Starting phenix.real_space_refine on Mon Jul 6 06:34:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nd7_12278/07_2026/7nd7_12278.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nd7_12278/07_2026/7nd7_12278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nd7_12278/07_2026/7nd7_12278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nd7_12278/07_2026/7nd7_12278.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7nd7_12278/07_2026/7nd7_12278.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nd7_12278/07_2026/7nd7_12278.cif" model { file = "/net/cci-nas-00/data/ceres_data/7nd7_12278/07_2026/7nd7_12278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nd7_12278/07_2026/7nd7_12278.cif" } resolution = 3.6 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= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4620 atoms to isotropic. 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 138 5.16 5 C 18767 2.51 5 N 4858 2.21 5 O 5828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29591 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "F" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "K" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.23, per 1000 atoms: 0.24 Number of scatterers: 29591 At special positions: 0 Unit cell: (139.4, 137.76, 198.44, 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 138 16.00 O 5828 8.00 N 4858 7.00 C 18767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 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=2.02 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 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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 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=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 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 X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " BETA1-6 " NAG Y 1 " - " FUC Y 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Z 1 " - " FUC Z 3 " " NAG a 1 " - " FUC a 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " " NAG Y 1 " - " ASN H 59 " " NAG Z 1 " - " ASN F 59 " " NAG a 1 " - " ASN J 59 " Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.3 seconds 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6858 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 63 sheets defined 23.0% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.848A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.404A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.631A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 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: 3.686A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.138A 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 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.886A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.650A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.101A 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 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.834A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.401A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.627A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 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: 3.694A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.102A 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 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.870A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.650A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.097A 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 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.821A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.401A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.635A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 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: 3.700A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.153A 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 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.896A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.655A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.090A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 81 through 85 Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.611A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.007A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 4.122A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.164A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.742A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.228A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.672A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.267A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) 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 654 through 655 removed outlier: 6.128A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.898A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.642A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.642A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.622A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.614A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.136A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.185A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.753A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.250A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.698A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.280A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.564A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.848A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.697A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.697A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.668A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.619A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 52 removed outlier: 7.026A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.215A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.714A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.257A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.249A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.564A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.536A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.536A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.639A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.662A pdb=" N TYR H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.957A pdb=" N TYR H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N MET H 100 " --> pdb=" O PHE H 109 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE H 109 " --> pdb=" O MET H 100 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.504A pdb=" N ALA L 86 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.504A pdb=" N ALA L 86 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.724A pdb=" N TYR F 33 " --> pdb=" O ASP F 99 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.984A pdb=" N TYR F 111 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N MET F 100 " --> pdb=" O PHE F 109 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N PHE F 109 " --> pdb=" O MET F 100 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.178A pdb=" N GLN G 39 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU G 48 " --> pdb=" O GLN G 39 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 9 through 12 Processing sheet with id=AG3, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AG4, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.710A pdb=" N TYR J 33 " --> pdb=" O ASP J 99 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.974A pdb=" N TYR J 111 " --> pdb=" O ARG J 98 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N MET J 100 " --> pdb=" O PHE J 109 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE J 109 " --> pdb=" O MET J 100 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.170A pdb=" N GLN K 39 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU K 48 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 9 through 12 Processing sheet with id=AG9, first strand: chain 'K' and resid 18 through 23 1237 hydrogen bonds defined for protein. 3294 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: 8.06 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9406 1.35 - 1.47: 7716 1.47 - 1.59: 12942 1.59 - 1.71: 1 1.71 - 1.83: 183 Bond restraints: 30248 Sorted by residual: bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.77e+00 bond pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.57e+00 ... (remaining 30243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 40911 2.93 - 5.87: 217 5.87 - 8.80: 8 8.80 - 11.73: 0 11.73 - 14.67: 1 Bond angle restraints: 41137 Sorted by residual: angle pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CD PRO C 527 " ideal model delta sigma weight residual 125.00 110.33 14.67 4.10e+00 5.95e-02 1.28e+01 angle pdb=" C VAL K 53 " pdb=" N SER K 54 " pdb=" CA SER K 54 " ideal model delta sigma weight residual 121.99 116.76 5.23 1.56e+00 4.11e-01 1.12e+01 angle pdb=" CA TYR C 904 " pdb=" CB TYR C 904 " pdb=" CG TYR C 904 " ideal model delta sigma weight residual 113.90 119.73 -5.83 1.80e+00 3.09e-01 1.05e+01 angle pdb=" CA TYR A 904 " pdb=" CB TYR A 904 " pdb=" CG TYR A 904 " ideal model delta sigma weight residual 113.90 119.71 -5.81 1.80e+00 3.09e-01 1.04e+01 angle pdb=" CA CYS C 760 " pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 114.40 121.79 -7.39 2.30e+00 1.89e-01 1.03e+01 ... (remaining 41132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 16584 17.54 - 35.09: 658 35.09 - 52.63: 117 52.63 - 70.18: 53 70.18 - 87.72: 30 Dihedral angle restraints: 17442 sinusoidal: 6744 harmonic: 10698 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -168.83 82.83 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -168.56 82.56 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -168.39 82.39 1 1.00e+01 1.00e-02 8.33e+01 ... (remaining 17439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3691 0.049 - 0.099: 843 0.099 - 0.148: 277 0.148 - 0.197: 3 0.197 - 0.247: 9 Chirality restraints: 4823 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN F 59 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN H 59 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA GLU K 52 " pdb=" N GLU K 52 " pdb=" C GLU K 52 " pdb=" CB GLU K 52 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 4820 not shown) Planarity restraints: 5273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " -0.107 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO C 527 " 0.283 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " -0.094 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " -0.058 5.00e-02 4.00e+02 8.79e-02 1.24e+01 pdb=" N PRO B 527 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 881 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C THR A 881 " -0.060 2.00e-02 2.50e+03 pdb=" O THR A 881 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 882 " 0.020 2.00e-02 2.50e+03 ... (remaining 5270 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4376 2.76 - 3.30: 27242 3.30 - 3.83: 49572 3.83 - 4.37: 58626 4.37 - 4.90: 101890 Nonbonded interactions: 241706 Sorted by model distance: nonbonded pdb=" O LEU B 492 " pdb=" ND2 ASN F 54 " model vdw 2.229 3.120 nonbonded pdb=" OG SER B1123 " pdb=" OD1 ASN C 914 " model vdw 2.270 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OD1 ASN B 914 " model vdw 2.298 3.040 nonbonded pdb=" O LEU C 492 " pdb=" ND2 ASN J 54 " model vdw 2.302 3.120 nonbonded pdb=" O LEU A 492 " pdb=" ND2 ASN H 54 " model vdw 2.304 3.120 ... (remaining 241701 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 27 through 1308) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' 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' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.590 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 30357 Z= 0.177 Angle : 0.638 14.667 41419 Z= 0.345 Chirality : 0.046 0.247 4823 Planarity : 0.004 0.164 5230 Dihedral : 10.997 87.722 10449 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.65 % Favored : 96.15 % Rotamer: Outliers : 0.38 % Allowed : 2.19 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 3639 helix: 0.18 (0.18), residues: 711 sheet: 0.10 (0.15), residues: 1041 loop : -0.15 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 815 TYR 0.017 0.001 TYR A1067 PHE 0.020 0.001 PHE B 329 TRP 0.011 0.001 TRP J 50 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (30248) covalent geometry : angle 0.63223 / 0.34 (41137) SS BOND : bond 0.00309 / 0.20 ( 45) SS BOND : angle 1.11081 / 0.70 ( 90) hydrogen bonds : bond 0.18512 / 12.19 ( 1181) hydrogen bonds : angle 7.88916 / 5.52 ( 3294) link_BETA1-4 : bond 0.00257 / 0.14 ( 18) link_BETA1-4 : angle 1.06442 / 0.74 ( 54) link_BETA1-6 : bond 0.00631 / 0.27 ( 3) link_BETA1-6 : angle 1.47857 / 0.85 ( 9) link_NAG-ASN : bond 0.00195 / 0.13 ( 43) link_NAG-ASN : angle 1.37431 / 0.98 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 757 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8615 (mt) cc_final: 0.8080 (mp) REVERT: A 392 PHE cc_start: 0.7065 (m-80) cc_final: 0.6843 (m-80) REVERT: A 513 LEU cc_start: 0.8680 (mt) cc_final: 0.8450 (mp) REVERT: A 902 MET cc_start: 0.7829 (mmm) cc_final: 0.7048 (mmm) REVERT: A 904 TYR cc_start: 0.5283 (m-10) cc_final: 0.4916 (m-10) REVERT: A 1037 SER cc_start: 0.7037 (t) cc_final: 0.6807 (t) REVERT: A 1122 VAL cc_start: 0.8289 (t) cc_final: 0.8089 (p) REVERT: B 88 ASP cc_start: 0.8350 (m-30) cc_final: 0.8129 (t0) REVERT: B 269 TYR cc_start: 0.6673 (m-80) cc_final: 0.6401 (m-80) REVERT: B 490 PHE cc_start: 0.8061 (t80) cc_final: 0.7201 (t80) REVERT: B 492 LEU cc_start: 0.8762 (mt) cc_final: 0.8405 (mt) REVERT: B 513 LEU cc_start: 0.8869 (mt) cc_final: 0.8635 (mp) REVERT: B 756 TYR cc_start: 0.8622 (m-80) cc_final: 0.8133 (m-80) REVERT: B 1029 MET cc_start: 0.8235 (tpp) cc_final: 0.7958 (tpp) REVERT: C 54 LEU cc_start: 0.8581 (mt) cc_final: 0.8056 (mt) REVERT: C 92 PHE cc_start: 0.6167 (t80) cc_final: 0.5161 (t80) REVERT: C 396 TYR cc_start: 0.5856 (m-80) cc_final: 0.4702 (m-10) REVERT: C 398 ASP cc_start: 0.6748 (m-30) cc_final: 0.6461 (m-30) REVERT: C 902 MET cc_start: 0.7392 (mmm) cc_final: 0.6622 (mmm) REVERT: H 76 ILE cc_start: 0.8989 (pt) cc_final: 0.8743 (pt) outliers start: 12 outliers final: 0 residues processed: 767 average time/residue: 0.1985 time to fit residues: 238.6116 Evaluate side-chains 373 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 450 ASN B1010 GLN B1011 GLN C 321 GLN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 762 GLN C 872 GLN C1010 GLN C1106 GLN C1135 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.188001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.149432 restraints weight = 57214.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.145184 restraints weight = 70487.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.142289 restraints weight = 48630.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.141127 restraints weight = 53080.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.141919 restraints weight = 48584.967| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 30357 Z= 0.164 Angle : 0.671 11.098 41419 Z= 0.344 Chirality : 0.047 0.211 4823 Planarity : 0.005 0.147 5230 Dihedral : 4.309 27.389 3963 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.79 % Favored : 98.19 % Rotamer: Outliers : 2.03 % Allowed : 9.17 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.13), residues: 3639 helix: 1.55 (0.20), residues: 699 sheet: 0.37 (0.15), residues: 1017 loop : -0.13 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1014 TYR 0.021 0.002 TYR G 88 PHE 0.030 0.002 PHE C 515 TRP 0.022 0.002 TRP A 104 HIS 0.008 0.001 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (30248) covalent geometry : angle 0.65849 / 0.34 (41137) SS BOND : bond 0.00403 / 0.26 ( 45) SS BOND : angle 2.02769 / 1.15 ( 90) hydrogen bonds : bond 0.04542 / 3.02 ( 1181) hydrogen bonds : angle 6.49423 / 4.54 ( 3294) link_BETA1-4 : bond 0.00639 / 0.34 ( 18) link_BETA1-4 : angle 1.19685 / 0.80 ( 54) link_BETA1-6 : bond 0.00946 / 0.39 ( 3) link_BETA1-6 : angle 1.51049 / 0.89 ( 9) link_NAG-ASN : bond 0.00321 / 0.19 ( 43) link_NAG-ASN : angle 1.62455 / 1.10 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 429 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8195 (p) cc_final: 0.7863 (t) REVERT: A 269 TYR cc_start: 0.6918 (m-80) cc_final: 0.6702 (m-80) REVERT: A 492 LEU cc_start: 0.8742 (mt) cc_final: 0.8431 (tp) REVERT: A 606 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7829 (t0) REVERT: A 902 MET cc_start: 0.7718 (mmm) cc_final: 0.6887 (mmm) REVERT: A 1037 SER cc_start: 0.7522 (t) cc_final: 0.7270 (t) REVERT: B 88 ASP cc_start: 0.7936 (m-30) cc_final: 0.7621 (t0) REVERT: B 293 LEU cc_start: 0.8209 (tt) cc_final: 0.7649 (tt) REVERT: B 490 PHE cc_start: 0.7910 (t80) cc_final: 0.7169 (t80) REVERT: B 492 LEU cc_start: 0.8716 (mt) cc_final: 0.8502 (mt) REVERT: B 756 TYR cc_start: 0.8775 (m-80) cc_final: 0.8070 (m-80) REVERT: C 42 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8736 (m) REVERT: C 425 LEU cc_start: 0.8450 (mp) cc_final: 0.8249 (mt) REVERT: C 902 MET cc_start: 0.7167 (mmm) cc_final: 0.6684 (mmm) REVERT: C 945 LEU cc_start: 0.8795 (mm) cc_final: 0.8563 (mt) REVERT: F 73 ASP cc_start: 0.6964 (t0) cc_final: 0.6591 (t0) REVERT: J 73 ASP cc_start: 0.6871 (t0) cc_final: 0.6414 (t0) outliers start: 65 outliers final: 33 residues processed: 474 average time/residue: 0.1874 time to fit residues: 139.6911 Evaluate side-chains 365 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 330 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain K residue 3 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 16 optimal weight: 0.1980 chunk 232 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 215 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 224 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 354 ASN B 450 ASN B 613 GLN B 955 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.186703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.146404 restraints weight = 57175.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.141921 restraints weight = 66604.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.136407 restraints weight = 45063.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.136807 restraints weight = 48508.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.137629 restraints weight = 42646.605| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30357 Z= 0.145 Angle : 0.624 9.196 41419 Z= 0.316 Chirality : 0.046 0.266 4823 Planarity : 0.004 0.128 5230 Dihedral : 4.334 23.687 3963 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.17 % Favored : 97.80 % Rotamer: Outliers : 2.00 % Allowed : 11.33 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3639 helix: 1.52 (0.20), residues: 720 sheet: 0.36 (0.15), residues: 1029 loop : -0.10 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 466 TYR 0.020 0.002 TYR K 89 PHE 0.022 0.001 PHE C 515 TRP 0.030 0.002 TRP C 104 HIS 0.004 0.001 HIS G 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (30248) covalent geometry : angle 0.61589 / 0.31 (41137) SS BOND : bond 0.00544 / 0.30 ( 45) SS BOND : angle 1.41284 / 0.89 ( 90) hydrogen bonds : bond 0.04038 / 2.69 ( 1181) hydrogen bonds : angle 6.19160 / 4.31 ( 3294) link_BETA1-4 : bond 0.00331 / 0.18 ( 18) link_BETA1-4 : angle 1.01649 / 0.70 ( 54) link_BETA1-6 : bond 0.00709 / 0.31 ( 3) link_BETA1-6 : angle 1.41383 / 0.84 ( 9) link_NAG-ASN : bond 0.00305 / 0.18 ( 43) link_NAG-ASN : angle 1.44431 / 0.98 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 358 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8240 (p) cc_final: 0.7832 (t) REVERT: A 269 TYR cc_start: 0.7077 (m-80) cc_final: 0.6785 (m-80) REVERT: A 365 TYR cc_start: 0.7361 (m-80) cc_final: 0.7155 (m-10) REVERT: A 511 VAL cc_start: 0.7747 (t) cc_final: 0.7546 (m) REVERT: A 606 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.7982 (t0) REVERT: A 740 MET cc_start: 0.8085 (ttt) cc_final: 0.7827 (ttm) REVERT: A 902 MET cc_start: 0.8080 (mmm) cc_final: 0.7204 (mmm) REVERT: A 1037 SER cc_start: 0.7665 (t) cc_final: 0.7402 (t) REVERT: B 90 VAL cc_start: 0.8101 (m) cc_final: 0.7808 (t) REVERT: B 269 TYR cc_start: 0.7017 (m-80) cc_final: 0.6583 (m-80) REVERT: B 466 ARG cc_start: 0.6784 (mtp180) cc_final: 0.6330 (mtp85) REVERT: B 490 PHE cc_start: 0.8052 (t80) cc_final: 0.7243 (t80) REVERT: B 492 LEU cc_start: 0.8894 (mt) cc_final: 0.8600 (mt) REVERT: B 756 TYR cc_start: 0.8809 (m-80) cc_final: 0.8068 (m-80) REVERT: C 42 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8763 (m) REVERT: C 189 LEU cc_start: 0.8065 (tp) cc_final: 0.7794 (tt) REVERT: C 291 CYS cc_start: 0.6255 (m) cc_final: 0.5967 (m) REVERT: C 492 LEU cc_start: 0.8535 (mt) cc_final: 0.8274 (tp) REVERT: C 787 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7820 (mp10) REVERT: C 902 MET cc_start: 0.7185 (mmm) cc_final: 0.6606 (mmm) REVERT: C 945 LEU cc_start: 0.8826 (mm) cc_final: 0.8553 (mt) REVERT: H 73 ASP cc_start: 0.6976 (t0) cc_final: 0.6680 (t0) REVERT: F 73 ASP cc_start: 0.7851 (t0) cc_final: 0.7381 (t0) REVERT: G 3 VAL cc_start: 0.5617 (OUTLIER) cc_final: 0.5396 (p) REVERT: J 70 MET cc_start: 0.1656 (mtt) cc_final: 0.0634 (mtt) REVERT: J 73 ASP cc_start: 0.7302 (t0) cc_final: 0.6884 (t0) outliers start: 64 outliers final: 41 residues processed: 404 average time/residue: 0.1737 time to fit residues: 112.2170 Evaluate side-chains 372 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 327 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 89 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 12 optimal weight: 0.8980 chunk 323 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 chunk 265 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 272 optimal weight: 0.7980 chunk 331 optimal weight: 20.0000 chunk 29 optimal weight: 0.4980 chunk 180 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1005 GLN B 52 GLN B 450 ASN C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.185472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.149183 restraints weight = 57612.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.143992 restraints weight = 80234.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.140676 restraints weight = 70135.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.141672 restraints weight = 60544.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.141769 restraints weight = 47604.932| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30357 Z= 0.146 Angle : 0.601 10.670 41419 Z= 0.304 Chirality : 0.045 0.258 4823 Planarity : 0.004 0.052 5230 Dihedral : 4.279 23.593 3963 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.47 % Allowed : 11.83 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3639 helix: 1.52 (0.20), residues: 720 sheet: 0.25 (0.15), residues: 1053 loop : -0.05 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 38 TYR 0.021 0.002 TYR L 89 PHE 0.025 0.001 PHE F 109 TRP 0.016 0.002 TRP H 47 HIS 0.010 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (30248) covalent geometry : angle 0.59378 / 0.30 (41137) SS BOND : bond 0.00451 / 0.31 ( 45) SS BOND : angle 1.27632 / 0.82 ( 90) hydrogen bonds : bond 0.03841 / 2.55 ( 1181) hydrogen bonds : angle 6.00751 / 4.20 ( 3294) link_BETA1-4 : bond 0.00325 / 0.18 ( 18) link_BETA1-4 : angle 0.97973 / 0.68 ( 54) link_BETA1-6 : bond 0.00601 / 0.26 ( 3) link_BETA1-6 : angle 1.56201 / 0.93 ( 9) link_NAG-ASN : bond 0.00249 / 0.16 ( 43) link_NAG-ASN : angle 1.31779 / 0.91 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 344 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7896 (t0) REVERT: A 902 MET cc_start: 0.7856 (mmm) cc_final: 0.7187 (mmm) REVERT: A 1037 SER cc_start: 0.7987 (t) cc_final: 0.7158 (p) REVERT: B 90 VAL cc_start: 0.8190 (m) cc_final: 0.7948 (t) REVERT: B 490 PHE cc_start: 0.7480 (t80) cc_final: 0.6983 (t80) REVERT: B 756 TYR cc_start: 0.8756 (m-80) cc_final: 0.8002 (m-80) REVERT: B 948 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8073 (mt) REVERT: C 42 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8689 (m) REVERT: C 109 THR cc_start: 0.7249 (p) cc_final: 0.7041 (p) REVERT: C 189 LEU cc_start: 0.7509 (tp) cc_final: 0.7269 (tt) REVERT: C 332 ILE cc_start: 0.6867 (mp) cc_final: 0.6659 (tp) REVERT: C 365 TYR cc_start: 0.6801 (m-80) cc_final: 0.6508 (m-80) REVERT: C 902 MET cc_start: 0.7535 (mmm) cc_final: 0.6630 (mmm) REVERT: C 992 GLN cc_start: 0.7965 (mp10) cc_final: 0.7707 (mp10) REVERT: L 49 MET cc_start: 0.3708 (tpp) cc_final: 0.3420 (ttm) REVERT: G 3 VAL cc_start: 0.4736 (OUTLIER) cc_final: 0.4468 (p) outliers start: 79 outliers final: 48 residues processed: 403 average time/residue: 0.1868 time to fit residues: 120.1623 Evaluate side-chains 343 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 291 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 32 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 5.9990 chunk 301 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 348 optimal weight: 1.9990 chunk 282 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 322 optimal weight: 0.7980 chunk 254 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 493 GLN C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.185215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.148468 restraints weight = 57298.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.144959 restraints weight = 85669.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.141501 restraints weight = 67674.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.142107 restraints weight = 63026.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.142274 restraints weight = 48857.010| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 30357 Z= 0.147 Angle : 0.596 15.220 41419 Z= 0.302 Chirality : 0.045 0.223 4823 Planarity : 0.004 0.045 5230 Dihedral : 4.266 25.542 3963 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.64 % Rotamer: Outliers : 2.50 % Allowed : 12.86 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3639 helix: 1.71 (0.21), residues: 696 sheet: 0.29 (0.16), residues: 1047 loop : -0.14 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1107 TYR 0.016 0.002 TYR A1067 PHE 0.017 0.001 PHE B 192 TRP 0.015 0.002 TRP J 47 HIS 0.004 0.001 HIS G 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (30248) covalent geometry : angle 0.58507 / 0.30 (41137) SS BOND : bond 0.00467 / 0.29 ( 45) SS BOND : angle 1.96590 / 1.07 ( 90) hydrogen bonds : bond 0.03769 / 2.48 ( 1181) hydrogen bonds : angle 5.91747 / 4.13 ( 3294) link_BETA1-4 : bond 0.00289 / 0.16 ( 18) link_BETA1-4 : angle 0.95940 / 0.66 ( 54) link_BETA1-6 : bond 0.00632 / 0.28 ( 3) link_BETA1-6 : angle 1.53346 / 0.91 ( 9) link_NAG-ASN : bond 0.00229 / 0.14 ( 43) link_NAG-ASN : angle 1.25743 / 0.87 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 318 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 ASN cc_start: 0.8371 (t0) cc_final: 0.7892 (t0) REVERT: A 902 MET cc_start: 0.8462 (mmm) cc_final: 0.7780 (mmm) REVERT: A 1037 SER cc_start: 0.7956 (t) cc_final: 0.7642 (t) REVERT: A 1104 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8654 (p) REVERT: B 90 VAL cc_start: 0.8135 (m) cc_final: 0.7902 (t) REVERT: B 301 CYS cc_start: 0.7250 (OUTLIER) cc_final: 0.7012 (m) REVERT: B 490 PHE cc_start: 0.7459 (t80) cc_final: 0.7001 (t80) REVERT: B 492 LEU cc_start: 0.7951 (mt) cc_final: 0.7654 (mm) REVERT: B 756 TYR cc_start: 0.8799 (m-80) cc_final: 0.8129 (m-80) REVERT: B 948 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7937 (mt) REVERT: C 189 LEU cc_start: 0.7484 (tp) cc_final: 0.7260 (tt) REVERT: C 231 ILE cc_start: 0.7763 (mm) cc_final: 0.7476 (tt) REVERT: C 365 TYR cc_start: 0.6782 (m-80) cc_final: 0.6507 (m-80) REVERT: C 450 ASN cc_start: 0.8111 (m110) cc_final: 0.7334 (t0) REVERT: C 740 MET cc_start: 0.8103 (ttt) cc_final: 0.7881 (ttt) REVERT: C 902 MET cc_start: 0.7743 (mmm) cc_final: 0.6800 (mmm) REVERT: C 992 GLN cc_start: 0.7988 (mp10) cc_final: 0.7706 (mp10) REVERT: L 34 TYR cc_start: 0.0353 (m-80) cc_final: -0.0054 (m-80) REVERT: L 49 MET cc_start: 0.3904 (tpp) cc_final: 0.3171 (ttm) REVERT: G 3 VAL cc_start: 0.5086 (OUTLIER) cc_final: 0.4833 (p) REVERT: K 37 TRP cc_start: 0.3795 (m100) cc_final: 0.3006 (m100) outliers start: 80 outliers final: 59 residues processed: 380 average time/residue: 0.1840 time to fit residues: 112.7674 Evaluate side-chains 350 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 287 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 89 TYR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 23 optimal weight: 5.9990 chunk 291 optimal weight: 0.8980 chunk 336 optimal weight: 10.0000 chunk 276 optimal weight: 0.8980 chunk 312 optimal weight: 0.0030 chunk 211 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 184 optimal weight: 0.4980 chunk 365 optimal weight: 9.9990 chunk 266 optimal weight: 1.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 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 = 0.4541 r_free = 0.4541 target = 0.184395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.142494 restraints weight = 56805.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.139186 restraints weight = 64923.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.132316 restraints weight = 46254.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.132520 restraints weight = 44778.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.133134 restraints weight = 39375.247| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 30357 Z= 0.147 Angle : 0.582 10.509 41419 Z= 0.294 Chirality : 0.045 0.187 4823 Planarity : 0.004 0.044 5230 Dihedral : 4.235 25.797 3963 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 2.57 % Allowed : 13.74 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3639 helix: 1.51 (0.21), residues: 714 sheet: 0.29 (0.16), residues: 1041 loop : -0.10 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.016 0.001 TYR A1067 PHE 0.020 0.001 PHE A 55 TRP 0.016 0.002 TRP C 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (30248) covalent geometry : angle 0.57375 / 0.29 (41137) SS BOND : bond 0.00344 / 0.22 ( 45) SS BOND : angle 1.50625 / 0.85 ( 90) hydrogen bonds : bond 0.03670 / 2.42 ( 1181) hydrogen bonds : angle 5.80103 / 4.05 ( 3294) link_BETA1-4 : bond 0.00330 / 0.17 ( 18) link_BETA1-4 : angle 0.98959 / 0.69 ( 54) link_BETA1-6 : bond 0.00556 / 0.24 ( 3) link_BETA1-6 : angle 1.44269 / 0.85 ( 9) link_NAG-ASN : bond 0.00248 / 0.16 ( 43) link_NAG-ASN : angle 1.23731 / 0.86 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 311 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7015 (m-80) cc_final: 0.6530 (m-80) REVERT: A 606 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8035 (t0) REVERT: A 902 MET cc_start: 0.8493 (mmm) cc_final: 0.7617 (mmm) REVERT: A 1037 SER cc_start: 0.8244 (t) cc_final: 0.7517 (p) REVERT: A 1101 HIS cc_start: 0.5523 (OUTLIER) cc_final: 0.5203 (t-90) REVERT: A 1104 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8619 (p) REVERT: B 90 VAL cc_start: 0.8045 (m) cc_final: 0.7785 (t) REVERT: B 490 PHE cc_start: 0.7985 (t80) cc_final: 0.7304 (t80) REVERT: B 492 LEU cc_start: 0.8374 (mt) cc_final: 0.7981 (mm) REVERT: B 756 TYR cc_start: 0.8834 (m-80) cc_final: 0.8155 (m-80) REVERT: B 948 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8064 (mt) REVERT: C 231 ILE cc_start: 0.7905 (mm) cc_final: 0.7596 (tt) REVERT: C 365 TYR cc_start: 0.7478 (m-80) cc_final: 0.7100 (m-80) REVERT: L 34 TYR cc_start: 0.0496 (m-80) cc_final: 0.0044 (m-80) REVERT: L 49 MET cc_start: 0.3954 (tpp) cc_final: 0.3248 (ttm) REVERT: G 3 VAL cc_start: 0.5889 (OUTLIER) cc_final: 0.5641 (p) outliers start: 82 outliers final: 61 residues processed: 372 average time/residue: 0.1827 time to fit residues: 110.2153 Evaluate side-chains 351 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 285 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 365 optimal weight: 30.0000 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 177 optimal weight: 0.1980 chunk 48 optimal weight: 7.9990 chunk 287 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.183004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.145737 restraints weight = 56881.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.142968 restraints weight = 85803.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.139173 restraints weight = 67811.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.139671 restraints weight = 66581.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.139821 restraints weight = 51113.662| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 30357 Z= 0.180 Angle : 0.600 10.314 41419 Z= 0.306 Chirality : 0.045 0.193 4823 Planarity : 0.004 0.045 5230 Dihedral : 4.312 28.319 3963 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 2.44 % Allowed : 14.68 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3639 helix: 1.39 (0.20), residues: 714 sheet: 0.30 (0.16), residues: 1038 loop : -0.12 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 67 TYR 0.021 0.002 TYR A 365 PHE 0.025 0.002 PHE A1103 TRP 0.016 0.002 TRP C 886 HIS 0.026 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (30248) covalent geometry : angle 0.59328 / 0.30 (41137) SS BOND : bond 0.00417 / 0.24 ( 45) SS BOND : angle 1.34179 / 0.78 ( 90) hydrogen bonds : bond 0.03781 / 2.50 ( 1181) hydrogen bonds : angle 5.81818 / 4.07 ( 3294) link_BETA1-4 : bond 0.00340 / 0.17 ( 18) link_BETA1-4 : angle 1.00225 / 0.69 ( 54) link_BETA1-6 : bond 0.00585 / 0.27 ( 3) link_BETA1-6 : angle 1.53533 / 0.91 ( 9) link_NAG-ASN : bond 0.00245 / 0.16 ( 43) link_NAG-ASN : angle 1.27181 / 0.89 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 297 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.6836 (m-80) cc_final: 0.6321 (m-80) REVERT: A 606 ASN cc_start: 0.8400 (t0) cc_final: 0.7952 (t0) REVERT: A 902 MET cc_start: 0.8569 (mmm) cc_final: 0.7548 (mmm) REVERT: A 1037 SER cc_start: 0.8203 (t) cc_final: 0.7244 (p) REVERT: A 1104 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8565 (p) REVERT: B 90 VAL cc_start: 0.8095 (m) cc_final: 0.7830 (t) REVERT: B 302 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8465 (t) REVERT: B 490 PHE cc_start: 0.7259 (t80) cc_final: 0.6986 (t80) REVERT: B 492 LEU cc_start: 0.8227 (mt) cc_final: 0.8001 (mm) REVERT: B 756 TYR cc_start: 0.8859 (m-80) cc_final: 0.8193 (m-80) REVERT: B 948 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8072 (mt) REVERT: C 291 CYS cc_start: 0.6345 (m) cc_final: 0.5915 (m) REVERT: C 902 MET cc_start: 0.8091 (mmm) cc_final: 0.7288 (mmm) REVERT: L 34 TYR cc_start: 0.0199 (m-80) cc_final: -0.0164 (m-80) REVERT: L 49 MET cc_start: 0.3642 (tpp) cc_final: 0.2591 (ttm) REVERT: G 3 VAL cc_start: 0.5034 (OUTLIER) cc_final: 0.4829 (p) REVERT: G 41 HIS cc_start: 0.5659 (m90) cc_final: 0.4977 (m-70) REVERT: J 100 MET cc_start: 0.1540 (tpt) cc_final: 0.1093 (tpt) REVERT: K 22 CYS cc_start: 0.0840 (OUTLIER) cc_final: 0.0248 (t) outliers start: 78 outliers final: 63 residues processed: 356 average time/residue: 0.1921 time to fit residues: 111.2619 Evaluate side-chains 346 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 278 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 32 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 112 optimal weight: 2.9990 chunk 336 optimal weight: 4.9990 chunk 59 optimal weight: 0.1980 chunk 137 optimal weight: 0.0000 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN B 394 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.183133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.146117 restraints weight = 57030.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.142819 restraints weight = 85662.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.139016 restraints weight = 66865.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.139151 restraints weight = 68116.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.139648 restraints weight = 51353.405| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 30357 Z= 0.165 Angle : 0.597 10.427 41419 Z= 0.304 Chirality : 0.045 0.200 4823 Planarity : 0.004 0.041 5230 Dihedral : 4.299 29.577 3963 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.78 % Favored : 97.20 % Rotamer: Outliers : 2.57 % Allowed : 15.09 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 3639 helix: 1.45 (0.20), residues: 708 sheet: 0.30 (0.16), residues: 1038 loop : -0.15 (0.15), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 67 TYR 0.019 0.002 TYR A 365 PHE 0.029 0.002 PHE C 392 TRP 0.026 0.002 TRP B 104 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (30248) covalent geometry : angle 0.58841 / 0.30 (41137) SS BOND : bond 0.00342 / 0.22 ( 45) SS BOND : angle 1.63753 / 0.98 ( 90) hydrogen bonds : bond 0.03710 / 2.45 ( 1181) hydrogen bonds : angle 5.76775 / 4.03 ( 3294) link_BETA1-4 : bond 0.00320 / 0.16 ( 18) link_BETA1-4 : angle 0.99449 / 0.69 ( 54) link_BETA1-6 : bond 0.00550 / 0.24 ( 3) link_BETA1-6 : angle 1.49519 / 0.88 ( 9) link_NAG-ASN : bond 0.00250 / 0.17 ( 43) link_NAG-ASN : angle 1.24930 / 0.88 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 295 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.6860 (m-80) cc_final: 0.6236 (m-80) REVERT: A 606 ASN cc_start: 0.8402 (t0) cc_final: 0.7963 (t0) REVERT: A 902 MET cc_start: 0.8563 (mmm) cc_final: 0.7515 (mmm) REVERT: B 90 VAL cc_start: 0.8086 (m) cc_final: 0.7791 (t) REVERT: B 490 PHE cc_start: 0.7510 (t80) cc_final: 0.7016 (t80) REVERT: B 492 LEU cc_start: 0.8290 (mt) cc_final: 0.8061 (mm) REVERT: B 756 TYR cc_start: 0.8859 (m-80) cc_final: 0.8225 (m-80) REVERT: B 948 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8106 (mt) REVERT: C 291 CYS cc_start: 0.5880 (m) cc_final: 0.5505 (m) REVERT: C 739 THR cc_start: 0.8341 (m) cc_final: 0.8120 (p) REVERT: C 902 MET cc_start: 0.8092 (mmm) cc_final: 0.7237 (mmm) REVERT: L 34 TYR cc_start: 0.0160 (m-80) cc_final: -0.0198 (m-80) REVERT: L 49 MET cc_start: 0.3703 (tpp) cc_final: 0.2639 (ttm) REVERT: G 3 VAL cc_start: 0.5121 (OUTLIER) cc_final: 0.4909 (p) REVERT: G 41 HIS cc_start: 0.5857 (m90) cc_final: 0.5332 (m-70) REVERT: K 22 CYS cc_start: 0.0901 (OUTLIER) cc_final: 0.0183 (t) REVERT: K 40 GLN cc_start: 0.4881 (tm-30) cc_final: 0.4601 (tm-30) outliers start: 82 outliers final: 70 residues processed: 358 average time/residue: 0.1896 time to fit residues: 110.8604 Evaluate side-chains 356 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 283 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 32 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 180 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.181536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.144165 restraints weight = 56870.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.140843 restraints weight = 85080.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.138204 restraints weight = 68485.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.138281 restraints weight = 65779.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.138323 restraints weight = 53592.053| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 30357 Z= 0.202 Angle : 0.633 14.467 41419 Z= 0.322 Chirality : 0.046 0.264 4823 Planarity : 0.004 0.059 5230 Dihedral : 4.402 26.975 3963 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 2.63 % Allowed : 15.40 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3639 helix: 1.31 (0.20), residues: 708 sheet: 0.23 (0.16), residues: 1008 loop : -0.20 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 67 TYR 0.029 0.002 TYR K 88 PHE 0.049 0.002 PHE C 392 TRP 0.037 0.002 TRP B 104 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (30248) covalent geometry : angle 0.62320 / 0.32 (41137) SS BOND : bond 0.00503 / 0.30 ( 45) SS BOND : angle 1.88476 / 1.14 ( 90) hydrogen bonds : bond 0.03826 / 2.52 ( 1181) hydrogen bonds : angle 5.80666 / 4.05 ( 3294) link_BETA1-4 : bond 0.00297 / 0.15 ( 18) link_BETA1-4 : angle 0.99328 / 0.69 ( 54) link_BETA1-6 : bond 0.00456 / 0.19 ( 3) link_BETA1-6 : angle 1.46250 / 0.87 ( 9) link_NAG-ASN : bond 0.00279 / 0.18 ( 43) link_NAG-ASN : angle 1.28586 / 0.91 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 290 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.6893 (m-80) cc_final: 0.6198 (m-80) REVERT: A 606 ASN cc_start: 0.8417 (t0) cc_final: 0.7994 (t0) REVERT: A 902 MET cc_start: 0.8543 (mmm) cc_final: 0.7445 (mmm) REVERT: B 490 PHE cc_start: 0.7480 (t80) cc_final: 0.7138 (t80) REVERT: B 948 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8067 (mt) REVERT: C 291 CYS cc_start: 0.6310 (m) cc_final: 0.5986 (m) REVERT: C 739 THR cc_start: 0.7923 (m) cc_final: 0.7719 (p) REVERT: C 902 MET cc_start: 0.8114 (mmm) cc_final: 0.7300 (mmm) REVERT: L 34 TYR cc_start: 0.0536 (m-80) cc_final: 0.0141 (m-80) REVERT: L 49 MET cc_start: 0.3723 (tpp) cc_final: 0.2641 (ttm) REVERT: G 41 HIS cc_start: 0.5670 (m90) cc_final: 0.5237 (m-70) REVERT: K 22 CYS cc_start: 0.0946 (OUTLIER) cc_final: 0.0249 (t) REVERT: K 40 GLN cc_start: 0.4863 (tm-30) cc_final: 0.4628 (tm-30) outliers start: 84 outliers final: 70 residues processed: 351 average time/residue: 0.1904 time to fit residues: 109.5727 Evaluate side-chains 348 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 276 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 32 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 310 optimal weight: 20.0000 chunk 274 optimal weight: 0.1980 chunk 251 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 265 optimal weight: 0.9990 chunk 342 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 155 optimal weight: 0.0870 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 271 GLN B 360 ASN B 450 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.182214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.145548 restraints weight = 57161.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.143958 restraints weight = 81718.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.142357 restraints weight = 66094.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.142093 restraints weight = 59953.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.141446 restraints weight = 51834.787| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 30357 Z= 0.168 Angle : 0.621 12.277 41419 Z= 0.312 Chirality : 0.045 0.275 4823 Planarity : 0.004 0.070 5230 Dihedral : 4.388 25.560 3963 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 2.32 % Allowed : 15.90 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3639 helix: 1.40 (0.20), residues: 708 sheet: 0.30 (0.16), residues: 978 loop : -0.24 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 67 TYR 0.026 0.002 TYR K 88 PHE 0.045 0.002 PHE C 392 TRP 0.038 0.002 TRP B 104 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (30248) covalent geometry : angle 0.61011 / 0.31 (41137) SS BOND : bond 0.00440 / 0.26 ( 45) SS BOND : angle 1.76322 / 1.07 ( 90) hydrogen bonds : bond 0.03673 / 2.43 ( 1181) hydrogen bonds : angle 5.75018 / 4.01 ( 3294) link_BETA1-4 : bond 0.00305 / 0.15 ( 18) link_BETA1-4 : angle 1.06299 / 0.73 ( 54) link_BETA1-6 : bond 0.00487 / 0.21 ( 3) link_BETA1-6 : angle 1.46987 / 0.87 ( 9) link_NAG-ASN : bond 0.00264 / 0.17 ( 43) link_NAG-ASN : angle 1.55535 / 1.00 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 287 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 ASN cc_start: 0.8405 (t0) cc_final: 0.8000 (t0) REVERT: A 902 MET cc_start: 0.8586 (mmm) cc_final: 0.7521 (mmm) REVERT: B 490 PHE cc_start: 0.7347 (t80) cc_final: 0.7094 (t80) REVERT: B 948 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7970 (mt) REVERT: C 291 CYS cc_start: 0.6380 (m) cc_final: 0.6028 (m) REVERT: C 739 THR cc_start: 0.7813 (m) cc_final: 0.7608 (p) REVERT: C 902 MET cc_start: 0.8153 (mmm) cc_final: 0.7319 (mmm) REVERT: L 49 MET cc_start: 0.3545 (tpp) cc_final: 0.2472 (ttm) REVERT: F 81 MET cc_start: 0.5955 (mmm) cc_final: 0.5449 (mmm) REVERT: G 41 HIS cc_start: 0.5336 (m90) cc_final: 0.5081 (m90) REVERT: K 22 CYS cc_start: 0.0798 (OUTLIER) cc_final: 0.0065 (t) REVERT: K 40 GLN cc_start: 0.4560 (tm-30) cc_final: 0.4347 (tm-30) outliers start: 74 outliers final: 67 residues processed: 337 average time/residue: 0.1915 time to fit residues: 106.1117 Evaluate side-chains 342 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 273 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 32 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 250 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 168 optimal weight: 0.0070 chunk 169 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 273 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 103 optimal weight: 0.0970 chunk 301 optimal weight: 9.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 606 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.182037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.144520 restraints weight = 57555.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.141620 restraints weight = 87034.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.138782 restraints weight = 67225.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.138827 restraints weight = 61597.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.138688 restraints weight = 50624.853| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.279 30357 Z= 0.257 Angle : 0.872 59.200 41419 Z= 0.512 Chirality : 0.048 0.819 4823 Planarity : 0.005 0.238 5230 Dihedral : 4.439 38.931 3963 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.98 % Rotamer: Outliers : 2.38 % Allowed : 15.99 % Favored : 81.63 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3639 helix: 1.42 (0.20), residues: 708 sheet: 0.28 (0.16), residues: 978 loop : -0.25 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 44 TYR 0.021 0.002 TYR K 88 PHE 0.063 0.002 PHE A 194 TRP 0.129 0.003 TRP A 104 HIS 0.389 0.005 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.26 (30248) covalent geometry : angle 0.86587 / 0.51 (41137) SS BOND : bond 0.00435 / 0.26 ( 45) SS BOND : angle 1.70154 / 1.03 ( 90) hydrogen bonds : bond 0.03681 / 2.44 ( 1181) hydrogen bonds : angle 5.75795 / 4.01 ( 3294) link_BETA1-4 : bond 0.00438 / 0.23 ( 18) link_BETA1-4 : angle 1.09466 / 0.76 ( 54) link_BETA1-6 : bond 0.00350 / 0.14 ( 3) link_BETA1-6 : angle 1.37531 / 0.82 ( 9) link_NAG-ASN : bond 0.00253 / 0.17 ( 43) link_NAG-ASN : angle 1.53417 / 0.99 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5082.72 seconds wall clock time: 88 minutes 58.72 seconds (5338.72 seconds total)