Starting phenix.real_space_refine on Fri Feb 6 17:19:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tf0_25857/02_2026/7tf0_25857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf0_25857/02_2026/7tf0_25857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tf0_25857/02_2026/7tf0_25857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf0_25857/02_2026/7tf0_25857.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tf0_25857/02_2026/7tf0_25857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf0_25857/02_2026/7tf0_25857.map" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 121 5.16 5 C 17086 2.51 5 N 4399 2.21 5 O 5243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26849 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 6513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6513 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 45, 'TRANS': 790} Chain breaks: 8 Chain: "B" Number of atoms: 8093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8093 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 56, 'TRANS': 978} Chain breaks: 7 Chain: "C" Number of atoms: 6513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6513 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 45, 'TRANS': 790} Chain breaks: 8 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.99, per 1000 atoms: 0.22 Number of scatterers: 26849 At special positions: 0 Unit cell: (141, 158, 236, 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 121 16.00 O 5243 8.00 N 4399 7.00 C 17086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 17 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6206 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 47 sheets defined 34.5% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.861A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.599A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.925A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.528A 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.182A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.673A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.048A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 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: 3.602A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.916A 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 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.058A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.542A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.581A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.748A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.915A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.057A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.072A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.770A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.133A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 155 removed outlier: 3.955A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.651A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.764A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.818A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.531A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.679A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.112A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.535A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.288A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.596A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 3.600A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.781A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.140A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 44 removed outlier: 5.319A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.115A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.993A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.444A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 141 through 144 removed outlier: 6.858A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.244A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.167A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.187A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.585A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.337A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.921A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.026A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.564A 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 55 removed outlier: 4.051A 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: 3.705A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 141 through 144 removed outlier: 6.872A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.738A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.930A 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: 5.183A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.433A 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: 3.989A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.051A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.713A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.549A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.549A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.276A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.245A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.092A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.794A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.735A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 140 through 144 removed outlier: 6.752A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.584A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.082A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.562A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.562A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.307A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.903A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.196A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.392A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1294 hydrogen bonds defined for protein. 3642 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: 6.60 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8512 1.35 - 1.47: 6971 1.47 - 1.60: 11812 1.60 - 1.72: 0 1.72 - 1.85: 166 Bond restraints: 27461 Sorted by residual: bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.90e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.81e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.28e+00 ... (remaining 27456 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 36117 2.05 - 4.09: 1147 4.09 - 6.14: 77 6.14 - 8.19: 26 8.19 - 10.23: 3 Bond angle restraints: 37370 Sorted by residual: angle pdb=" C LYS B 528 " pdb=" N LYS B 529 " pdb=" CA LYS B 529 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.26 -5.56 1.22e+00 6.72e-01 2.08e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.22 -5.52 1.22e+00 6.72e-01 2.04e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.13 -5.43 1.22e+00 6.72e-01 1.98e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.36 128.54 -6.18 1.42e+00 4.96e-01 1.90e+01 ... (remaining 37365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 15787 17.82 - 35.64: 1075 35.64 - 53.45: 210 53.45 - 71.27: 58 71.27 - 89.09: 34 Dihedral angle restraints: 17164 sinusoidal: 7546 harmonic: 9618 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -51.75 -34.25 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual 79.00 17.20 61.80 1 2.00e+01 2.50e-03 1.27e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 65.65 27.35 1 1.00e+01 1.00e-02 1.07e+01 ... (remaining 17161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3579 0.074 - 0.148: 748 0.148 - 0.221: 61 0.221 - 0.295: 7 0.295 - 0.369: 2 Chirality restraints: 4397 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 4394 not shown) Planarity restraints: 4796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 550 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C GLY C 550 " -0.049 2.00e-02 2.50e+03 pdb=" O GLY C 550 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL C 551 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.046 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO E 590 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 499 " -0.044 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO E 500 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 500 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 500 " -0.037 5.00e-02 4.00e+02 ... (remaining 4793 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6503 2.80 - 3.32: 23098 3.32 - 3.85: 45804 3.85 - 4.37: 52442 4.37 - 4.90: 90912 Nonbonded interactions: 218759 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.286 3.040 nonbonded pdb=" OD1 ASN A 540 " pdb=" OG1 THR A 549 " model vdw 2.288 3.040 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.296 3.040 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.322 3.040 ... (remaining 218754 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 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.390 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 27559 Z= 0.241 Angle : 0.842 15.066 37628 Z= 0.458 Chirality : 0.057 0.369 4397 Planarity : 0.006 0.075 4752 Dihedral : 13.051 89.092 10850 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.45 % Favored : 98.52 % Rotamer: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.64 (0.13), residues: 3249 helix: 1.74 (0.14), residues: 987 sheet: 1.15 (0.20), residues: 591 loop : -0.65 (0.13), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 158 TYR 0.032 0.002 TYR E 385 PHE 0.028 0.002 PHE A 238 TRP 0.024 0.002 TRP E 69 HIS 0.007 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00483 (27461) covalent geometry : angle 0.81080 (37370) SS BOND : bond 0.00284 ( 36) SS BOND : angle 1.58550 ( 72) hydrogen bonds : bond 0.12671 ( 1246) hydrogen bonds : angle 6.97897 ( 3642) link_BETA1-4 : bond 0.00606 ( 18) link_BETA1-4 : angle 1.41869 ( 54) link_NAG-ASN : bond 0.00752 ( 44) link_NAG-ASN : angle 3.69507 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 341 time to evaluate : 0.894 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: A 52 GLN cc_start: 0.7348 (tp-100) cc_final: 0.7124 (tp-100) REVERT: A 200 TYR cc_start: 0.8610 (m-80) cc_final: 0.8408 (m-80) REVERT: A 238 PHE cc_start: 0.7691 (p90) cc_final: 0.7264 (p90) REVERT: B 188 ASN cc_start: 0.7190 (m-40) cc_final: 0.6817 (m-40) REVERT: C 197 ILE cc_start: 0.8663 (mm) cc_final: 0.8354 (mp) REVERT: C 237 ARG cc_start: 0.8969 (mtp180) cc_final: 0.8705 (mtm-85) REVERT: C 787 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8061 (mm-40) REVERT: C 823 PHE cc_start: 0.8237 (m-80) cc_final: 0.7945 (m-10) REVERT: E 63 ASN cc_start: 0.8335 (m-40) cc_final: 0.8119 (m-40) REVERT: E 240 LEU cc_start: 0.6644 (tp) cc_final: 0.6423 (mt) REVERT: E 552 GLN cc_start: 0.7526 (tp-100) cc_final: 0.6903 (tm-30) REVERT: E 554 LEU cc_start: 0.5980 (tp) cc_final: 0.5595 (tp) outliers start: 3 outliers final: 0 residues processed: 344 average time/residue: 0.1898 time to fit residues: 100.7762 Evaluate side-chains 138 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 121 ASN A 824 ASN A 907 ASN A1002 GLN A1071 HIS B 188 ASN B 957 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 HIS C 218 GLN C 824 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 HIS E 64 ASN E 374 HIS E 493 HIS E 586 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.118523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.078239 restraints weight = 86776.940| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.65 r_work: 0.3083 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 27559 Z= 0.230 Angle : 0.645 11.180 37628 Z= 0.322 Chirality : 0.046 0.248 4397 Planarity : 0.004 0.067 4752 Dihedral : 6.284 59.941 4823 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 0.95 % Favored : 99.02 % Rotamer: Outliers : 1.03 % Allowed : 6.90 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 1.00 (0.14), residues: 3249 helix: 2.30 (0.16), residues: 993 sheet: 0.82 (0.20), residues: 606 loop : -0.42 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 34 TYR 0.025 0.002 TYR A 170 PHE 0.025 0.002 PHE A 133 TRP 0.024 0.002 TRP E 168 HIS 0.008 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00519 (27461) covalent geometry : angle 0.61877 (37370) SS BOND : bond 0.00304 ( 36) SS BOND : angle 1.09037 ( 72) hydrogen bonds : bond 0.04581 ( 1246) hydrogen bonds : angle 5.64939 ( 3642) link_BETA1-4 : bond 0.00165 ( 18) link_BETA1-4 : angle 1.08918 ( 54) link_NAG-ASN : bond 0.00606 ( 44) link_NAG-ASN : angle 2.98230 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6846 (p90) cc_final: 0.6506 (p90) REVERT: A 200 TYR cc_start: 0.8920 (m-80) cc_final: 0.8628 (m-80) REVERT: A 1138 TYR cc_start: 0.8689 (t80) cc_final: 0.8409 (t80) REVERT: B 92 PHE cc_start: 0.8814 (t80) cc_final: 0.8299 (t80) REVERT: B 188 ASN cc_start: 0.7711 (m110) cc_final: 0.7244 (m-40) REVERT: B 394 ASN cc_start: 0.9065 (m-40) cc_final: 0.8828 (t0) REVERT: C 900 MET cc_start: 0.8960 (mtp) cc_final: 0.8711 (mtp) REVERT: E 240 LEU cc_start: 0.6600 (tp) cc_final: 0.6339 (mt) outliers start: 30 outliers final: 16 residues processed: 169 average time/residue: 0.1693 time to fit residues: 46.5525 Evaluate side-chains 129 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 10 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 307 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 273 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 257 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 314 GLN A 613 GLN B 448 ASN B 450 ASN B 493 GLN B 907 ASN B1005 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.116574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.076739 restraints weight = 86633.709| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.54 r_work: 0.3106 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27559 Z= 0.145 Angle : 0.558 10.650 37628 Z= 0.279 Chirality : 0.044 0.262 4397 Planarity : 0.004 0.058 4752 Dihedral : 5.789 59.245 4823 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.31 % Allowed : 7.93 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 1.07 (0.14), residues: 3249 helix: 2.47 (0.16), residues: 999 sheet: 0.63 (0.19), residues: 649 loop : -0.39 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 482 TYR 0.023 0.001 TYR B1067 PHE 0.022 0.001 PHE A 133 TRP 0.015 0.001 TRP E 165 HIS 0.007 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00322 (27461) covalent geometry : angle 0.53350 (37370) SS BOND : bond 0.00171 ( 36) SS BOND : angle 0.89659 ( 72) hydrogen bonds : bond 0.04048 ( 1246) hydrogen bonds : angle 5.36816 ( 3642) link_BETA1-4 : bond 0.00271 ( 18) link_BETA1-4 : angle 0.93137 ( 54) link_NAG-ASN : bond 0.00536 ( 44) link_NAG-ASN : angle 2.70838 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.9059 (tpp) cc_final: 0.8854 (tpp) REVERT: A 983 ARG cc_start: 0.8418 (mtp180) cc_final: 0.7982 (tpm170) REVERT: B 92 PHE cc_start: 0.8787 (t80) cc_final: 0.8258 (t80) REVERT: B 118 LEU cc_start: 0.8731 (tp) cc_final: 0.8514 (tt) REVERT: B 188 ASN cc_start: 0.7684 (m110) cc_final: 0.7188 (m-40) REVERT: E 190 MET cc_start: 0.3915 (ppp) cc_final: 0.3469 (ppp) REVERT: E 215 TYR cc_start: 0.3883 (OUTLIER) cc_final: 0.3593 (t80) REVERT: E 240 LEU cc_start: 0.6534 (tp) cc_final: 0.6237 (mt) REVERT: E 455 MET cc_start: 0.5450 (ptm) cc_final: 0.5233 (ptm) outliers start: 38 outliers final: 19 residues processed: 151 average time/residue: 0.1500 time to fit residues: 38.9073 Evaluate side-chains 131 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 124 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 278 optimal weight: 6.9990 chunk 256 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 125 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** E 228 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 = 0.4103 r_free = 0.4103 target = 0.103825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.063231 restraints weight = 87196.772| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.62 r_work: 0.3065 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27559 Z= 0.181 Angle : 0.570 10.562 37628 Z= 0.282 Chirality : 0.044 0.267 4397 Planarity : 0.004 0.054 4752 Dihedral : 5.474 56.292 4823 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.38 % Allowed : 8.41 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.97 (0.14), residues: 3249 helix: 2.56 (0.16), residues: 992 sheet: 0.38 (0.20), residues: 598 loop : -0.44 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 214 TYR 0.023 0.001 TYR A1138 PHE 0.025 0.001 PHE A 133 TRP 0.016 0.001 TRP B 258 HIS 0.009 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00410 (27461) covalent geometry : angle 0.54661 (37370) SS BOND : bond 0.00179 ( 36) SS BOND : angle 0.85481 ( 72) hydrogen bonds : bond 0.04017 ( 1246) hydrogen bonds : angle 5.25200 ( 3642) link_BETA1-4 : bond 0.00202 ( 18) link_BETA1-4 : angle 1.03509 ( 54) link_NAG-ASN : bond 0.00539 ( 44) link_NAG-ASN : angle 2.65568 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8886 (tpp) cc_final: 0.8635 (tpp) REVERT: A 983 ARG cc_start: 0.8352 (mtp180) cc_final: 0.7978 (tpm170) REVERT: B 92 PHE cc_start: 0.8773 (t80) cc_final: 0.8237 (t80) REVERT: B 188 ASN cc_start: 0.7651 (m110) cc_final: 0.7158 (m-40) REVERT: E 240 LEU cc_start: 0.6653 (tp) cc_final: 0.6327 (mt) outliers start: 40 outliers final: 25 residues processed: 142 average time/residue: 0.1587 time to fit residues: 38.1498 Evaluate side-chains 122 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 51 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 172 optimal weight: 3.9990 chunk 307 optimal weight: 20.0000 chunk 217 optimal weight: 0.7980 chunk 201 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 208 optimal weight: 0.2980 chunk 145 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.105746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.065669 restraints weight = 87451.205| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.45 r_work: 0.3078 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 27559 Z= 0.158 Angle : 0.541 10.278 37628 Z= 0.269 Chirality : 0.043 0.272 4397 Planarity : 0.003 0.050 4752 Dihedral : 5.258 54.716 4823 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.14 % Allowed : 9.17 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.99 (0.14), residues: 3249 helix: 2.53 (0.16), residues: 998 sheet: 0.41 (0.19), residues: 642 loop : -0.44 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 158 TYR 0.022 0.001 TYR A1067 PHE 0.025 0.001 PHE A 133 TRP 0.013 0.001 TRP E 165 HIS 0.006 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00353 (27461) covalent geometry : angle 0.51849 (37370) SS BOND : bond 0.00160 ( 36) SS BOND : angle 0.79655 ( 72) hydrogen bonds : bond 0.03854 ( 1246) hydrogen bonds : angle 5.17087 ( 3642) link_BETA1-4 : bond 0.00252 ( 18) link_BETA1-4 : angle 0.95825 ( 54) link_NAG-ASN : bond 0.00515 ( 44) link_NAG-ASN : angle 2.55106 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8933 (tpp) cc_final: 0.8676 (tpp) REVERT: A 983 ARG cc_start: 0.8314 (mtp180) cc_final: 0.7953 (tpm170) REVERT: B 92 PHE cc_start: 0.8761 (t80) cc_final: 0.8212 (t80) REVERT: B 188 ASN cc_start: 0.7717 (m110) cc_final: 0.7186 (m-40) REVERT: E 240 LEU cc_start: 0.6658 (tp) cc_final: 0.6333 (mt) outliers start: 33 outliers final: 25 residues processed: 134 average time/residue: 0.1535 time to fit residues: 35.6671 Evaluate side-chains 125 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 309 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 315 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 321 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 241 optimal weight: 0.9980 chunk 305 optimal weight: 20.0000 chunk 174 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 GLN B 125 ASN B 824 ASN B 907 ASN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN E 86 GLN E 239 HIS E 580 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.102079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.061120 restraints weight = 87656.161| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.60 r_work: 0.3006 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 27559 Z= 0.311 Angle : 0.672 10.409 37628 Z= 0.334 Chirality : 0.047 0.286 4397 Planarity : 0.004 0.053 4752 Dihedral : 5.722 54.443 4823 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.55 % Allowed : 9.62 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.60 (0.14), residues: 3249 helix: 2.16 (0.16), residues: 1005 sheet: 0.14 (0.18), residues: 707 loop : -0.66 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 190 TYR 0.025 0.002 TYR B1067 PHE 0.028 0.002 PHE A 133 TRP 0.017 0.002 TRP E 165 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00706 (27461) covalent geometry : angle 0.65109 (37370) SS BOND : bond 0.00278 ( 36) SS BOND : angle 0.98398 ( 72) hydrogen bonds : bond 0.04578 ( 1246) hydrogen bonds : angle 5.48345 ( 3642) link_BETA1-4 : bond 0.00215 ( 18) link_BETA1-4 : angle 1.20632 ( 54) link_NAG-ASN : bond 0.00706 ( 44) link_NAG-ASN : angle 2.77814 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8988 (tpp) cc_final: 0.8740 (tpp) REVERT: A 983 ARG cc_start: 0.8236 (mtp180) cc_final: 0.7966 (tpm170) REVERT: B 92 PHE cc_start: 0.8813 (t80) cc_final: 0.8211 (t80) REVERT: B 188 ASN cc_start: 0.7646 (m110) cc_final: 0.7126 (m-40) REVERT: B 867 ASP cc_start: 0.8808 (m-30) cc_final: 0.8452 (t0) REVERT: E 240 LEU cc_start: 0.6587 (tp) cc_final: 0.6224 (mt) REVERT: E 408 MET cc_start: 0.7117 (mmp) cc_final: 0.6868 (tpp) REVERT: E 557 MET cc_start: 0.5279 (ptp) cc_final: 0.4959 (ptp) outliers start: 45 outliers final: 30 residues processed: 137 average time/residue: 0.1628 time to fit residues: 38.2032 Evaluate side-chains 122 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 555 PHE Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 160 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 233 optimal weight: 0.8980 chunk 317 optimal weight: 20.0000 chunk 232 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 613 GLN B 907 ASN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN E 86 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.104907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064219 restraints weight = 87536.674| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.46 r_work: 0.3087 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27559 Z= 0.116 Angle : 0.537 10.244 37628 Z= 0.268 Chirality : 0.043 0.288 4397 Planarity : 0.003 0.050 4752 Dihedral : 5.194 57.517 4823 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.10 % Allowed : 10.55 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.84 (0.14), residues: 3249 helix: 2.43 (0.16), residues: 1004 sheet: 0.17 (0.19), residues: 686 loop : -0.50 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.021 0.001 TYR A1067 PHE 0.028 0.001 PHE A 133 TRP 0.010 0.001 TRP E 165 HIS 0.005 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00254 (27461) covalent geometry : angle 0.51577 (37370) SS BOND : bond 0.00161 ( 36) SS BOND : angle 0.78366 ( 72) hydrogen bonds : bond 0.03787 ( 1246) hydrogen bonds : angle 5.17100 ( 3642) link_BETA1-4 : bond 0.00316 ( 18) link_BETA1-4 : angle 0.87360 ( 54) link_NAG-ASN : bond 0.00494 ( 44) link_NAG-ASN : angle 2.48626 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8951 (tpp) cc_final: 0.8745 (tpp) REVERT: A 983 ARG cc_start: 0.8212 (mtp180) cc_final: 0.7950 (tpm170) REVERT: B 92 PHE cc_start: 0.8807 (t80) cc_final: 0.8211 (t80) REVERT: B 188 ASN cc_start: 0.7761 (m110) cc_final: 0.7269 (m-40) REVERT: E 190 MET cc_start: 0.3418 (ppp) cc_final: 0.2795 (ppp) REVERT: E 240 LEU cc_start: 0.6771 (tp) cc_final: 0.6380 (mt) REVERT: E 408 MET cc_start: 0.7210 (mmp) cc_final: 0.6974 (tpp) REVERT: E 557 MET cc_start: 0.5225 (ptp) cc_final: 0.4925 (ptp) outliers start: 32 outliers final: 23 residues processed: 129 average time/residue: 0.1514 time to fit residues: 34.2096 Evaluate side-chains 120 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 188 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 165 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 141 optimal weight: 0.4980 chunk 207 optimal weight: 3.9990 chunk 158 optimal weight: 0.0020 chunk 260 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.113731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.074235 restraints weight = 87052.480| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.56 r_work: 0.3097 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27559 Z= 0.104 Angle : 0.526 11.054 37628 Z= 0.261 Chirality : 0.043 0.284 4397 Planarity : 0.003 0.048 4752 Dihedral : 4.878 57.149 4823 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.90 % Allowed : 10.76 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.96 (0.14), residues: 3249 helix: 2.53 (0.16), residues: 998 sheet: 0.21 (0.20), residues: 630 loop : -0.38 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.021 0.001 TYR A1067 PHE 0.031 0.001 PHE A 133 TRP 0.010 0.001 TRP E 594 HIS 0.005 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00225 (27461) covalent geometry : angle 0.50637 (37370) SS BOND : bond 0.00142 ( 36) SS BOND : angle 0.74783 ( 72) hydrogen bonds : bond 0.03606 ( 1246) hydrogen bonds : angle 5.01739 ( 3642) link_BETA1-4 : bond 0.00283 ( 18) link_BETA1-4 : angle 0.90631 ( 54) link_NAG-ASN : bond 0.00483 ( 44) link_NAG-ASN : angle 2.39375 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 983 ARG cc_start: 0.8230 (mtp180) cc_final: 0.7946 (tpm170) REVERT: B 92 PHE cc_start: 0.8836 (t80) cc_final: 0.8250 (t80) REVERT: B 188 ASN cc_start: 0.7660 (m110) cc_final: 0.7196 (m-40) REVERT: E 190 MET cc_start: 0.3466 (ppp) cc_final: 0.2918 (ppp) REVERT: E 240 LEU cc_start: 0.6780 (tp) cc_final: 0.6437 (mt) REVERT: E 408 MET cc_start: 0.7169 (mmp) cc_final: 0.6958 (tpp) REVERT: E 557 MET cc_start: 0.5033 (ptp) cc_final: 0.3983 (ptp) outliers start: 26 outliers final: 21 residues processed: 124 average time/residue: 0.1517 time to fit residues: 32.8684 Evaluate side-chains 116 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 261 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 308 optimal weight: 30.0000 chunk 39 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.113409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.073769 restraints weight = 87108.891| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.61 r_work: 0.3086 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27559 Z= 0.124 Angle : 0.526 10.142 37628 Z= 0.260 Chirality : 0.043 0.287 4397 Planarity : 0.003 0.050 4752 Dihedral : 4.740 57.030 4823 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.00 % Allowed : 10.86 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 1.02 (0.15), residues: 3249 helix: 2.57 (0.16), residues: 998 sheet: 0.29 (0.19), residues: 650 loop : -0.37 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.021 0.001 TYR A1067 PHE 0.027 0.001 PHE A 133 TRP 0.012 0.001 TRP E 594 HIS 0.005 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00276 (27461) covalent geometry : angle 0.50604 (37370) SS BOND : bond 0.00137 ( 36) SS BOND : angle 0.73968 ( 72) hydrogen bonds : bond 0.03588 ( 1246) hydrogen bonds : angle 4.96767 ( 3642) link_BETA1-4 : bond 0.00264 ( 18) link_BETA1-4 : angle 0.92367 ( 54) link_NAG-ASN : bond 0.00481 ( 44) link_NAG-ASN : angle 2.37438 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6273 (p90) cc_final: 0.5494 (p90) REVERT: A 983 ARG cc_start: 0.8233 (mtp180) cc_final: 0.7932 (tpm170) REVERT: B 92 PHE cc_start: 0.8824 (t80) cc_final: 0.8271 (t80) REVERT: B 188 ASN cc_start: 0.7688 (m110) cc_final: 0.7206 (m-40) REVERT: B 396 TYR cc_start: 0.8387 (m-10) cc_final: 0.8159 (m-10) REVERT: B 867 ASP cc_start: 0.8777 (m-30) cc_final: 0.8378 (t0) REVERT: C 740 MET cc_start: 0.9158 (tpp) cc_final: 0.8794 (tpp) REVERT: E 240 LEU cc_start: 0.6776 (tp) cc_final: 0.6444 (mt) REVERT: E 249 MET cc_start: 0.3637 (mmm) cc_final: 0.3401 (mpp) REVERT: E 323 MET cc_start: 0.4386 (tmm) cc_final: 0.3043 (ppp) REVERT: E 535 HIS cc_start: 0.5202 (OUTLIER) cc_final: 0.4805 (t-90) REVERT: E 557 MET cc_start: 0.4265 (ptp) cc_final: 0.4007 (ptp) outliers start: 29 outliers final: 24 residues processed: 125 average time/residue: 0.1505 time to fit residues: 32.9235 Evaluate side-chains 123 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 232 optimal weight: 7.9990 chunk 257 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 296 optimal weight: 8.9990 chunk 126 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 323 optimal weight: 0.2980 chunk 107 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 184 optimal weight: 0.5980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN E 86 GLN E 572 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.112902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.073301 restraints weight = 87230.639| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.53 r_work: 0.3074 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27559 Z= 0.151 Angle : 0.539 10.122 37628 Z= 0.267 Chirality : 0.044 0.290 4397 Planarity : 0.003 0.049 4752 Dihedral : 4.780 56.948 4823 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.00 % Allowed : 11.17 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 1.00 (0.15), residues: 3249 helix: 2.54 (0.16), residues: 1000 sheet: 0.28 (0.19), residues: 685 loop : -0.39 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 190 TYR 0.021 0.001 TYR A1067 PHE 0.028 0.001 PHE A 133 TRP 0.012 0.001 TRP E 165 HIS 0.009 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00341 (27461) covalent geometry : angle 0.51988 (37370) SS BOND : bond 0.00147 ( 36) SS BOND : angle 0.77443 ( 72) hydrogen bonds : bond 0.03676 ( 1246) hydrogen bonds : angle 5.02054 ( 3642) link_BETA1-4 : bond 0.00251 ( 18) link_BETA1-4 : angle 0.95200 ( 54) link_NAG-ASN : bond 0.00491 ( 44) link_NAG-ASN : angle 2.39361 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6146 (p90) cc_final: 0.5391 (p90) REVERT: A 983 ARG cc_start: 0.8189 (mtp180) cc_final: 0.7926 (tpm170) REVERT: A 1144 GLU cc_start: 0.8611 (mm-30) cc_final: 0.7701 (tm-30) REVERT: B 92 PHE cc_start: 0.8827 (t80) cc_final: 0.8290 (t80) REVERT: B 188 ASN cc_start: 0.7672 (m110) cc_final: 0.7191 (m-40) REVERT: B 396 TYR cc_start: 0.8369 (m-10) cc_final: 0.8150 (m-10) REVERT: B 867 ASP cc_start: 0.8779 (m-30) cc_final: 0.8377 (t0) REVERT: C 740 MET cc_start: 0.9176 (tpp) cc_final: 0.8757 (tpp) REVERT: E 190 MET cc_start: 0.3639 (ppp) cc_final: 0.3053 (ppp) REVERT: E 240 LEU cc_start: 0.6795 (tp) cc_final: 0.6474 (mt) REVERT: E 249 MET cc_start: 0.3691 (mmm) cc_final: 0.3419 (mpp) REVERT: E 323 MET cc_start: 0.4740 (tmm) cc_final: 0.3421 (ppp) REVERT: E 408 MET cc_start: 0.7249 (mmp) cc_final: 0.6921 (tpp) REVERT: E 535 HIS cc_start: 0.5300 (OUTLIER) cc_final: 0.4925 (t-90) REVERT: E 557 MET cc_start: 0.4308 (ptp) cc_final: 0.4058 (ptp) outliers start: 29 outliers final: 25 residues processed: 121 average time/residue: 0.1520 time to fit residues: 32.2831 Evaluate side-chains 124 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 555 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 232 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 254 optimal weight: 0.7980 chunk 311 optimal weight: 20.0000 chunk 201 optimal weight: 0.0030 chunk 316 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.102701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.063359 restraints weight = 87763.906| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.41 r_work: 0.3052 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27559 Z= 0.211 Angle : 0.577 10.103 37628 Z= 0.286 Chirality : 0.044 0.295 4397 Planarity : 0.004 0.049 4752 Dihedral : 4.935 56.613 4823 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.97 % Allowed : 11.24 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.90 (0.15), residues: 3249 helix: 2.48 (0.16), residues: 1000 sheet: 0.20 (0.19), residues: 694 loop : -0.45 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.022 0.001 TYR A1067 PHE 0.027 0.001 PHE A 133 TRP 0.014 0.001 TRP E 165 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00480 (27461) covalent geometry : angle 0.55777 (37370) SS BOND : bond 0.00171 ( 36) SS BOND : angle 0.83527 ( 72) hydrogen bonds : bond 0.03876 ( 1246) hydrogen bonds : angle 5.11977 ( 3642) link_BETA1-4 : bond 0.00225 ( 18) link_BETA1-4 : angle 0.99252 ( 54) link_NAG-ASN : bond 0.00542 ( 44) link_NAG-ASN : angle 2.47266 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10359.57 seconds wall clock time: 177 minutes 19.05 seconds (10639.05 seconds total)