Starting phenix.real_space_refine on Fri Mar 6 18:52:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9k_25760/03_2026/7t9k_25760.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9k_25760/03_2026/7t9k_25760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t9k_25760/03_2026/7t9k_25760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9k_25760/03_2026/7t9k_25760.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9k_25760/03_2026/7t9k_25760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9k_25760/03_2026/7t9k_25760.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 161 5.16 5 C 21312 2.51 5 N 5454 2.21 5 O 6471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33398 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "B" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "C" Number of atoms: 6502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6502 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 45, 'TRANS': 787} Chain breaks: 9 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "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: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 7.98, per 1000 atoms: 0.24 Number of scatterers: 33398 At special positions: 0 Unit cell: (136, 158, 236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 161 16.00 O 6471 8.00 N 5454 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " 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 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " NAG F 1 " - " ASN A 17 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1074 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 17 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.3 seconds 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7698 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 44 sheets defined 38.2% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.686A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.041A 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: 3.608A 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: 3.936A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.000A 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 337 through 343 removed outlier: 3.582A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.678A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.763A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.972A 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: 3.582A 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: 3.938A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.053A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.586A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.824A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.606A 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 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.952A 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: 3.567A 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 1032 removed outlier: 4.092A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.737A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.271A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.567A pdb=" N SER D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 Proline residue: D 178 - end of helix removed outlier: 3.804A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 221 through 252 removed outlier: 4.037A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.816A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.538A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.863A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 4.382A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.588A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.415A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.800A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.338A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.517A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.710A 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 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.260A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.637A pdb=" N SER E 155 " --> pdb=" O ILE E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.790A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 221 through 252 removed outlier: 4.028A 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: 3.855A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.547A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.852A 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: 4.348A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA E 413 " --> pdb=" O SER E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.642A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.406A 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: 3.844A 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: 4.356A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.656A 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: 3.511A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.902A 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 removed outlier: 7.946A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.881A 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: 3.854A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.022A 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: 3.809A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.712A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.843A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.758A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.925A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.694A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.504A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.504A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.339A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.664A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.130A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.126A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.694A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.834A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.105A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.223A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.834A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.717A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.509A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 448 through 454 removed outlier: 6.133A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.721A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.857A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.455A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.530A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.530A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.340A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.047A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.063A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.819A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 11.664A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.675A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.611A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.928A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.939A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.467A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.467A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.344A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.800A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.187A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.925A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.174A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1580 hydrogen bonds defined for protein. 4494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.04 Time building geometry restraints manager: 3.86 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: 10338 1.34 - 1.46: 8517 1.46 - 1.58: 15111 1.58 - 1.71: 0 1.71 - 1.83: 230 Bond restraints: 34196 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.04e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.16e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.19e+00 ... (remaining 34191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 45443 2.50 - 4.99: 928 4.99 - 7.49: 99 7.49 - 9.98: 18 9.98 - 12.48: 10 Bond angle restraints: 46498 Sorted by residual: angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.46 128.98 -6.52 1.41e+00 5.03e-01 2.14e+01 angle pdb=" CB LYS E 534 " pdb=" CG LYS E 534 " pdb=" CD LYS E 534 " ideal model delta sigma weight residual 111.30 121.68 -10.38 2.30e+00 1.89e-01 2.04e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.18 -5.48 1.22e+00 6.72e-01 2.02e+01 angle pdb=" CB LYS D 534 " pdb=" CG LYS D 534 " pdb=" CD LYS D 534 " ideal model delta sigma weight residual 111.30 121.51 -10.21 2.30e+00 1.89e-01 1.97e+01 angle pdb=" C SER A 359 " pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 122.46 128.72 -6.26 1.41e+00 5.03e-01 1.97e+01 ... (remaining 46493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 19432 17.98 - 35.95: 1441 35.95 - 53.93: 266 53.93 - 71.90: 88 71.90 - 89.88: 38 Dihedral angle restraints: 21265 sinusoidal: 9331 harmonic: 11934 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 93.00 37.86 55.14 1 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 38.91 54.09 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CA GLN E 139 " pdb=" C GLN E 139 " pdb=" N GLU E 140 " pdb=" CA GLU E 140 " ideal model delta harmonic sigma weight residual 180.00 158.67 21.33 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 21262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4556 0.083 - 0.165: 768 0.165 - 0.248: 37 0.248 - 0.330: 1 0.330 - 0.413: 3 Chirality restraints: 5365 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 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 ... (remaining 5362 not shown) Planarity restraints: 5964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO B 337 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 954 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C HIS C 954 " -0.064 2.00e-02 2.50e+03 pdb=" O HIS C 954 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN C 955 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 958 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ALA C 958 " -0.060 2.00e-02 2.50e+03 pdb=" O ALA C 958 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU C 959 " 0.020 2.00e-02 2.50e+03 ... (remaining 5961 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7564 2.79 - 3.32: 29172 3.32 - 3.84: 57497 3.84 - 4.37: 65767 4.37 - 4.90: 113961 Nonbonded interactions: 273961 Sorted by model distance: nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.263 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.285 3.040 ... (remaining 273956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.270 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 0.084 34306 Z= 0.249 Angle : 0.890 15.414 46788 Z= 0.475 Chirality : 0.057 0.413 5365 Planarity : 0.007 0.102 5912 Dihedral : 13.590 89.877 13447 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.12), residues: 4027 helix: 0.53 (0.13), residues: 1367 sheet: 0.96 (0.19), residues: 665 loop : -0.76 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 582 TYR 0.038 0.002 TYR C1067 PHE 0.040 0.002 PHE B 981 TRP 0.036 0.002 TRP A 886 HIS 0.026 0.002 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00511 (34196) covalent geometry : angle 0.87047 (46498) SS BOND : bond 0.00271 ( 40) SS BOND : angle 1.29650 ( 80) hydrogen bonds : bond 0.12659 ( 1534) hydrogen bonds : angle 6.89191 ( 4494) link_BETA1-4 : bond 0.00579 ( 18) link_BETA1-4 : angle 1.62142 ( 54) link_NAG-ASN : bond 0.00681 ( 52) link_NAG-ASN : angle 3.17080 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 441 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.6173 (m-80) cc_final: 0.5451 (m-80) REVERT: A 508 TYR cc_start: 0.5819 (m-80) cc_final: 0.5449 (m-10) REVERT: B 140 PHE cc_start: 0.7087 (p90) cc_final: 0.6701 (p90) REVERT: B 207 HIS cc_start: 0.7929 (t-170) cc_final: 0.7713 (m-70) REVERT: B 238 PHE cc_start: 0.6509 (p90) cc_final: 0.5804 (p90) REVERT: B 534 VAL cc_start: 0.8821 (t) cc_final: 0.8574 (m) REVERT: B 973 ILE cc_start: 0.8906 (pt) cc_final: 0.8474 (mp) REVERT: B 978 ASN cc_start: 0.7725 (m-40) cc_final: 0.7091 (t0) REVERT: C 242 LEU cc_start: 0.7678 (mt) cc_final: 0.7051 (tp) REVERT: C 1142 GLN cc_start: 0.8673 (tp40) cc_final: 0.8054 (tp-100) REVERT: D 383 MET cc_start: 0.4491 (mtp) cc_final: 0.4269 (tmm) REVERT: E 22 GLU cc_start: 0.3216 (tm-30) cc_final: 0.1814 (pm20) REVERT: E 53 ASN cc_start: 0.3957 (t0) cc_final: 0.3383 (t0) REVERT: E 98 GLN cc_start: 0.4358 (mt0) cc_final: 0.4075 (mm110) REVERT: E 249 MET cc_start: 0.0399 (ttm) cc_final: 0.0008 (tmt) REVERT: E 383 MET cc_start: 0.1904 (mtp) cc_final: 0.1167 (tmm) REVERT: E 398 GLU cc_start: 0.2195 (pt0) cc_final: 0.1640 (mt-10) REVERT: E 441 LYS cc_start: 0.0970 (tttp) cc_final: 0.0536 (pptt) REVERT: E 484 ILE cc_start: 0.1073 (mt) cc_final: 0.0802 (mp) REVERT: E 495 GLU cc_start: 0.3320 (mp0) cc_final: 0.1811 (mt-10) REVERT: E 555 PHE cc_start: 0.2446 (t80) cc_final: 0.2084 (t80) REVERT: E 579 MET cc_start: 0.1953 (ptp) cc_final: 0.1280 (mpp) outliers start: 1 outliers final: 5 residues processed: 442 average time/residue: 0.6688 time to fit residues: 353.9150 Evaluate side-chains 209 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 204 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain E residue 142 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN A1142 GLN B 188 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN B 824 ASN C 907 ASN C1005 GLN D 117 ASN D 195 HIS D 374 HIS D 442 GLN D 522 GLN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS E 552 GLN E 586 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.186583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.111085 restraints weight = 68520.803| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.26 r_work: 0.3241 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 34306 Z= 0.200 Angle : 0.627 11.494 46788 Z= 0.316 Chirality : 0.046 0.269 5365 Planarity : 0.005 0.050 5912 Dihedral : 6.742 59.980 5854 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.72 % Allowed : 9.20 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.13), residues: 4027 helix: 1.30 (0.13), residues: 1390 sheet: 0.77 (0.20), residues: 617 loop : -0.51 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 192 TYR 0.027 0.002 TYR C1067 PHE 0.027 0.002 PHE D 315 TRP 0.024 0.002 TRP E 566 HIS 0.016 0.001 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00454 (34196) covalent geometry : angle 0.60356 (46498) SS BOND : bond 0.00230 ( 40) SS BOND : angle 0.93192 ( 80) hydrogen bonds : bond 0.04706 ( 1534) hydrogen bonds : angle 5.51563 ( 4494) link_BETA1-4 : bond 0.00252 ( 18) link_BETA1-4 : angle 1.22182 ( 54) link_NAG-ASN : bond 0.00529 ( 52) link_NAG-ASN : angle 2.89192 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 TYR cc_start: 0.6003 (m-80) cc_final: 0.5642 (m-10) REVERT: A 533 LEU cc_start: 0.7603 (tp) cc_final: 0.7255 (tp) REVERT: A 759 PHE cc_start: 0.8025 (m-80) cc_final: 0.7795 (m-80) REVERT: B 309 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8522 (mp0) REVERT: B 314 GLN cc_start: 0.8936 (tt0) cc_final: 0.8702 (tt0) REVERT: B 752 LEU cc_start: 0.9145 (mp) cc_final: 0.8723 (mp) REVERT: B 755 GLN cc_start: 0.8355 (mp10) cc_final: 0.7819 (mp10) REVERT: B 973 ILE cc_start: 0.8994 (pt) cc_final: 0.8680 (mp) REVERT: B 978 ASN cc_start: 0.7854 (m-40) cc_final: 0.7164 (t0) REVERT: B 985 ASP cc_start: 0.7798 (p0) cc_final: 0.7511 (p0) REVERT: C 320 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7762 (m) REVERT: D 152 MET cc_start: 0.1578 (pp-130) cc_final: 0.0654 (mmt) REVERT: D 270 MET cc_start: 0.1385 (ttm) cc_final: -0.0123 (mpp) REVERT: D 297 MET cc_start: -0.2172 (ttt) cc_final: -0.2599 (mtt) REVERT: D 383 MET cc_start: 0.4577 (mtp) cc_final: 0.4040 (tmm) REVERT: D 557 MET cc_start: 0.3602 (ptm) cc_final: 0.3130 (ptm) REVERT: D 572 ASN cc_start: 0.3510 (m-40) cc_final: 0.3071 (t0) REVERT: E 53 ASN cc_start: 0.3172 (t0) cc_final: 0.2771 (t0) REVERT: E 207 TYR cc_start: -0.1567 (m-80) cc_final: -0.2200 (m-10) REVERT: E 249 MET cc_start: 0.1702 (ttm) cc_final: 0.1255 (tmt) REVERT: E 366 MET cc_start: 0.3036 (tmm) cc_final: 0.2653 (tpt) REVERT: E 383 MET cc_start: 0.1866 (mtp) cc_final: 0.1149 (tmm) REVERT: E 495 GLU cc_start: 0.3654 (mp0) cc_final: 0.3252 (mt-10) REVERT: E 513 ILE cc_start: -0.0352 (OUTLIER) cc_final: -0.0912 (pt) REVERT: E 555 PHE cc_start: 0.2629 (t80) cc_final: 0.2421 (t80) outliers start: 62 outliers final: 13 residues processed: 248 average time/residue: 0.6814 time to fit residues: 204.1010 Evaluate side-chains 188 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 245 ARG Chi-restraints excluded: chain E residue 513 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 117 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 274 optimal weight: 3.9990 chunk 344 optimal weight: 20.0000 chunk 282 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 290 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 564 GLN A 755 GLN A 762 GLN A 907 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN C 314 GLN C 824 ASN C 978 ASN D 154 ASN D 175 GLN D 250 ASN D 374 HIS D 442 GLN D 524 GLN D 535 HIS ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN E 522 GLN E 535 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.182308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.105361 restraints weight = 68521.742| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.43 r_work: 0.3187 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 34306 Z= 0.229 Angle : 0.615 11.180 46788 Z= 0.309 Chirality : 0.046 0.282 5365 Planarity : 0.004 0.054 5912 Dihedral : 6.253 59.975 5842 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.06 % Allowed : 11.00 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.13), residues: 4027 helix: 1.51 (0.14), residues: 1396 sheet: 0.37 (0.20), residues: 612 loop : -0.50 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 518 TYR 0.027 0.002 TYR A 200 PHE 0.021 0.002 PHE C 275 TRP 0.030 0.002 TRP E 566 HIS 0.008 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00526 (34196) covalent geometry : angle 0.59459 (46498) SS BOND : bond 0.00275 ( 40) SS BOND : angle 0.83214 ( 80) hydrogen bonds : bond 0.04542 ( 1534) hydrogen bonds : angle 5.38761 ( 4494) link_BETA1-4 : bond 0.00220 ( 18) link_BETA1-4 : angle 1.18017 ( 54) link_NAG-ASN : bond 0.00583 ( 52) link_NAG-ASN : angle 2.71443 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 201 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6754 (t80) cc_final: 0.6436 (t80) REVERT: A 226 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.6999 (pt) REVERT: A 508 TYR cc_start: 0.6089 (m-80) cc_final: 0.5779 (m-10) REVERT: A 532 ASN cc_start: 0.9080 (m-40) cc_final: 0.8785 (t0) REVERT: A 533 LEU cc_start: 0.7677 (tp) cc_final: 0.7465 (tp) REVERT: B 200 TYR cc_start: 0.8207 (m-80) cc_final: 0.7589 (t80) REVERT: B 309 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8559 (mp0) REVERT: B 314 GLN cc_start: 0.8998 (tt0) cc_final: 0.8744 (tt0) REVERT: B 433 VAL cc_start: 0.3917 (OUTLIER) cc_final: 0.3658 (t) REVERT: B 752 LEU cc_start: 0.9171 (mp) cc_final: 0.8741 (mp) REVERT: B 755 GLN cc_start: 0.8476 (mp10) cc_final: 0.7986 (mp10) REVERT: B 978 ASN cc_start: 0.8083 (m-40) cc_final: 0.7413 (t0) REVERT: C 66 HIS cc_start: 0.6840 (t-90) cc_final: 0.6630 (t-90) REVERT: C 258 TRP cc_start: 0.0397 (p90) cc_final: 0.0174 (p90) REVERT: C 320 VAL cc_start: 0.7970 (OUTLIER) cc_final: 0.7766 (m) REVERT: C 983 ARG cc_start: 0.8140 (mtm180) cc_final: 0.7835 (mtp-110) REVERT: C 1092 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8448 (mm-30) REVERT: D 152 MET cc_start: 0.1440 (pp-130) cc_final: 0.0767 (mmt) REVERT: D 183 TYR cc_start: -0.0432 (OUTLIER) cc_final: -0.0936 (t80) REVERT: D 270 MET cc_start: 0.1740 (ttm) cc_final: 0.0232 (mpp) REVERT: D 292 ASP cc_start: 0.2757 (t0) cc_final: 0.2307 (p0) REVERT: D 297 MET cc_start: -0.1943 (ttt) cc_final: -0.2413 (mtt) REVERT: D 323 MET cc_start: 0.0500 (OUTLIER) cc_final: 0.0252 (mmt) REVERT: D 383 MET cc_start: 0.4643 (mtp) cc_final: 0.4402 (tmm) REVERT: D 557 MET cc_start: 0.3269 (ptm) cc_final: 0.2622 (ptm) REVERT: D 566 TRP cc_start: -0.0349 (p-90) cc_final: -0.0729 (p-90) REVERT: D 572 ASN cc_start: 0.3421 (m-40) cc_final: 0.3008 (t0) REVERT: D 579 MET cc_start: 0.1225 (mpp) cc_final: 0.0373 (mpm) REVERT: E 53 ASN cc_start: 0.2602 (t0) cc_final: 0.2227 (t0) REVERT: E 249 MET cc_start: 0.1961 (ttm) cc_final: 0.1498 (tmt) REVERT: E 323 MET cc_start: 0.1309 (tpt) cc_final: 0.0167 (tpt) REVERT: E 325 GLN cc_start: 0.2295 (OUTLIER) cc_final: 0.1781 (mm-40) REVERT: E 366 MET cc_start: 0.3116 (tmm) cc_final: 0.2871 (tpt) REVERT: E 383 MET cc_start: 0.2046 (mtp) cc_final: 0.1683 (tmm) REVERT: E 495 GLU cc_start: 0.3825 (mp0) cc_final: 0.3408 (mt-10) outliers start: 74 outliers final: 23 residues processed: 259 average time/residue: 0.6308 time to fit residues: 200.3452 Evaluate side-chains 205 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 123 optimal weight: 20.0000 chunk 98 optimal weight: 0.5980 chunk 406 optimal weight: 9.9990 chunk 246 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 218 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN D 221 GLN D 442 GLN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN E 522 GLN E 552 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.182542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.107021 restraints weight = 67433.971| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.89 r_work: 0.3216 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34306 Z= 0.189 Angle : 0.576 11.044 46788 Z= 0.289 Chirality : 0.045 0.279 5365 Planarity : 0.004 0.039 5912 Dihedral : 5.958 59.487 5842 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.61 % Allowed : 12.50 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.13), residues: 4027 helix: 1.62 (0.14), residues: 1405 sheet: 0.37 (0.20), residues: 588 loop : -0.47 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 518 TYR 0.023 0.001 TYR C1067 PHE 0.028 0.002 PHE E 555 TRP 0.029 0.001 TRP E 566 HIS 0.005 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00431 (34196) covalent geometry : angle 0.55581 (46498) SS BOND : bond 0.00230 ( 40) SS BOND : angle 0.69380 ( 80) hydrogen bonds : bond 0.04203 ( 1534) hydrogen bonds : angle 5.26087 ( 4494) link_BETA1-4 : bond 0.00258 ( 18) link_BETA1-4 : angle 1.13317 ( 54) link_NAG-ASN : bond 0.00542 ( 52) link_NAG-ASN : angle 2.59404 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 189 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6761 (t80) cc_final: 0.6554 (t80) REVERT: A 508 TYR cc_start: 0.6018 (m-80) cc_final: 0.5703 (m-10) REVERT: A 532 ASN cc_start: 0.8859 (m-40) cc_final: 0.8568 (t0) REVERT: A 960 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8392 (m110) REVERT: B 200 TYR cc_start: 0.8193 (m-80) cc_final: 0.7627 (t80) REVERT: B 309 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8524 (mp0) REVERT: B 314 GLN cc_start: 0.8966 (tt0) cc_final: 0.8754 (tp40) REVERT: B 433 VAL cc_start: 0.3822 (OUTLIER) cc_final: 0.3437 (t) REVERT: B 752 LEU cc_start: 0.9216 (mt) cc_final: 0.8760 (mp) REVERT: B 755 GLN cc_start: 0.8556 (mp10) cc_final: 0.7990 (mp10) REVERT: B 978 ASN cc_start: 0.8075 (m-40) cc_final: 0.7394 (t0) REVERT: C 258 TRP cc_start: 0.0210 (p90) cc_final: -0.0148 (p90) REVERT: C 983 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7809 (mtp-110) REVERT: D 152 MET cc_start: 0.1408 (pp-130) cc_final: 0.0713 (mmt) REVERT: D 183 TYR cc_start: -0.0401 (OUTLIER) cc_final: -0.0816 (t80) REVERT: D 270 MET cc_start: 0.1858 (ttm) cc_final: 0.0271 (mpp) REVERT: D 292 ASP cc_start: 0.2899 (t0) cc_final: 0.2404 (p0) REVERT: D 297 MET cc_start: -0.1941 (ttm) cc_final: -0.2442 (mtt) REVERT: D 383 MET cc_start: 0.4671 (mtp) cc_final: 0.4373 (tmm) REVERT: D 557 MET cc_start: 0.3678 (ptm) cc_final: 0.3200 (ptm) REVERT: D 572 ASN cc_start: 0.3347 (m-40) cc_final: 0.3099 (t0) REVERT: E 53 ASN cc_start: 0.2892 (t0) cc_final: 0.2469 (t0) REVERT: E 249 MET cc_start: 0.1636 (ttm) cc_final: 0.1098 (tmt) REVERT: E 291 ILE cc_start: 0.0279 (OUTLIER) cc_final: -0.0257 (tp) REVERT: E 323 MET cc_start: 0.0799 (tpt) cc_final: -0.0141 (tpt) REVERT: E 325 GLN cc_start: 0.2955 (OUTLIER) cc_final: 0.2597 (mm-40) REVERT: E 366 MET cc_start: 0.3069 (tmm) cc_final: 0.2768 (tpt) REVERT: E 383 MET cc_start: 0.2126 (mtp) cc_final: 0.1745 (tmm) REVERT: E 495 GLU cc_start: 0.3943 (mp0) cc_final: 0.3484 (mt-10) outliers start: 58 outliers final: 22 residues processed: 238 average time/residue: 0.6303 time to fit residues: 184.1999 Evaluate side-chains 193 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 325 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 336 optimal weight: 30.0000 chunk 231 optimal weight: 0.5980 chunk 368 optimal weight: 8.9990 chunk 373 optimal weight: 9.9990 chunk 214 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 383 optimal weight: 30.0000 chunk 330 optimal weight: 3.9990 chunk 334 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1142 GLN D 42 GLN D 221 GLN D 442 GLN E 76 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN E 522 GLN E 552 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.182849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.112362 restraints weight = 67069.984| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.60 r_work: 0.3159 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 34306 Z= 0.228 Angle : 0.602 11.010 46788 Z= 0.301 Chirality : 0.046 0.285 5365 Planarity : 0.004 0.105 5912 Dihedral : 5.933 58.520 5842 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.31 % Allowed : 12.50 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.13), residues: 4027 helix: 1.60 (0.14), residues: 1405 sheet: 0.21 (0.20), residues: 601 loop : -0.50 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.023 0.002 TYR C1067 PHE 0.032 0.002 PHE E 555 TRP 0.031 0.002 TRP E 566 HIS 0.013 0.001 HIS E 241 Details of bonding type rmsd covalent geometry : bond 0.00523 (34196) covalent geometry : angle 0.58210 (46498) SS BOND : bond 0.00277 ( 40) SS BOND : angle 0.75167 ( 80) hydrogen bonds : bond 0.04342 ( 1534) hydrogen bonds : angle 5.28981 ( 4494) link_BETA1-4 : bond 0.00220 ( 18) link_BETA1-4 : angle 1.18794 ( 54) link_NAG-ASN : bond 0.00587 ( 52) link_NAG-ASN : angle 2.61608 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 177 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.4513 (OUTLIER) cc_final: 0.3948 (tpm170) REVERT: A 79 PHE cc_start: 0.7042 (t80) cc_final: 0.6710 (t80) REVERT: A 118 LEU cc_start: 0.7841 (tm) cc_final: 0.7397 (mt) REVERT: A 532 ASN cc_start: 0.8755 (m-40) cc_final: 0.8423 (t0) REVERT: A 960 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8320 (m110) REVERT: B 200 TYR cc_start: 0.8142 (m-80) cc_final: 0.7584 (t80) REVERT: B 309 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8494 (mp0) REVERT: B 433 VAL cc_start: 0.3784 (OUTLIER) cc_final: 0.3495 (t) REVERT: B 752 LEU cc_start: 0.9124 (mt) cc_final: 0.8607 (mp) REVERT: B 755 GLN cc_start: 0.8534 (mp10) cc_final: 0.7954 (mp10) REVERT: B 978 ASN cc_start: 0.8157 (m-40) cc_final: 0.7430 (t0) REVERT: C 51 THR cc_start: 0.8590 (p) cc_final: 0.8385 (p) REVERT: C 537 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8431 (mtmm) REVERT: C 983 ARG cc_start: 0.8202 (mtm180) cc_final: 0.7890 (mtp-110) REVERT: C 995 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7987 (ptm160) REVERT: D 152 MET cc_start: 0.1412 (pp-130) cc_final: 0.1000 (pp-130) REVERT: D 183 TYR cc_start: -0.0241 (OUTLIER) cc_final: -0.0766 (t80) REVERT: D 270 MET cc_start: 0.2132 (ttm) cc_final: 0.1139 (mpp) REVERT: D 292 ASP cc_start: 0.2757 (t0) cc_final: 0.2400 (p0) REVERT: D 297 MET cc_start: -0.1874 (ttm) cc_final: -0.2353 (mtt) REVERT: D 383 MET cc_start: 0.4807 (mtp) cc_final: 0.4492 (tmm) REVERT: D 557 MET cc_start: 0.3412 (ptm) cc_final: 0.2981 (ptm) REVERT: D 572 ASN cc_start: 0.3344 (m-40) cc_final: 0.3048 (t0) REVERT: D 579 MET cc_start: 0.1996 (mpp) cc_final: 0.1059 (mpm) REVERT: E 53 ASN cc_start: 0.2527 (t0) cc_final: 0.2111 (t0) REVERT: E 249 MET cc_start: 0.1380 (ttm) cc_final: 0.0942 (tmt) REVERT: E 291 ILE cc_start: 0.0272 (OUTLIER) cc_final: -0.0370 (tp) REVERT: E 323 MET cc_start: 0.1149 (tpt) cc_final: -0.0148 (tpt) REVERT: E 325 GLN cc_start: 0.2979 (pp30) cc_final: 0.2608 (mm110) REVERT: E 366 MET cc_start: 0.3146 (tmm) cc_final: 0.2891 (tpt) REVERT: E 383 MET cc_start: 0.2229 (mtp) cc_final: 0.1980 (tmm) REVERT: E 495 GLU cc_start: 0.3767 (mp0) cc_final: 0.3398 (mt-10) outliers start: 83 outliers final: 36 residues processed: 239 average time/residue: 0.5834 time to fit residues: 172.7967 Evaluate side-chains 206 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 558 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 290 optimal weight: 20.0000 chunk 253 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 319 optimal weight: 10.0000 chunk 230 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 377 optimal weight: 9.9990 chunk 347 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B 965 GLN D 221 GLN D 290 ASN D 522 GLN E 96 GLN E 325 GLN E 552 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.182653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.112113 restraints weight = 66523.021| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.70 r_work: 0.3181 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 34306 Z= 0.213 Angle : 0.590 10.221 46788 Z= 0.295 Chirality : 0.046 0.290 5365 Planarity : 0.004 0.081 5912 Dihedral : 5.853 58.997 5842 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.25 % Allowed : 13.23 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.13), residues: 4027 helix: 1.61 (0.14), residues: 1411 sheet: 0.10 (0.20), residues: 612 loop : -0.51 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 78 TYR 0.023 0.002 TYR C1067 PHE 0.038 0.002 PHE E 555 TRP 0.035 0.002 TRP E 566 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00490 (34196) covalent geometry : angle 0.57118 (46498) SS BOND : bond 0.00254 ( 40) SS BOND : angle 0.72124 ( 80) hydrogen bonds : bond 0.04198 ( 1534) hydrogen bonds : angle 5.24391 ( 4494) link_BETA1-4 : bond 0.00240 ( 18) link_BETA1-4 : angle 1.16094 ( 54) link_NAG-ASN : bond 0.00543 ( 52) link_NAG-ASN : angle 2.55335 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 171 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7002 (t80) cc_final: 0.6649 (t80) REVERT: A 118 LEU cc_start: 0.8017 (tm) cc_final: 0.7576 (mt) REVERT: A 532 ASN cc_start: 0.8862 (m-40) cc_final: 0.8520 (t0) REVERT: B 200 TYR cc_start: 0.8186 (m-80) cc_final: 0.7726 (t80) REVERT: B 309 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8508 (mp0) REVERT: B 433 VAL cc_start: 0.3913 (OUTLIER) cc_final: 0.3615 (t) REVERT: B 752 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8630 (mp) REVERT: B 755 GLN cc_start: 0.8487 (mp10) cc_final: 0.7928 (mp10) REVERT: C 235 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6951 (mt) REVERT: C 537 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8414 (mtmm) REVERT: C 995 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8018 (ptm160) REVERT: C 1092 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8583 (mm-30) REVERT: D 152 MET cc_start: 0.1701 (pp-130) cc_final: 0.1212 (pp-130) REVERT: D 169 ARG cc_start: 0.0320 (OUTLIER) cc_final: 0.0097 (mmm160) REVERT: D 183 TYR cc_start: -0.0550 (OUTLIER) cc_final: -0.0784 (t80) REVERT: D 270 MET cc_start: 0.1934 (ttm) cc_final: 0.1640 (mpp) REVERT: D 292 ASP cc_start: 0.2872 (t0) cc_final: 0.2350 (p0) REVERT: D 297 MET cc_start: -0.2231 (ttm) cc_final: -0.2699 (mtt) REVERT: D 383 MET cc_start: 0.4747 (mtp) cc_final: 0.4476 (tmm) REVERT: D 557 MET cc_start: 0.3722 (ptm) cc_final: 0.3320 (ptm) REVERT: D 572 ASN cc_start: 0.3294 (m-40) cc_final: 0.2880 (t0) REVERT: D 579 MET cc_start: 0.0942 (mpp) cc_final: 0.0124 (mpm) REVERT: E 53 ASN cc_start: 0.3622 (t0) cc_final: 0.3060 (t0) REVERT: E 249 MET cc_start: 0.0885 (ttm) cc_final: 0.0397 (tmt) REVERT: E 291 ILE cc_start: 0.0093 (OUTLIER) cc_final: -0.0272 (tp) REVERT: E 323 MET cc_start: 0.0698 (tpt) cc_final: 0.0347 (ttt) REVERT: E 325 GLN cc_start: 0.2218 (OUTLIER) cc_final: 0.1868 (mm-40) REVERT: E 366 MET cc_start: 0.2838 (tmm) cc_final: 0.2568 (tpt) REVERT: E 383 MET cc_start: 0.2204 (mtp) cc_final: 0.1976 (mmt) REVERT: E 495 GLU cc_start: 0.3568 (mp0) cc_final: 0.2715 (mt-10) outliers start: 81 outliers final: 39 residues processed: 230 average time/residue: 0.5460 time to fit residues: 156.1774 Evaluate side-chains 206 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 558 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 244 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 321 optimal weight: 0.0070 chunk 83 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 957 GLN C 218 GLN C1010 GLN D 221 GLN D 442 GLN E 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.179026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.111327 restraints weight = 70219.961| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.43 r_work: 0.3286 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34306 Z= 0.128 Angle : 0.554 11.500 46788 Z= 0.275 Chirality : 0.044 0.291 5365 Planarity : 0.004 0.082 5912 Dihedral : 5.517 55.307 5842 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.89 % Allowed : 13.92 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.13), residues: 4027 helix: 1.76 (0.14), residues: 1411 sheet: 0.22 (0.19), residues: 643 loop : -0.43 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 454 TYR 0.022 0.001 TYR D 215 PHE 0.023 0.001 PHE C 168 TRP 0.036 0.001 TRP E 566 HIS 0.005 0.001 HIS E 241 Details of bonding type rmsd covalent geometry : bond 0.00284 (34196) covalent geometry : angle 0.53592 (46498) SS BOND : bond 0.00164 ( 40) SS BOND : angle 0.59873 ( 80) hydrogen bonds : bond 0.03803 ( 1534) hydrogen bonds : angle 5.07175 ( 4494) link_BETA1-4 : bond 0.00281 ( 18) link_BETA1-4 : angle 1.07774 ( 54) link_NAG-ASN : bond 0.00503 ( 52) link_NAG-ASN : angle 2.39354 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 178 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6994 (t80) cc_final: 0.6700 (t80) REVERT: A 118 LEU cc_start: 0.7935 (tm) cc_final: 0.7473 (mt) REVERT: A 532 ASN cc_start: 0.8967 (m-40) cc_final: 0.8719 (t0) REVERT: A 960 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8294 (m110) REVERT: B 200 TYR cc_start: 0.8181 (m-80) cc_final: 0.7697 (t80) REVERT: B 309 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8545 (mp0) REVERT: B 752 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8691 (mp) REVERT: B 755 GLN cc_start: 0.8481 (mp10) cc_final: 0.7963 (mp10) REVERT: B 981 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7449 (m-80) REVERT: C 51 THR cc_start: 0.8710 (p) cc_final: 0.8406 (p) REVERT: C 240 THR cc_start: 0.8819 (t) cc_final: 0.8572 (m) REVERT: C 537 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8353 (mtmm) REVERT: C 995 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8155 (ptm160) REVERT: C 1092 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8460 (mm-30) REVERT: D 152 MET cc_start: 0.1942 (pp-130) cc_final: 0.1483 (pp-130) REVERT: D 270 MET cc_start: 0.1795 (ttm) cc_final: 0.1288 (mpp) REVERT: D 297 MET cc_start: -0.2221 (ttm) cc_final: -0.2685 (mtt) REVERT: D 323 MET cc_start: -0.0348 (OUTLIER) cc_final: -0.1060 (mmt) REVERT: D 383 MET cc_start: 0.4726 (mtp) cc_final: 0.4380 (tmm) REVERT: D 557 MET cc_start: 0.3854 (ptm) cc_final: 0.3499 (ptm) REVERT: D 572 ASN cc_start: 0.3151 (m-40) cc_final: 0.2829 (t0) REVERT: D 579 MET cc_start: 0.1110 (mpp) cc_final: 0.0333 (mpm) REVERT: E 53 ASN cc_start: 0.4081 (t0) cc_final: 0.3380 (t0) REVERT: E 62 MET cc_start: -0.1019 (OUTLIER) cc_final: -0.1755 (ptm) REVERT: E 249 MET cc_start: 0.0905 (ttm) cc_final: 0.0492 (tmt) REVERT: E 291 ILE cc_start: 0.0179 (OUTLIER) cc_final: -0.0195 (tp) REVERT: E 323 MET cc_start: 0.0405 (tpt) cc_final: 0.0099 (ttt) REVERT: E 325 GLN cc_start: 0.2280 (pp30) cc_final: 0.2051 (mm-40) REVERT: E 366 MET cc_start: 0.2788 (tmm) cc_final: 0.2525 (tpt) REVERT: E 495 GLU cc_start: 0.3775 (mp0) cc_final: 0.3125 (mt-10) REVERT: E 606 TRP cc_start: 0.2634 (p90) cc_final: 0.2351 (p90) outliers start: 68 outliers final: 29 residues processed: 225 average time/residue: 0.6408 time to fit residues: 176.4334 Evaluate side-chains 196 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 981 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 441 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 61 optimal weight: 4.9990 chunk 345 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 354 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 149 optimal weight: 0.4980 chunk 234 optimal weight: 7.9990 chunk 274 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN D 221 GLN D 442 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.179657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.104083 restraints weight = 67678.219| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.33 r_work: 0.3155 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 34306 Z= 0.274 Angle : 0.639 12.818 46788 Z= 0.318 Chirality : 0.048 0.303 5365 Planarity : 0.004 0.083 5912 Dihedral : 5.834 53.751 5842 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.03 % Allowed : 14.09 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.13), residues: 4027 helix: 1.54 (0.14), residues: 1413 sheet: -0.15 (0.20), residues: 612 loop : -0.56 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 169 TYR 0.022 0.002 TYR C1067 PHE 0.023 0.002 PHE A 898 TRP 0.039 0.002 TRP E 566 HIS 0.007 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00636 (34196) covalent geometry : angle 0.62075 (46498) SS BOND : bond 0.00319 ( 40) SS BOND : angle 0.75093 ( 80) hydrogen bonds : bond 0.04496 ( 1534) hydrogen bonds : angle 5.33401 ( 4494) link_BETA1-4 : bond 0.00223 ( 18) link_BETA1-4 : angle 1.25377 ( 54) link_NAG-ASN : bond 0.00626 ( 52) link_NAG-ASN : angle 2.63131 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 162 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6998 (t80) cc_final: 0.6632 (t80) REVERT: A 118 LEU cc_start: 0.8041 (tm) cc_final: 0.7600 (mt) REVERT: A 532 ASN cc_start: 0.9045 (m-40) cc_final: 0.8800 (t0) REVERT: A 960 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8278 (m110) REVERT: B 135 PHE cc_start: 0.6369 (OUTLIER) cc_final: 0.5740 (m-80) REVERT: B 141 LEU cc_start: 0.6747 (mp) cc_final: 0.6013 (tp) REVERT: B 200 TYR cc_start: 0.8233 (m-80) cc_final: 0.7681 (t80) REVERT: B 309 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8553 (mp0) REVERT: B 433 VAL cc_start: 0.3900 (OUTLIER) cc_final: 0.3641 (t) REVERT: B 752 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8675 (mp) REVERT: B 755 GLN cc_start: 0.8490 (mp10) cc_final: 0.7966 (mp10) REVERT: C 95 ILE cc_start: 0.8212 (mm) cc_final: 0.7619 (tp) REVERT: C 537 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8424 (mtmm) REVERT: C 1092 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8517 (mm-30) REVERT: D 152 MET cc_start: 0.1726 (pp-130) cc_final: 0.1404 (pp-130) REVERT: D 270 MET cc_start: 0.3248 (ttm) cc_final: 0.1758 (mpp) REVERT: D 297 MET cc_start: -0.2065 (ttm) cc_final: -0.2531 (mtt) REVERT: D 557 MET cc_start: 0.3370 (ptm) cc_final: 0.2858 (ptm) REVERT: D 572 ASN cc_start: 0.3328 (m-40) cc_final: 0.3010 (t0) REVERT: E 53 ASN cc_start: 0.2728 (t0) cc_final: 0.2211 (t0) REVERT: E 62 MET cc_start: -0.0918 (OUTLIER) cc_final: -0.1779 (ttt) REVERT: E 249 MET cc_start: 0.1228 (ttm) cc_final: 0.0849 (tmt) REVERT: E 271 TRP cc_start: 0.2111 (OUTLIER) cc_final: 0.1043 (p90) REVERT: E 291 ILE cc_start: 0.0140 (OUTLIER) cc_final: -0.0265 (tp) REVERT: E 495 GLU cc_start: 0.3889 (mp0) cc_final: 0.3458 (mt-10) outliers start: 73 outliers final: 41 residues processed: 217 average time/residue: 0.5810 time to fit residues: 157.5676 Evaluate side-chains 200 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 441 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 229 optimal weight: 0.5980 chunk 182 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 326 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 332 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 957 GLN E 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.178263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.109837 restraints weight = 69716.858| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.40 r_work: 0.3283 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34306 Z= 0.147 Angle : 0.580 11.320 46788 Z= 0.287 Chirality : 0.045 0.299 5365 Planarity : 0.004 0.076 5912 Dihedral : 5.550 53.008 5842 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.61 % Allowed : 14.89 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.13), residues: 4027 helix: 1.70 (0.14), residues: 1409 sheet: -0.02 (0.20), residues: 561 loop : -0.44 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 169 TYR 0.023 0.001 TYR B 170 PHE 0.027 0.001 PHE E 512 TRP 0.042 0.001 TRP E 566 HIS 0.005 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00331 (34196) covalent geometry : angle 0.56342 (46498) SS BOND : bond 0.00188 ( 40) SS BOND : angle 0.62510 ( 80) hydrogen bonds : bond 0.03886 ( 1534) hydrogen bonds : angle 5.13832 ( 4494) link_BETA1-4 : bond 0.00272 ( 18) link_BETA1-4 : angle 1.06941 ( 54) link_NAG-ASN : bond 0.00495 ( 52) link_NAG-ASN : angle 2.40341 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 167 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7071 (t80) cc_final: 0.6696 (t80) REVERT: A 118 LEU cc_start: 0.7862 (tm) cc_final: 0.7416 (mt) REVERT: A 532 ASN cc_start: 0.8969 (m-40) cc_final: 0.8727 (t0) REVERT: A 960 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8197 (m110) REVERT: B 140 PHE cc_start: 0.7373 (p90) cc_final: 0.7052 (p90) REVERT: B 141 LEU cc_start: 0.6757 (mp) cc_final: 0.6035 (tp) REVERT: B 200 TYR cc_start: 0.8172 (m-80) cc_final: 0.7767 (t80) REVERT: B 309 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8509 (mp0) REVERT: C 240 THR cc_start: 0.8829 (t) cc_final: 0.8559 (m) REVERT: C 537 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8291 (mtmm) REVERT: C 995 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8145 (ptm160) REVERT: D 152 MET cc_start: 0.2150 (pp-130) cc_final: 0.1687 (pp-130) REVERT: D 270 MET cc_start: 0.2778 (ttm) cc_final: 0.1171 (mpp) REVERT: D 297 MET cc_start: -0.2221 (ttm) cc_final: -0.2693 (mtt) REVERT: D 363 LYS cc_start: 0.3733 (mmtm) cc_final: 0.3466 (mppt) REVERT: D 383 MET cc_start: 0.5532 (tmm) cc_final: 0.5171 (mtt) REVERT: D 557 MET cc_start: 0.3889 (ptm) cc_final: 0.3417 (ptm) REVERT: D 572 ASN cc_start: 0.3164 (m-40) cc_final: 0.2819 (t0) REVERT: E 53 ASN cc_start: 0.3931 (t0) cc_final: 0.3350 (t0) REVERT: E 62 MET cc_start: -0.1041 (OUTLIER) cc_final: -0.2408 (ttt) REVERT: E 190 MET cc_start: -0.2400 (ptt) cc_final: -0.2710 (ttp) REVERT: E 249 MET cc_start: 0.0935 (ttm) cc_final: 0.0525 (tmt) REVERT: E 271 TRP cc_start: 0.2199 (OUTLIER) cc_final: 0.1028 (p90) REVERT: E 291 ILE cc_start: 0.0197 (OUTLIER) cc_final: -0.0355 (tp) REVERT: E 495 GLU cc_start: 0.4022 (mp0) cc_final: 0.3412 (mt-10) outliers start: 58 outliers final: 36 residues processed: 208 average time/residue: 0.5393 time to fit residues: 140.8492 Evaluate side-chains 197 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 291 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 198 optimal weight: 0.7980 chunk 303 optimal weight: 10.0000 chunk 121 optimal weight: 0.0670 chunk 73 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 366 optimal weight: 20.0000 chunk 274 optimal weight: 3.9990 chunk 302 optimal weight: 0.9990 chunk 329 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 262 optimal weight: 0.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.178642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.111161 restraints weight = 69642.354| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.37 r_work: 0.3303 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34306 Z= 0.120 Angle : 0.567 12.711 46788 Z= 0.279 Chirality : 0.044 0.294 5365 Planarity : 0.004 0.069 5912 Dihedral : 5.213 53.042 5842 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.25 % Allowed : 15.37 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.13), residues: 4027 helix: 1.87 (0.14), residues: 1397 sheet: 0.09 (0.20), residues: 577 loop : -0.38 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 169 TYR 0.021 0.001 TYR A1067 PHE 0.020 0.001 PHE A 400 TRP 0.043 0.001 TRP E 566 HIS 0.006 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00266 (34196) covalent geometry : angle 0.55120 (46498) SS BOND : bond 0.00150 ( 40) SS BOND : angle 0.62081 ( 80) hydrogen bonds : bond 0.03663 ( 1534) hydrogen bonds : angle 5.00767 ( 4494) link_BETA1-4 : bond 0.00288 ( 18) link_BETA1-4 : angle 1.05397 ( 54) link_NAG-ASN : bond 0.00480 ( 52) link_NAG-ASN : angle 2.32082 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6941 (t80) cc_final: 0.6608 (t80) REVERT: A 118 LEU cc_start: 0.7902 (tm) cc_final: 0.7472 (mt) REVERT: A 532 ASN cc_start: 0.9012 (m-40) cc_final: 0.8797 (t0) REVERT: B 140 PHE cc_start: 0.7436 (p90) cc_final: 0.7078 (p90) REVERT: B 141 LEU cc_start: 0.6759 (mp) cc_final: 0.6022 (tp) REVERT: B 200 TYR cc_start: 0.8119 (m-80) cc_final: 0.7784 (t80) REVERT: B 309 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8449 (mp0) REVERT: C 240 THR cc_start: 0.8827 (t) cc_final: 0.8553 (m) REVERT: C 537 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8256 (mtmm) REVERT: C 995 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8214 (ptm160) REVERT: D 152 MET cc_start: 0.2130 (pp-130) cc_final: 0.1725 (pp-130) REVERT: D 270 MET cc_start: 0.2829 (ttm) cc_final: 0.1229 (mpp) REVERT: D 297 MET cc_start: -0.2186 (ttm) cc_final: -0.2656 (mtt) REVERT: D 363 LYS cc_start: 0.3600 (mmtm) cc_final: 0.3342 (mppt) REVERT: D 383 MET cc_start: 0.5900 (tmm) cc_final: 0.5543 (mtt) REVERT: D 557 MET cc_start: 0.3892 (ptm) cc_final: 0.3425 (ptm) REVERT: D 572 ASN cc_start: 0.3325 (m-40) cc_final: 0.2961 (t0) REVERT: E 53 ASN cc_start: 0.3808 (t0) cc_final: 0.3257 (t0) REVERT: E 62 MET cc_start: -0.1527 (OUTLIER) cc_final: -0.2772 (ttt) REVERT: E 190 MET cc_start: -0.2373 (ptt) cc_final: -0.2762 (ttp) REVERT: E 249 MET cc_start: 0.0973 (ttm) cc_final: 0.0575 (tmt) REVERT: E 271 TRP cc_start: 0.2143 (OUTLIER) cc_final: 0.0999 (p90) REVERT: E 291 ILE cc_start: 0.0150 (OUTLIER) cc_final: -0.0246 (tp) REVERT: E 495 GLU cc_start: 0.4130 (mp0) cc_final: 0.3529 (mt-10) outliers start: 45 outliers final: 33 residues processed: 205 average time/residue: 0.5886 time to fit residues: 150.8130 Evaluate side-chains 194 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 291 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 57 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 chunk 403 optimal weight: 9.9990 chunk 137 optimal weight: 30.0000 chunk 89 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 299 optimal weight: 8.9990 chunk 293 optimal weight: 20.0000 chunk 357 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 233 optimal weight: 0.8980 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 ASN B 907 ASN C 580 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.186748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.118351 restraints weight = 64195.075| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 4.14 r_work: 0.3113 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 34306 Z= 0.354 Angle : 0.717 13.822 46788 Z= 0.356 Chirality : 0.051 0.326 5365 Planarity : 0.005 0.084 5912 Dihedral : 6.124 57.908 5842 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.56 % Allowed : 15.17 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.13), residues: 4027 helix: 1.39 (0.14), residues: 1385 sheet: -0.32 (0.19), residues: 619 loop : -0.62 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 169 TYR 0.023 0.002 TYR C1067 PHE 0.027 0.002 PHE C 565 TRP 0.044 0.002 TRP E 566 HIS 0.008 0.002 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00827 (34196) covalent geometry : angle 0.69796 (46498) SS BOND : bond 0.00402 ( 40) SS BOND : angle 0.85600 ( 80) hydrogen bonds : bond 0.04862 ( 1534) hydrogen bonds : angle 5.51227 ( 4494) link_BETA1-4 : bond 0.00296 ( 18) link_BETA1-4 : angle 1.42555 ( 54) link_NAG-ASN : bond 0.00709 ( 52) link_NAG-ASN : angle 2.84425 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28588.85 seconds wall clock time: 482 minutes 57.15 seconds (28977.15 seconds total)