 13.05 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.12), residues: 4272 helix: 1.73 (0.14), residues: 1431 sheet: 0.58 (0.18), residues: 681 loop : -0.30 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 273 TYR 0.023 0.002 TYR A1067 PHE 0.060 0.002 PHE C 855 TRP 0.038 0.002 TRP E 165 HIS 0.009 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00512 (36130) covalent geometry : angle 0.58365 (49135) SS BOND : bond 0.00308 ( 46) SS BOND : angle 0.99051 ( 92) hydrogen bonds : bond 0.04534 ( 1615) hydrogen bonds : angle 5.23541 ( 4806) link_BETA1-4 : bond 0.00437 ( 18) link_BETA1-4 : angle 1.34854 ( 54) link_NAG-ASN : bond 0.00491 ( 51) link_NAG-ASN : angle 2.51517 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 162 time to evaluate : 1.368 Fit side-chains REVERT: A 170 TYR cc_start: 0.7820 (t80) cc_final: 0.7559 (t80) REVERT: A 220 PHE cc_start: 0.7405 (t80) cc_final: 0.7064 (t80) REVERT: B 314 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8647 (tm-30) REVERT: B 533 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7712 (tt) REVERT: B 697 MET cc_start: 0.9465 (ptt) cc_final: 0.9182 (ptt) REVERT: B 869 MET cc_start: 0.9476 (mtm) cc_final: 0.9060 (mtp) REVERT: B 1141 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8034 (tm) REVERT: C 88 ASP cc_start: 0.8278 (m-30) cc_final: 0.7845 (p0) REVERT: C 983 ARG cc_start: 0.8316 (mtm110) cc_final: 0.8080 (tmm-80) REVERT: D 224 GLU cc_start: 0.1812 (OUTLIER) cc_final: 0.1348 (mp0) REVERT: D 309 LYS cc_start: 0.6012 (mmtt) cc_final: 0.5734 (tmmm) REVERT: D 312 GLU cc_start: 0.4990 (OUTLIER) cc_final: 0.4728 (mm-30) REVERT: D 323 MET cc_start: 0.1175 (OUTLIER) cc_final: -0.0550 (tpt) REVERT: D 383 MET cc_start: 0.4949 (ptm) cc_final: 0.4215 (ppp) REVERT: D 526 GLN cc_start: 0.2187 (tp40) cc_final: 0.1942 (pt0) REVERT: E 62 MET cc_start: 0.1227 (ttp) cc_final: 0.0466 (tmm) REVERT: E 82 MET cc_start: 0.4076 (OUTLIER) cc_final: 0.2948 (mmt) REVERT: E 332 MET cc_start: -0.1223 (ttp) cc_final: -0.1707 (mmt) REVERT: E 400 PHE cc_start: 0.0989 (m-10) cc_final: 0.0787 (m-80) REVERT: E 557 MET cc_start: 0.1313 (tmm) cc_final: -0.0316 (mmp) REVERT: E 579 MET cc_start: 0.0455 (ttt) cc_final: -0.2283 (ptp) outliers start: 65 outliers final: 24 residues processed: 213 average time/residue: 0.6544 time to fit residues: 172.6347 Evaluate side-chains 177 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 107 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 398 optimal weight: 4.9990 chunk 385 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 chunk 309 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 339 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 125 ASN B1010 GLN ** C 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN E 442 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.196148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.121173 restraints weight = 69766.996| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 5.33 r_work: 0.3209 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36245 Z= 0.127 Angle : 0.544 11.104 49434 Z= 0.273 Chirality : 0.043 0.191 5640 Planarity : 0.004 0.046 6261 Dihedral : 5.436 59.288 6094 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.39 % Allowed : 13.99 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.13), residues: 4272 helix: 1.83 (0.14), residues: 1428 sheet: 0.58 (0.18), residues: 671 loop : -0.24 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 403 TYR 0.064 0.001 TYR E 521 PHE 0.066 0.001 PHE C 855 TRP 0.033 0.001 TRP E 165 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00275 (36130) covalent geometry : angle 0.52872 (49135) SS BOND : bond 0.00247 ( 46) SS BOND : angle 0.89047 ( 92) hydrogen bonds : bond 0.03909 ( 1615) hydrogen bonds : angle 5.05233 ( 4806) link_BETA1-4 : bond 0.00244 ( 18) link_BETA1-4 : angle 1.13650 ( 54) link_NAG-ASN : bond 0.00326 ( 51) link_NAG-ASN : angle 2.22270 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 165 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7881 (t80) cc_final: 0.7522 (t80) REVERT: A 177 MET cc_start: 0.6720 (pmm) cc_final: 0.5413 (mmt) REVERT: A 220 PHE cc_start: 0.7380 (t80) cc_final: 0.7049 (t80) REVERT: B 533 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7718 (tt) REVERT: B 697 MET cc_start: 0.9404 (ptt) cc_final: 0.9152 (ptt) REVERT: B 869 MET cc_start: 0.9286 (mtm) cc_final: 0.9022 (mtp) REVERT: C 88 ASP cc_start: 0.8206 (m-30) cc_final: 0.7785 (p0) REVERT: D 171 GLU cc_start: 0.3810 (mm-30) cc_final: 0.3605 (pp20) REVERT: D 224 GLU cc_start: 0.1730 (OUTLIER) cc_final: 0.1281 (mp0) REVERT: D 309 LYS cc_start: 0.6091 (mmtt) cc_final: 0.5817 (tmmm) REVERT: D 312 GLU cc_start: 0.5026 (OUTLIER) cc_final: 0.4779 (mm-30) REVERT: D 323 MET cc_start: 0.1123 (OUTLIER) cc_final: -0.0642 (tpt) REVERT: D 383 MET cc_start: 0.4917 (ptm) cc_final: 0.4157 (ppp) REVERT: E 62 MET cc_start: 0.1212 (ttp) cc_final: 0.0444 (tmm) REVERT: E 82 MET cc_start: 0.3986 (OUTLIER) cc_final: 0.2713 (mmt) REVERT: E 332 MET cc_start: -0.1101 (ttp) cc_final: -0.1496 (mmt) REVERT: E 400 PHE cc_start: 0.0851 (m-10) cc_final: 0.0651 (m-80) REVERT: E 455 MET cc_start: 0.4292 (tpt) cc_final: 0.3837 (tmm) REVERT: E 521 TYR cc_start: 0.2180 (m-80) cc_final: 0.1933 (m-80) REVERT: E 557 MET cc_start: 0.1256 (tmm) cc_final: -0.0349 (mmp) REVERT: E 579 MET cc_start: -0.0493 (ttt) cc_final: -0.3627 (ptp) outliers start: 53 outliers final: 22 residues processed: 206 average time/residue: 0.6260 time to fit residues: 161.2528 Evaluate side-chains 174 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 111 optimal weight: 9.9990 chunk 282 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 330 optimal weight: 20.0000 chunk 302 optimal weight: 0.8980 chunk 340 optimal weight: 4.9990 chunk 286 optimal weight: 0.5980 chunk 344 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 907 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.193412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.120599 restraints weight = 70968.064| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 4.72 r_work: 0.3177 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 36245 Z= 0.201 Angle : 0.592 11.448 49434 Z= 0.297 Chirality : 0.045 0.213 5640 Planarity : 0.004 0.048 6261 Dihedral : 5.579 58.984 6094 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.39 % Allowed : 14.41 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.12), residues: 4272 helix: 1.83 (0.14), residues: 1418 sheet: 0.48 (0.18), residues: 667 loop : -0.27 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 983 TYR 0.041 0.002 TYR E 521 PHE 0.019 0.002 PHE D 28 TRP 0.033 0.002 TRP E 165 HIS 0.007 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00460 (36130) covalent geometry : angle 0.57591 (49135) SS BOND : bond 0.00366 ( 46) SS BOND : angle 0.94172 ( 92) hydrogen bonds : bond 0.04308 ( 1615) hydrogen bonds : angle 5.19110 ( 4806) link_BETA1-4 : bond 0.00242 ( 18) link_BETA1-4 : angle 1.30943 ( 54) link_NAG-ASN : bond 0.00446 ( 51) link_NAG-ASN : angle 2.37327 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 156 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7817 (t80) cc_final: 0.7534 (t80) REVERT: A 177 MET cc_start: 0.6769 (pmm) cc_final: 0.5420 (mmt) REVERT: A 220 PHE cc_start: 0.7422 (t80) cc_final: 0.7084 (t80) REVERT: B 314 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8597 (tm-30) REVERT: B 533 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7693 (tt) REVERT: B 697 MET cc_start: 0.9439 (ptt) cc_final: 0.9188 (ptt) REVERT: B 869 MET cc_start: 0.9389 (mtm) cc_final: 0.9020 (mtp) REVERT: B 1141 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7962 (tm) REVERT: C 88 ASP cc_start: 0.8236 (m-30) cc_final: 0.7838 (p0) REVERT: D 171 GLU cc_start: 0.3648 (mm-30) cc_final: 0.3444 (pp20) REVERT: D 224 GLU cc_start: 0.1880 (OUTLIER) cc_final: 0.1319 (mp0) REVERT: D 309 LYS cc_start: 0.6119 (mmtt) cc_final: 0.5794 (tmmm) REVERT: D 312 GLU cc_start: 0.5097 (OUTLIER) cc_final: 0.4888 (mm-30) REVERT: D 323 MET cc_start: 0.0819 (OUTLIER) cc_final: -0.0767 (tpt) REVERT: D 383 MET cc_start: 0.4601 (ptm) cc_final: 0.3854 (ppp) REVERT: E 62 MET cc_start: 0.1099 (ttp) cc_final: 0.0416 (tmt) REVERT: E 82 MET cc_start: 0.3711 (OUTLIER) cc_final: 0.2209 (mmt) REVERT: E 332 MET cc_start: -0.1330 (ttp) cc_final: -0.1530 (mmt) REVERT: E 521 TYR cc_start: 0.2137 (m-80) cc_final: 0.1699 (m-80) REVERT: E 557 MET cc_start: 0.1390 (tmm) cc_final: -0.0267 (mmp) REVERT: E 579 MET cc_start: -0.0837 (ttt) cc_final: -0.3746 (ptp) outliers start: 53 outliers final: 26 residues processed: 199 average time/residue: 0.6312 time to fit residues: 156.2318 Evaluate side-chains 185 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 293 optimal weight: 2.9990 chunk 180 optimal weight: 0.0670 chunk 96 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 304 optimal weight: 0.5980 chunk 209 optimal weight: 4.9990 chunk 401 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 206 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN E 442 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.193698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.121477 restraints weight = 71866.186| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.82 r_work: 0.3247 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36245 Z= 0.111 Angle : 0.551 10.766 49434 Z= 0.276 Chirality : 0.043 0.188 5640 Planarity : 0.004 0.050 6261 Dihedral : 5.242 59.606 6094 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.21 % Allowed : 14.65 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.13), residues: 4272 helix: 1.94 (0.14), residues: 1420 sheet: 0.52 (0.18), residues: 673 loop : -0.18 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.041 0.001 TYR E 521 PHE 0.056 0.001 PHE C 855 TRP 0.032 0.001 TRP E 165 HIS 0.004 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00237 (36130) covalent geometry : angle 0.53782 (49135) SS BOND : bond 0.00309 ( 46) SS BOND : angle 0.85568 ( 92) hydrogen bonds : bond 0.03788 ( 1615) hydrogen bonds : angle 4.99899 ( 4806) link_BETA1-4 : bond 0.00316 ( 18) link_BETA1-4 : angle 1.13207 ( 54) link_NAG-ASN : bond 0.00314 ( 51) link_NAG-ASN : angle 2.09275 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 167 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7801 (t80) cc_final: 0.7429 (t80) REVERT: A 171 VAL cc_start: 0.8270 (t) cc_final: 0.8035 (p) REVERT: A 177 MET cc_start: 0.6635 (pmm) cc_final: 0.5345 (mmt) REVERT: A 220 PHE cc_start: 0.7405 (t80) cc_final: 0.7095 (t80) REVERT: A 571 ASP cc_start: 0.8701 (t0) cc_final: 0.8340 (t0) REVERT: A 855 PHE cc_start: 0.7354 (m-80) cc_final: 0.7072 (t80) REVERT: B 18 LEU cc_start: 0.7204 (mm) cc_final: 0.6874 (mp) REVERT: B 314 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8595 (tm-30) REVERT: B 697 MET cc_start: 0.9387 (ptt) cc_final: 0.9128 (ptt) REVERT: B 869 MET cc_start: 0.9224 (mtm) cc_final: 0.9010 (mtp) REVERT: C 88 ASP cc_start: 0.8125 (m-30) cc_final: 0.7804 (p0) REVERT: D 57 GLU cc_start: 0.2414 (pm20) cc_final: 0.2112 (mt-10) REVERT: D 224 GLU cc_start: 0.1779 (OUTLIER) cc_final: 0.1254 (mp0) REVERT: D 309 LYS cc_start: 0.6113 (mmtt) cc_final: 0.5827 (tmmm) REVERT: D 312 GLU cc_start: 0.4996 (OUTLIER) cc_final: 0.4764 (mm-30) REVERT: D 323 MET cc_start: 0.1179 (OUTLIER) cc_final: -0.0620 (tpt) REVERT: D 383 MET cc_start: 0.4770 (ptm) cc_final: 0.3942 (ppp) REVERT: E 62 MET cc_start: 0.1172 (ttp) cc_final: 0.0478 (tmt) REVERT: E 82 MET cc_start: 0.3965 (OUTLIER) cc_final: 0.2652 (mmt) REVERT: E 332 MET cc_start: -0.1100 (ttp) cc_final: -0.1557 (mmt) REVERT: E 521 TYR cc_start: 0.1609 (m-80) cc_final: 0.1384 (m-80) REVERT: E 557 MET cc_start: 0.1133 (tmm) cc_final: -0.0431 (mmp) REVERT: E 579 MET cc_start: -0.0319 (ttt) cc_final: -0.3394 (ptp) outliers start: 46 outliers final: 22 residues processed: 204 average time/residue: 0.6500 time to fit residues: 164.9987 Evaluate side-chains 184 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 38 optimal weight: 9.9990 chunk 162 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 110 optimal weight: 0.0470 chunk 364 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 177 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 960 ASN D 373 HIS E 442 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.194393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.120320 restraints weight = 69599.157| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 4.82 r_work: 0.3209 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 36245 Z= 0.195 Angle : 0.603 12.486 49434 Z= 0.302 Chirality : 0.045 0.214 5640 Planarity : 0.004 0.049 6261 Dihedral : 5.403 58.935 6094 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.08 % Allowed : 14.91 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.13), residues: 4272 helix: 1.79 (0.14), residues: 1435 sheet: 0.49 (0.18), residues: 678 loop : -0.24 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.035 0.001 TYR E 521 PHE 0.027 0.002 PHE A 855 TRP 0.041 0.002 TRP E 165 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00445 (36130) covalent geometry : angle 0.58873 (49135) SS BOND : bond 0.00349 ( 46) SS BOND : angle 0.88825 ( 92) hydrogen bonds : bond 0.04250 ( 1615) hydrogen bonds : angle 5.17620 ( 4806) link_BETA1-4 : bond 0.00254 ( 18) link_BETA1-4 : angle 1.30727 ( 54) link_NAG-ASN : bond 0.00404 ( 51) link_NAG-ASN : angle 2.26707 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7925 (t80) cc_final: 0.7300 (t80) REVERT: A 177 MET cc_start: 0.6655 (pmm) cc_final: 0.5418 (mmt) REVERT: A 220 PHE cc_start: 0.7509 (t80) cc_final: 0.7143 (t80) REVERT: B 18 LEU cc_start: 0.7298 (mm) cc_final: 0.6961 (mp) REVERT: B 314 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8632 (tm-30) REVERT: B 697 MET cc_start: 0.9403 (ptt) cc_final: 0.9141 (ptt) REVERT: B 869 MET cc_start: 0.9385 (mtm) cc_final: 0.8991 (mtp) REVERT: C 88 ASP cc_start: 0.8267 (m-30) cc_final: 0.7809 (p0) REVERT: D 224 GLU cc_start: 0.1883 (OUTLIER) cc_final: 0.1341 (mp0) REVERT: D 309 LYS cc_start: 0.6262 (mmtt) cc_final: 0.5915 (tmmm) REVERT: D 312 GLU cc_start: 0.4909 (OUTLIER) cc_final: 0.4654 (mm-30) REVERT: D 323 MET cc_start: 0.1389 (OUTLIER) cc_final: -0.0608 (tpt) REVERT: D 383 MET cc_start: 0.4752 (ptm) cc_final: 0.3953 (ppp) REVERT: E 62 MET cc_start: 0.1127 (ttp) cc_final: 0.0431 (tmt) REVERT: E 82 MET cc_start: 0.3798 (OUTLIER) cc_final: 0.2344 (mmt) REVERT: E 332 MET cc_start: -0.1241 (ttp) cc_final: -0.1544 (mmt) REVERT: E 521 TYR cc_start: 0.1796 (m-80) cc_final: 0.1540 (m-80) REVERT: E 557 MET cc_start: 0.1134 (tmm) cc_final: -0.0366 (mmp) REVERT: E 579 MET cc_start: -0.0667 (ttt) cc_final: -0.3542 (ptp) outliers start: 41 outliers final: 22 residues processed: 192 average time/residue: 0.6095 time to fit residues: 148.0199 Evaluate side-chains 178 residues out of total 3802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 349 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 362 optimal weight: 3.9990 chunk 292 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 263 optimal weight: 0.3980 chunk 420 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.192287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.118722 restraints weight = 71036.942| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.74 r_work: 0.3201 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 36245 Z= 0.181 Angle : 0.604 16.736 49434 Z= 0.301 Chirality : 0.045 0.224 5640 Planarity : 0.004 0.049 6261 Dihedral : 5.449 59.641 6094 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.05 % Allowed : 15.15 % Favored : 83.80 % 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 aren not related in a simple way. whole: 0.77 (0.13), residues: 4272 helix: 1.76 (0.14), residues: 1430 sheet: 0.40 (0.18), residues: 682 loop : -0.26 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.040 0.001 TYR E 127 PHE 0.065 0.001 PHE C 855 TRP 0.039 0.002 TRP E 165 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00412 (36130) covalent geometry : angle 0.59092 (49135) SS BOND : bond 0.00340 ( 46) SS BOND : angle 0.91240 ( 92) hydrogen bonds : bond 0.04165 ( 1615) hydrogen bonds : angle 5.17452 ( 4806) link_BETA1-4 : bond 0.00297 ( 18) link_BETA1-4 : angle 1.23467 ( 54) link_NAG-ASN : bond 0.00356 ( 51) link_NAG-ASN : angle 2.19819 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26207.25 seconds wall clock time: 444 minutes 1.96 seconds (26641.96 seconds total)