Starting phenix.real_space_refine on Fri Feb 6 17:33:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sxx_25509/02_2026/7sxx_25509.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxx_25509/02_2026/7sxx_25509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sxx_25509/02_2026/7sxx_25509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxx_25509/02_2026/7sxx_25509.map" model { file = "/net/cci-nas-00/data/ceres_data/7sxx_25509/02_2026/7sxx_25509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxx_25509/02_2026/7sxx_25509.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 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 124 5.16 5 C 17164 2.51 5 N 4407 2.21 5 O 5277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s 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: 26972 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 6555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6555 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 45, 'TRANS': 795} Chain breaks: 8 Chain: "B" Number of atoms: 8132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8132 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 6555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6555 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 45, 'TRANS': 795} Chain breaks: 8 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "B" 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: 6.47, per 1000 atoms: 0.24 Number of scatterers: 26972 At special positions: 0 Unit cell: (140, 156, 235, 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 124 16.00 O 5277 8.00 N 4407 7.00 C 17164 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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: 2.73 Conformation dependent library (CDL) restraints added in 1.1 seconds 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6236 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 38 sheets defined 34.0% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.893A 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: 3.619A 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: 3.941A 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: 3.569A 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 1032 removed outlier: 4.242A 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 364 through 370 removed outlier: 4.378A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.664A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.094A 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: 3.604A 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: 3.936A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.501A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.057A 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: 3.525A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.975A 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: 3.584A 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 897 through 909 removed outlier: 3.543A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.912A 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 removed outlier: 3.503A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.114A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.798A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.794A 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: 4.077A 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: 3.944A 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: 3.704A 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: 3.740A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.889A 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: 3.823A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.528A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.689A 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: 4.186A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.961A 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: 3.540A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.382A 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: 3.781A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.375A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.578A 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: 3.910A 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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 78 through 79 current: chain 'A' and resid 188 through 197 removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.280A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.177A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.025A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 163 removed outlier: 9.514A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.391A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.340A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.253A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.048A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.065A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.630A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1078 removed outlier: 3.906A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.288A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.946A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 6.374A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.054A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 11.426A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.521A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.694A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.160A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.081A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.068A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.840A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.922A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.251A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 6.183A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.122A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 85 current: chain 'C' and resid 116 through 121 removed outlier: 6.843A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 154 through 172 current: chain 'C' and resid 259 through 260 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.586A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.032A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1078 removed outlier: 3.907A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.341A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.736A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.020A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.316A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1107 hydrogen bonds defined for protein. 3125 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: 6.44 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8501 1.34 - 1.47: 6926 1.47 - 1.59: 11985 1.59 - 1.72: 0 1.72 - 1.85: 172 Bond restraints: 27584 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.57e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.49e+00 ... (remaining 27579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 36215 2.00 - 4.00: 1192 4.00 - 6.00: 87 6.00 - 7.99: 28 7.99 - 9.99: 10 Bond angle restraints: 37532 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.31 -5.61 1.22e+00 6.72e-01 2.12e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.36 128.86 -6.50 1.42e+00 4.96e-01 2.10e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.18 -5.48 1.22e+00 6.72e-01 2.02e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.07 -5.37 1.22e+00 6.72e-01 1.94e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 123.58 -9.18 2.30e+00 1.89e-01 1.59e+01 ... (remaining 37527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 15862 17.91 - 35.83: 1083 35.83 - 53.74: 202 53.74 - 71.66: 61 71.66 - 89.57: 37 Dihedral angle restraints: 17245 sinusoidal: 7582 harmonic: 9663 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 -46.45 -39.55 1 1.00e+01 1.00e-02 2.20e+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 19.57 59.43 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ALA E 396 " pdb=" C ALA E 396 " pdb=" N ASN E 397 " pdb=" CA ASN E 397 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 17242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3506 0.068 - 0.136: 783 0.136 - 0.204: 111 0.204 - 0.271: 10 0.271 - 0.339: 3 Chirality restraints: 4413 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 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+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 -2.09 -0.31 2.00e-01 2.50e+01 2.37e+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 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 4410 not shown) Planarity restraints: 4819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.64e+00 pdb=" C ARG E 169 " -0.054 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.020 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 902 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C MET A 902 " 0.051 2.00e-02 2.50e+03 pdb=" O MET A 902 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA A 903 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 319 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C ARG C 319 " -0.046 2.00e-02 2.50e+03 pdb=" O ARG C 319 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL C 320 " 0.016 2.00e-02 2.50e+03 ... (remaining 4816 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7622 2.82 - 3.34: 23438 3.34 - 3.86: 46856 3.86 - 4.38: 53185 4.38 - 4.90: 91280 Nonbonded interactions: 222381 Sorted by model distance: nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.298 3.040 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.305 3.040 nonbonded pdb=" OD1 ASN A 540 " pdb=" OG1 THR A 549 " model vdw 2.315 3.040 ... (remaining 222376 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.320 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 0.059 27682 Z= 0.239 Angle : 0.838 14.879 37790 Z= 0.444 Chirality : 0.057 0.339 4413 Planarity : 0.006 0.065 4775 Dihedral : 13.195 89.574 10901 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -0.02 (0.13), residues: 3264 helix: 0.85 (0.14), residues: 994 sheet: 0.53 (0.20), residues: 630 loop : -0.75 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 328 TYR 0.032 0.002 TYR E 385 PHE 0.033 0.002 PHE C 238 TRP 0.022 0.002 TRP A 886 HIS 0.007 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00488 (27584) covalent geometry : angle 0.80470 (37532) SS BOND : bond 0.00288 ( 36) SS BOND : angle 1.64928 ( 72) hydrogen bonds : bond 0.12332 ( 1107) hydrogen bonds : angle 6.71830 ( 3125) link_BETA1-4 : bond 0.00513 ( 18) link_BETA1-4 : angle 1.62129 ( 54) link_NAG-ASN : bond 0.00690 ( 44) link_NAG-ASN : angle 3.80142 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7300 (m-80) cc_final: 0.6448 (m-80) REVERT: A 173 GLN cc_start: 0.8667 (mp10) cc_final: 0.8347 (tp-100) REVERT: A 174 PRO cc_start: 0.6589 (Cg_endo) cc_final: 0.5203 (Cg_exo) REVERT: A 200 TYR cc_start: 0.8856 (m-80) cc_final: 0.8377 (t80) REVERT: A 1029 MET cc_start: 0.9147 (tpp) cc_final: 0.8861 (tpp) REVERT: B 340 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8459 (pt0) REVERT: B 365 TYR cc_start: 0.8763 (m-80) cc_final: 0.8469 (m-80) REVERT: B 378 LYS cc_start: 0.9340 (tptt) cc_final: 0.8985 (tptm) REVERT: B 380 TYR cc_start: 0.8061 (m-80) cc_final: 0.7470 (m-80) REVERT: B 1029 MET cc_start: 0.9201 (tpp) cc_final: 0.8946 (tpp) REVERT: C 54 LEU cc_start: 0.9058 (mm) cc_final: 0.8614 (mt) REVERT: C 79 PHE cc_start: 0.7282 (t80) cc_final: 0.6864 (t80) REVERT: C 129 LYS cc_start: 0.8302 (mtmt) cc_final: 0.8006 (tttp) REVERT: C 197 ILE cc_start: 0.9039 (mm) cc_final: 0.8715 (mp) REVERT: C 571 ASP cc_start: 0.8491 (m-30) cc_final: 0.8163 (p0) REVERT: C 1029 MET cc_start: 0.9156 (tpp) cc_final: 0.8905 (tpt) REVERT: E 360 MET cc_start: 0.4014 (ttm) cc_final: 0.3765 (ttt) REVERT: E 474 MET cc_start: -0.0013 (mmt) cc_final: -0.1355 (mtp) outliers start: 0 outliers final: 1 residues processed: 220 average time/residue: 0.7760 time to fit residues: 195.7664 Evaluate side-chains 105 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 213 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN E 374 HIS E 472 GLN E 552 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.095622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.058212 restraints weight = 96135.969| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.59 r_work: 0.2989 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27682 Z= 0.192 Angle : 0.604 10.597 37790 Z= 0.301 Chirality : 0.044 0.263 4413 Planarity : 0.004 0.052 4775 Dihedral : 6.540 99.921 4839 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.03 % Allowed : 6.00 % Favored : 92.97 % 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: 0.58 (0.14), residues: 3264 helix: 1.88 (0.16), residues: 992 sheet: 0.40 (0.20), residues: 614 loop : -0.53 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 319 TYR 0.017 0.001 TYR B1067 PHE 0.019 0.001 PHE C 135 TRP 0.019 0.002 TRP E 606 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00429 (27584) covalent geometry : angle 0.57717 (37532) SS BOND : bond 0.00237 ( 36) SS BOND : angle 1.06527 ( 72) hydrogen bonds : bond 0.04455 ( 1107) hydrogen bonds : angle 5.40797 ( 3125) link_BETA1-4 : bond 0.00199 ( 18) link_BETA1-4 : angle 1.07275 ( 54) link_NAG-ASN : bond 0.00563 ( 44) link_NAG-ASN : angle 2.91101 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7443 (m-80) cc_final: 0.6996 (m-80) REVERT: A 173 GLN cc_start: 0.8780 (mp10) cc_final: 0.8307 (tp-100) REVERT: A 174 PRO cc_start: 0.6905 (Cg_endo) cc_final: 0.5479 (Cg_exo) REVERT: A 200 TYR cc_start: 0.9057 (m-80) cc_final: 0.8651 (t80) REVERT: A 1029 MET cc_start: 0.9532 (tpp) cc_final: 0.9295 (tpp) REVERT: B 175 PHE cc_start: 0.5802 (m-10) cc_final: 0.5420 (m-10) REVERT: B 314 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8220 (tm-30) REVERT: B 340 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8620 (pt0) REVERT: B 365 TYR cc_start: 0.8865 (m-80) cc_final: 0.8372 (m-80) REVERT: B 378 LYS cc_start: 0.9229 (tptt) cc_final: 0.9022 (tptm) REVERT: B 387 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8363 (mm) REVERT: B 950 ASP cc_start: 0.8875 (m-30) cc_final: 0.8650 (m-30) REVERT: C 79 PHE cc_start: 0.7527 (t80) cc_final: 0.7057 (t80) REVERT: C 238 PHE cc_start: 0.6557 (p90) cc_final: 0.6316 (p90) REVERT: C 571 ASP cc_start: 0.8749 (m-30) cc_final: 0.8426 (p0) REVERT: E 474 MET cc_start: -0.0093 (mmt) cc_final: -0.0767 (ttm) outliers start: 30 outliers final: 6 residues processed: 135 average time/residue: 0.7448 time to fit residues: 116.1925 Evaluate side-chains 100 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain E residue 341 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 110 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 824 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN E 524 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.094981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.057517 restraints weight = 95421.990| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.52 r_work: 0.2956 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27682 Z= 0.200 Angle : 0.585 10.178 37790 Z= 0.288 Chirality : 0.044 0.278 4413 Planarity : 0.004 0.055 4775 Dihedral : 5.859 53.914 4837 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.20 % Allowed : 6.76 % Favored : 92.04 % 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: 0.76 (0.14), residues: 3264 helix: 2.15 (0.16), residues: 1001 sheet: 0.41 (0.21), residues: 586 loop : -0.46 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.018 0.001 TYR B1067 PHE 0.019 0.001 PHE A 133 TRP 0.017 0.001 TRP E 606 HIS 0.004 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00447 (27584) covalent geometry : angle 0.55820 (37532) SS BOND : bond 0.00228 ( 36) SS BOND : angle 0.97194 ( 72) hydrogen bonds : bond 0.04253 ( 1107) hydrogen bonds : angle 5.16189 ( 3125) link_BETA1-4 : bond 0.00195 ( 18) link_BETA1-4 : angle 1.17132 ( 54) link_NAG-ASN : bond 0.00593 ( 44) link_NAG-ASN : angle 2.87733 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.8710 (mp10) cc_final: 0.8254 (tp-100) REVERT: A 174 PRO cc_start: 0.6906 (Cg_endo) cc_final: 0.5450 (Cg_exo) REVERT: A 200 TYR cc_start: 0.9042 (m-80) cc_final: 0.8599 (t80) REVERT: A 1145 LEU cc_start: 0.7783 (tp) cc_final: 0.7484 (pp) REVERT: B 118 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8198 (mm) REVERT: B 314 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: B 340 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8661 (pt0) REVERT: B 365 TYR cc_start: 0.9005 (m-80) cc_final: 0.8400 (m-80) REVERT: B 378 LYS cc_start: 0.9212 (tptt) cc_final: 0.8950 (tptp) REVERT: B 380 TYR cc_start: 0.8522 (m-80) cc_final: 0.8044 (m-80) REVERT: B 387 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8480 (mm) REVERT: B 390 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8850 (tm) REVERT: B 950 ASP cc_start: 0.8903 (m-30) cc_final: 0.8629 (m-30) REVERT: C 79 PHE cc_start: 0.7612 (t80) cc_final: 0.7144 (t80) REVERT: C 571 ASP cc_start: 0.8906 (m-30) cc_final: 0.8496 (p0) REVERT: E 285 PHE cc_start: 0.4616 (OUTLIER) cc_final: 0.4041 (m-80) REVERT: E 474 MET cc_start: 0.0044 (mmt) cc_final: -0.0473 (mtp) outliers start: 35 outliers final: 10 residues processed: 127 average time/residue: 0.6288 time to fit residues: 94.0334 Evaluate side-chains 104 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain E residue 341 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 149 optimal weight: 5.9990 chunk 157 optimal weight: 0.0170 chunk 330 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.094269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.056716 restraints weight = 95414.312| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.53 r_work: 0.2932 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 27682 Z= 0.214 Angle : 0.579 10.400 37790 Z= 0.285 Chirality : 0.044 0.283 4413 Planarity : 0.004 0.054 4775 Dihedral : 5.612 55.750 4837 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.30 % Allowed : 7.79 % Favored : 90.91 % 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: 0.82 (0.14), residues: 3264 helix: 2.25 (0.16), residues: 994 sheet: 0.26 (0.20), residues: 603 loop : -0.38 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 214 TYR 0.018 0.001 TYR B1067 PHE 0.020 0.001 PHE B 175 TRP 0.022 0.001 TRP A 104 HIS 0.004 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00481 (27584) covalent geometry : angle 0.55827 (37532) SS BOND : bond 0.00229 ( 36) SS BOND : angle 0.82116 ( 72) hydrogen bonds : bond 0.04199 ( 1107) hydrogen bonds : angle 5.04878 ( 3125) link_BETA1-4 : bond 0.00175 ( 18) link_BETA1-4 : angle 1.23447 ( 54) link_NAG-ASN : bond 0.00655 ( 44) link_NAG-ASN : angle 2.54054 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7467 (m-80) cc_final: 0.6975 (m-10) REVERT: A 173 GLN cc_start: 0.8633 (mp10) cc_final: 0.8200 (tp-100) REVERT: A 174 PRO cc_start: 0.7051 (Cg_endo) cc_final: 0.5471 (Cg_exo) REVERT: A 200 TYR cc_start: 0.9062 (m-80) cc_final: 0.8599 (t80) REVERT: A 1145 LEU cc_start: 0.7861 (tp) cc_final: 0.7539 (pp) REVERT: B 118 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8225 (mm) REVERT: B 314 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8234 (tm-30) REVERT: B 340 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8713 (pt0) REVERT: B 378 LYS cc_start: 0.9248 (tptt) cc_final: 0.9017 (tptm) REVERT: B 380 TYR cc_start: 0.8561 (m-80) cc_final: 0.8171 (m-80) REVERT: C 129 LYS cc_start: 0.8397 (mtmt) cc_final: 0.8023 (tttp) REVERT: C 1002 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: E 285 PHE cc_start: 0.4525 (OUTLIER) cc_final: 0.3963 (m-80) REVERT: E 474 MET cc_start: 0.0233 (mmt) cc_final: -0.0397 (mtp) REVERT: E 549 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7403 (mp0) outliers start: 38 outliers final: 8 residues processed: 121 average time/residue: 0.7632 time to fit residues: 107.4298 Evaluate side-chains 98 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain E residue 549 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 82 optimal weight: 0.9980 chunk 312 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 304 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 564 GLN B 907 ASN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.095227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.058246 restraints weight = 94911.014| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.51 r_work: 0.2973 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 27682 Z= 0.109 Angle : 0.528 10.325 37790 Z= 0.260 Chirality : 0.043 0.287 4413 Planarity : 0.003 0.067 4775 Dihedral : 5.241 56.460 4837 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.10 % Allowed : 8.71 % Favored : 90.19 % 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: 0.98 (0.14), residues: 3264 helix: 2.42 (0.16), residues: 997 sheet: 0.40 (0.22), residues: 533 loop : -0.31 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 214 TYR 0.015 0.001 TYR C1067 PHE 0.013 0.001 PHE B 898 TRP 0.024 0.001 TRP A 104 HIS 0.011 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00234 (27584) covalent geometry : angle 0.50871 (37532) SS BOND : bond 0.00146 ( 36) SS BOND : angle 0.64758 ( 72) hydrogen bonds : bond 0.03800 ( 1107) hydrogen bonds : angle 4.86662 ( 3125) link_BETA1-4 : bond 0.00322 ( 18) link_BETA1-4 : angle 1.05045 ( 54) link_NAG-ASN : bond 0.00507 ( 44) link_NAG-ASN : angle 2.35655 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7317 (m-80) cc_final: 0.6666 (m-10) REVERT: A 173 GLN cc_start: 0.8609 (mp10) cc_final: 0.8197 (tp-100) REVERT: A 174 PRO cc_start: 0.6998 (Cg_endo) cc_final: 0.5413 (Cg_exo) REVERT: A 200 TYR cc_start: 0.9071 (m-80) cc_final: 0.8557 (t80) REVERT: A 780 GLU cc_start: 0.9337 (OUTLIER) cc_final: 0.8657 (mp0) REVERT: B 118 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8235 (mm) REVERT: B 340 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8658 (pt0) REVERT: B 365 TYR cc_start: 0.8887 (m-80) cc_final: 0.8478 (m-80) REVERT: B 378 LYS cc_start: 0.9248 (tptt) cc_final: 0.9022 (tptm) REVERT: B 380 TYR cc_start: 0.8526 (m-80) cc_final: 0.8096 (m-10) REVERT: B 486 PHE cc_start: 0.8018 (t80) cc_final: 0.7678 (t80) REVERT: C 113 LYS cc_start: 0.9309 (tppt) cc_final: 0.9005 (tptp) REVERT: C 129 LYS cc_start: 0.8390 (mtmt) cc_final: 0.8013 (tttp) REVERT: E 82 MET cc_start: 0.7602 (mpp) cc_final: 0.7262 (tmm) REVERT: E 285 PHE cc_start: 0.4454 (OUTLIER) cc_final: 0.3791 (m-80) REVERT: E 323 MET cc_start: 0.7552 (mmp) cc_final: 0.7173 (mmm) REVERT: E 474 MET cc_start: -0.0198 (mmt) cc_final: -0.0765 (mtp) REVERT: E 579 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5493 (tpp) outliers start: 32 outliers final: 9 residues processed: 117 average time/residue: 0.7661 time to fit residues: 104.4320 Evaluate side-chains 102 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 609 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 307 optimal weight: 30.0000 chunk 229 optimal weight: 4.9990 chunk 292 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 824 ASN B 907 ASN C 245 HIS C 824 ASN C 872 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.091917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.054354 restraints weight = 96201.752| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.45 r_work: 0.2874 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 27682 Z= 0.399 Angle : 0.733 11.972 37790 Z= 0.360 Chirality : 0.049 0.305 4413 Planarity : 0.004 0.059 4775 Dihedral : 6.020 55.977 4837 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.10 % Allowed : 9.61 % Favored : 89.30 % 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: 0.47 (0.14), residues: 3264 helix: 1.94 (0.16), residues: 984 sheet: -0.09 (0.19), residues: 653 loop : -0.50 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1039 TYR 0.022 0.002 TYR B1067 PHE 0.024 0.002 PHE B 898 TRP 0.027 0.002 TRP A 104 HIS 0.005 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00904 (27584) covalent geometry : angle 0.71355 (37532) SS BOND : bond 0.00367 ( 36) SS BOND : angle 0.91105 ( 72) hydrogen bonds : bond 0.04983 ( 1107) hydrogen bonds : angle 5.28778 ( 3125) link_BETA1-4 : bond 0.00459 ( 18) link_BETA1-4 : angle 1.82992 ( 54) link_NAG-ASN : bond 0.00906 ( 44) link_NAG-ASN : angle 2.72224 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8408 (m-30) cc_final: 0.8119 (p0) REVERT: A 133 PHE cc_start: 0.7407 (m-80) cc_final: 0.6893 (m-10) REVERT: A 173 GLN cc_start: 0.8645 (mp10) cc_final: 0.8242 (tp-100) REVERT: A 174 PRO cc_start: 0.7172 (Cg_endo) cc_final: 0.5711 (Cg_exo) REVERT: A 200 TYR cc_start: 0.9065 (m-80) cc_final: 0.8559 (t80) REVERT: A 1145 LEU cc_start: 0.8147 (tp) cc_final: 0.7858 (pp) REVERT: B 340 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8791 (pt0) REVERT: B 378 LYS cc_start: 0.9222 (tptt) cc_final: 0.8944 (tptm) REVERT: B 380 TYR cc_start: 0.8484 (m-80) cc_final: 0.7849 (m-80) REVERT: B 486 PHE cc_start: 0.8064 (t80) cc_final: 0.7742 (t80) REVERT: C 129 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8139 (tttp) REVERT: E 82 MET cc_start: 0.7616 (mpp) cc_final: 0.7302 (tmm) REVERT: E 267 LEU cc_start: 0.3697 (OUTLIER) cc_final: 0.3477 (pp) REVERT: E 285 PHE cc_start: 0.4670 (OUTLIER) cc_final: 0.4119 (m-80) REVERT: E 455 MET cc_start: 0.5969 (pp-130) cc_final: 0.5609 (ptm) REVERT: E 474 MET cc_start: 0.0675 (mmt) cc_final: -0.0365 (ttm) REVERT: E 557 MET cc_start: 0.7903 (tmm) cc_final: 0.7678 (tmm) outliers start: 32 outliers final: 7 residues processed: 109 average time/residue: 0.7194 time to fit residues: 91.7630 Evaluate side-chains 89 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 285 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 295 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 184 optimal weight: 0.7980 chunk 320 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 250 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN B 907 ASN C 907 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.093973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.056767 restraints weight = 94285.272| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.45 r_work: 0.2946 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27682 Z= 0.133 Angle : 0.552 9.872 37790 Z= 0.273 Chirality : 0.043 0.278 4413 Planarity : 0.004 0.068 4775 Dihedral : 5.486 55.758 4837 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.65 % Allowed : 10.26 % Favored : 89.09 % 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: 0.81 (0.14), residues: 3264 helix: 2.33 (0.16), residues: 984 sheet: 0.13 (0.21), residues: 578 loop : -0.37 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 214 TYR 0.022 0.001 TYR E 385 PHE 0.014 0.001 PHE B 898 TRP 0.029 0.001 TRP A 104 HIS 0.004 0.001 BHIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00294 (27584) covalent geometry : angle 0.53433 (37532) SS BOND : bond 0.00148 ( 36) SS BOND : angle 0.60773 ( 72) hydrogen bonds : bond 0.03987 ( 1107) hydrogen bonds : angle 4.92493 ( 3125) link_BETA1-4 : bond 0.00282 ( 18) link_BETA1-4 : angle 1.08804 ( 54) link_NAG-ASN : bond 0.00512 ( 44) link_NAG-ASN : angle 2.32434 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7427 (m-80) cc_final: 0.6976 (m-10) REVERT: A 173 GLN cc_start: 0.8507 (mp10) cc_final: 0.8199 (tp-100) REVERT: A 174 PRO cc_start: 0.7110 (Cg_endo) cc_final: 0.5572 (Cg_exo) REVERT: A 200 TYR cc_start: 0.9086 (m-80) cc_final: 0.8646 (m-80) REVERT: B 340 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8699 (pt0) REVERT: B 378 LYS cc_start: 0.9268 (tptt) cc_final: 0.9049 (tptm) REVERT: B 380 TYR cc_start: 0.8492 (m-80) cc_final: 0.8074 (m-10) REVERT: B 486 PHE cc_start: 0.8035 (t80) cc_final: 0.7710 (t80) REVERT: B 979 ASP cc_start: 0.8746 (m-30) cc_final: 0.8274 (t0) REVERT: C 135 PHE cc_start: 0.7792 (m-80) cc_final: 0.7579 (m-80) REVERT: E 285 PHE cc_start: 0.4581 (OUTLIER) cc_final: 0.3922 (m-80) REVERT: E 323 MET cc_start: 0.7918 (mmp) cc_final: 0.7526 (mmm) REVERT: E 455 MET cc_start: 0.5848 (pp-130) cc_final: 0.5472 (ptm) REVERT: E 474 MET cc_start: 0.0218 (mmt) cc_final: -0.0496 (mtp) outliers start: 19 outliers final: 5 residues processed: 100 average time/residue: 0.7724 time to fit residues: 89.7572 Evaluate side-chains 88 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain E residue 285 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 9 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 chunk 324 optimal weight: 20.0000 chunk 295 optimal weight: 9.9990 chunk 207 optimal weight: 0.2980 chunk 290 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 292 optimal weight: 20.0000 chunk 267 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN B 907 ASN C 907 ASN C1083 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.091137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.052070 restraints weight = 96455.227| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.05 r_work: 0.2890 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.066 27682 Z= 0.462 Angle : 0.775 13.404 37790 Z= 0.381 Chirality : 0.051 0.304 4413 Planarity : 0.005 0.057 4775 Dihedral : 6.245 53.853 4837 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.79 % Allowed : 10.33 % Favored : 88.89 % 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: 0.21 (0.14), residues: 3264 helix: 1.84 (0.16), residues: 983 sheet: -0.26 (0.19), residues: 674 loop : -0.74 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 214 TYR 0.024 0.002 TYR E 83 PHE 0.025 0.002 PHE B 898 TRP 0.030 0.002 TRP A 104 HIS 0.007 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.01048 (27584) covalent geometry : angle 0.75515 (37532) SS BOND : bond 0.00414 ( 36) SS BOND : angle 0.92058 ( 72) hydrogen bonds : bond 0.05057 ( 1107) hydrogen bonds : angle 5.36322 ( 3125) link_BETA1-4 : bond 0.00526 ( 18) link_BETA1-4 : angle 1.94538 ( 54) link_NAG-ASN : bond 0.00985 ( 44) link_NAG-ASN : angle 2.80286 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8366 (m-30) cc_final: 0.8080 (p0) REVERT: A 133 PHE cc_start: 0.7392 (m-80) cc_final: 0.7043 (m-10) REVERT: A 200 TYR cc_start: 0.9076 (m-80) cc_final: 0.8598 (t80) REVERT: C 135 PHE cc_start: 0.7836 (m-80) cc_final: 0.7590 (m-80) REVERT: E 82 MET cc_start: 0.8377 (tmm) cc_final: 0.8156 (mpt) REVERT: E 285 PHE cc_start: 0.4195 (OUTLIER) cc_final: 0.3414 (m-80) REVERT: E 455 MET cc_start: 0.5834 (pp-130) cc_final: 0.5441 (ptm) REVERT: E 474 MET cc_start: 0.0494 (mmt) cc_final: -0.0476 (ttm) outliers start: 23 outliers final: 6 residues processed: 99 average time/residue: 0.6463 time to fit residues: 75.4782 Evaluate side-chains 84 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain E residue 285 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 188 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 chunk 302 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 259 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 314 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 907 ASN C 907 ASN C 925 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.093326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.056596 restraints weight = 95885.250| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.64 r_work: 0.2929 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27682 Z= 0.126 Angle : 0.576 12.720 37790 Z= 0.283 Chirality : 0.044 0.278 4413 Planarity : 0.004 0.083 4775 Dihedral : 5.569 56.026 4837 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.62 % Allowed : 10.84 % Favored : 88.54 % 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: 0.67 (0.14), residues: 3264 helix: 2.34 (0.16), residues: 981 sheet: -0.19 (0.20), residues: 608 loop : -0.43 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 214 TYR 0.020 0.001 TYR E 385 PHE 0.022 0.001 PHE E 315 TRP 0.037 0.001 TRP A 104 HIS 0.005 0.001 BHIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00277 (27584) covalent geometry : angle 0.55950 (37532) SS BOND : bond 0.00154 ( 36) SS BOND : angle 0.64598 ( 72) hydrogen bonds : bond 0.03929 ( 1107) hydrogen bonds : angle 4.93957 ( 3125) link_BETA1-4 : bond 0.00338 ( 18) link_BETA1-4 : angle 1.08631 ( 54) link_NAG-ASN : bond 0.00511 ( 44) link_NAG-ASN : angle 2.32432 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8344 (m-30) cc_final: 0.7971 (p0) REVERT: A 133 PHE cc_start: 0.7301 (m-80) cc_final: 0.7066 (m-10) REVERT: A 200 TYR cc_start: 0.9089 (m-80) cc_final: 0.8678 (m-80) REVERT: A 957 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8055 (tm-30) REVERT: B 354 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.8006 (m-40) REVERT: B 365 TYR cc_start: 0.8815 (m-80) cc_final: 0.8424 (m-80) REVERT: B 979 ASP cc_start: 0.8725 (m-30) cc_final: 0.8208 (t0) REVERT: B 1092 GLU cc_start: 0.8441 (pm20) cc_final: 0.7936 (tm-30) REVERT: C 135 PHE cc_start: 0.7776 (m-80) cc_final: 0.7574 (m-80) REVERT: E 285 PHE cc_start: 0.4179 (OUTLIER) cc_final: 0.3558 (m-80) REVERT: E 323 MET cc_start: 0.7840 (mmp) cc_final: 0.7398 (mmm) REVERT: E 474 MET cc_start: 0.0499 (mmt) cc_final: -0.0196 (mtp) REVERT: E 579 MET cc_start: 0.6165 (OUTLIER) cc_final: 0.5585 (tpp) outliers start: 18 outliers final: 8 residues processed: 97 average time/residue: 0.7415 time to fit residues: 83.9074 Evaluate side-chains 91 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 262 optimal weight: 0.4980 chunk 147 optimal weight: 0.0670 chunk 85 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 328 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN E 250 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.094152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.057439 restraints weight = 95029.452| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.60 r_work: 0.2960 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27682 Z= 0.110 Angle : 0.561 13.709 37790 Z= 0.273 Chirality : 0.043 0.274 4413 Planarity : 0.004 0.055 4775 Dihedral : 5.082 54.836 4837 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.51 % Allowed : 11.01 % Favored : 88.47 % 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 (0.15), residues: 3264 helix: 2.48 (0.16), residues: 979 sheet: -0.08 (0.21), residues: 618 loop : -0.32 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 214 TYR 0.016 0.001 TYR E 385 PHE 0.021 0.001 PHE E 315 TRP 0.038 0.001 TRP A 104 HIS 0.004 0.001 BHIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00240 (27584) covalent geometry : angle 0.54404 (37532) SS BOND : bond 0.00143 ( 36) SS BOND : angle 0.59780 ( 72) hydrogen bonds : bond 0.03769 ( 1107) hydrogen bonds : angle 4.78971 ( 3125) link_BETA1-4 : bond 0.00216 ( 18) link_BETA1-4 : angle 1.17161 ( 54) link_NAG-ASN : bond 0.00492 ( 44) link_NAG-ASN : angle 2.24490 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.9021 (m-80) cc_final: 0.8604 (m-80) REVERT: A 780 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.8948 (mp0) REVERT: A 957 GLN cc_start: 0.8316 (tm-30) cc_final: 0.8049 (tm-30) REVERT: B 354 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8171 (m-40) REVERT: B 365 TYR cc_start: 0.8868 (m-80) cc_final: 0.8507 (m-80) REVERT: B 979 ASP cc_start: 0.8706 (m-30) cc_final: 0.8206 (t0) REVERT: B 1092 GLU cc_start: 0.8467 (pm20) cc_final: 0.8045 (tm-30) REVERT: E 82 MET cc_start: 0.8484 (tmm) cc_final: 0.8111 (mpt) REVERT: E 285 PHE cc_start: 0.4529 (OUTLIER) cc_final: 0.3920 (m-80) REVERT: E 323 MET cc_start: 0.7747 (mmp) cc_final: 0.7301 (mmm) REVERT: E 455 MET cc_start: 0.5942 (pp-130) cc_final: 0.5652 (ptm) REVERT: E 474 MET cc_start: 0.0455 (mmt) cc_final: -0.0358 (mtp) REVERT: E 579 MET cc_start: 0.6218 (OUTLIER) cc_final: 0.5595 (tpp) outliers start: 15 outliers final: 5 residues processed: 95 average time/residue: 0.7506 time to fit residues: 83.4430 Evaluate side-chains 86 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 311 optimal weight: 20.0000 chunk 219 optimal weight: 9.9990 chunk 275 optimal weight: 20.0000 chunk 76 optimal weight: 0.0870 chunk 297 optimal weight: 0.6980 chunk 259 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 97 optimal weight: 30.0000 chunk 203 optimal weight: 9.9990 chunk 187 optimal weight: 0.6980 overall best weight: 1.2560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1011 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.093879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.057072 restraints weight = 95059.655| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.61 r_work: 0.2947 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27682 Z= 0.137 Angle : 0.569 12.920 37790 Z= 0.276 Chirality : 0.043 0.277 4413 Planarity : 0.004 0.061 4775 Dihedral : 4.989 54.643 4837 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.27 % Allowed : 11.39 % 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: 0.89 (0.15), residues: 3264 helix: 2.52 (0.16), residues: 981 sheet: -0.06 (0.21), residues: 618 loop : -0.30 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 214 TYR 0.022 0.001 TYR B 380 PHE 0.036 0.001 PHE A 133 TRP 0.035 0.001 TRP A 104 HIS 0.004 0.001 BHIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00308 (27584) covalent geometry : angle 0.55286 (37532) SS BOND : bond 0.00143 ( 36) SS BOND : angle 0.61726 ( 72) hydrogen bonds : bond 0.03770 ( 1107) hydrogen bonds : angle 4.75960 ( 3125) link_BETA1-4 : bond 0.00222 ( 18) link_BETA1-4 : angle 1.14083 ( 54) link_NAG-ASN : bond 0.00491 ( 44) link_NAG-ASN : angle 2.23025 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14621.47 seconds wall clock time: 248 minutes 46.61 seconds (14926.61 seconds total)