Starting phenix.real_space_refine on Mon Jul 6 06:48:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t9k_25760/07_2026/7t9k_25760.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9k_25760/07_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_25760/07_2026/7t9k_25760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9k_25760/07_2026/7t9k_25760.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9k_25760/07_2026/7t9k_25760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9k_25760/07_2026/7t9k_25760.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7t9k_25760/07_2026/7t9k_25760.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t9k_25760/07_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-6108/lib/python3.11/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 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 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 chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "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 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 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 chiralities: 6 Time building chain proxies: 7.04, per 1000 atoms: 0.21 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: 2.95 Conformation dependent library (CDL) restraints added in 1.5 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: 1.32 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: 8.85 Time building geometry restraints manager: 3.94 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: 18108 17.98 - 35.95: 1363 35.95 - 53.93: 218 53.93 - 71.90: 68 71.90 - 89.88: 38 Dihedral angle restraints: 19795 sinusoidal: 7861 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 19792 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: 5.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 33.060 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 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:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 13.678 89.877 11977 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/Z covalent geometry : bond 0.00511 / 0.25 (34196) covalent geometry : angle 0.87047 / 0.47 (46498) SS BOND : bond 0.00271 / 0.17 ( 40) SS BOND : angle 1.29650 / 0.85 ( 80) hydrogen bonds : bond 0.12659 / 8.34 ( 1534) hydrogen bonds : angle 6.89191 / 4.81 ( 4494) link_BETA1-4 : bond 0.00579 / 0.39 ( 18) link_BETA1-4 : angle 1.62142 / 1.07 ( 54) link_NAG-ASN : bond 0.00681 / 0.36 ( 52) link_NAG-ASN : angle 3.17080 / 2.16 ( 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 : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.6651 time to fit residues: 354.1340 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 : 1.262 ------------------------------------------------------------------------------- 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... ** 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 C 978 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.182585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.106768 restraints weight = 68907.597| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.04 r_work: 0.3238 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 34306 Z= 0.202 Angle : 0.628 11.361 46788 Z= 0.317 Chirality : 0.046 0.246 5365 Planarity : 0.005 0.052 5912 Dihedral : 4.472 25.116 4384 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.69 % Allowed : 9.28 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.13), 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 0.006 0.001 ARG D 192 TYR 0.027 0.002 TYR C1067 PHE 0.027 0.002 PHE D 315 TRP 0.025 0.002 TRP E 566 HIS 0.015 0.001 HIS D 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (34196) covalent geometry : angle 0.60566 / 0.31 (46498) SS BOND : bond 0.00227 / 0.15 ( 40) SS BOND : angle 0.93141 / 0.61 ( 80) hydrogen bonds : bond 0.04656 / 3.02 ( 1534) hydrogen bonds : angle 5.51219 / 3.81 ( 4494) link_BETA1-4 : bond 0.00216 / 0.12 ( 18) link_BETA1-4 : angle 1.12481 / 0.74 ( 54) link_NAG-ASN : bond 0.00504 / 0.28 ( 52) link_NAG-ASN : angle 2.85500 / 1.83 ( 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 269 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 TYR cc_start: 0.6065 (m-80) cc_final: 0.5712 (m-10) REVERT: A 533 LEU cc_start: 0.7602 (tp) cc_final: 0.7252 (tp) REVERT: A 759 PHE cc_start: 0.8125 (m-80) cc_final: 0.7896 (m-80) REVERT: B 207 HIS cc_start: 0.7948 (t-170) cc_final: 0.7747 (m-70) REVERT: B 309 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8538 (mp0) REVERT: B 314 GLN cc_start: 0.9016 (tt0) cc_final: 0.8813 (tt0) REVERT: B 752 LEU cc_start: 0.9165 (mp) cc_final: 0.8743 (mp) REVERT: B 755 GLN cc_start: 0.8362 (mp10) cc_final: 0.7839 (mp10) REVERT: B 973 ILE cc_start: 0.8995 (pt) cc_final: 0.8671 (mp) REVERT: B 978 ASN cc_start: 0.7859 (m-40) cc_final: 0.7172 (t0) REVERT: B 985 ASP cc_start: 0.7818 (p0) cc_final: 0.7535 (p0) REVERT: C 320 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7730 (m) REVERT: D 152 MET cc_start: 0.1566 (pp-130) cc_final: 0.0699 (mmt) REVERT: D 270 MET cc_start: 0.1335 (ttm) cc_final: -0.0123 (mpp) REVERT: D 297 MET cc_start: -0.2191 (ttt) cc_final: -0.2602 (mtt) REVERT: D 383 MET cc_start: 0.4462 (mtp) cc_final: 0.4064 (tmm) REVERT: D 557 MET cc_start: 0.3482 (ptm) cc_final: 0.2997 (ptm) REVERT: D 572 ASN cc_start: 0.3549 (m-40) cc_final: 0.3131 (t0) REVERT: E 53 ASN cc_start: 0.3102 (t0) cc_final: 0.2739 (t0) REVERT: E 207 TYR cc_start: -0.1539 (m-80) cc_final: -0.2169 (m-10) REVERT: E 249 MET cc_start: 0.1712 (ttm) cc_final: 0.1266 (tmt) REVERT: E 323 MET cc_start: 0.2039 (mmt) cc_final: 0.1810 (tpt) REVERT: E 366 MET cc_start: 0.3029 (tmm) cc_final: 0.2654 (tpt) REVERT: E 383 MET cc_start: 0.1870 (mtp) cc_final: 0.1207 (tmm) REVERT: E 495 GLU cc_start: 0.3660 (mp0) cc_final: 0.3259 (mt-10) REVERT: E 513 ILE cc_start: -0.0366 (OUTLIER) cc_final: -0.0852 (pt) REVERT: E 579 MET cc_start: 0.2025 (ptp) cc_final: 0.1823 (mpp) outliers start: 61 outliers final: 17 residues processed: 249 average time/residue: 0.6276 time to fit residues: 189.5183 Evaluate side-chains 193 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 79 PHE 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 794 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 541 LYS 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: 0.5980 chunk 227 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 chunk 344 optimal weight: 20.0000 chunk 282 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 290 optimal weight: 20.0000 chunk 139 optimal weight: 8.9990 chunk 220 optimal weight: 0.2980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 564 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN D 175 GLN D 250 ASN D 374 HIS D 442 GLN D 524 GLN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN E 325 GLN E 522 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.186227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.110229 restraints weight = 67563.046| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.24 r_work: 0.3248 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34306 Z= 0.151 Angle : 0.566 11.054 46788 Z= 0.283 Chirality : 0.044 0.259 5365 Planarity : 0.004 0.046 5912 Dihedral : 4.222 19.081 4372 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.72 % Allowed : 10.70 % Favored : 87.58 % 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: 0.71 (0.13), residues: 4027 helix: 1.66 (0.14), residues: 1400 sheet: 0.57 (0.20), residues: 601 loop : -0.38 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 518 TYR 0.024 0.001 TYR C1067 PHE 0.021 0.001 PHE B 79 TRP 0.029 0.001 TRP E 566 HIS 0.008 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (34196) covalent geometry : angle 0.54670 / 0.28 (46498) SS BOND : bond 0.00182 / 0.12 ( 40) SS BOND : angle 0.72320 / 0.50 ( 80) hydrogen bonds : bond 0.04139 / 2.67 ( 1534) hydrogen bonds : angle 5.24602 / 3.63 ( 4494) link_BETA1-4 : bond 0.00238 / 0.17 ( 18) link_BETA1-4 : angle 1.04473 / 0.69 ( 54) link_NAG-ASN : bond 0.00528 / 0.32 ( 52) link_NAG-ASN : angle 2.55152 / 1.63 ( 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 266 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 204 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6698 (t80) cc_final: 0.6396 (t80) REVERT: A 269 TYR cc_start: 0.6724 (m-80) cc_final: 0.5998 (m-80) REVERT: A 508 TYR cc_start: 0.6070 (m-80) cc_final: 0.5693 (m-10) REVERT: A 533 LEU cc_start: 0.7673 (tp) cc_final: 0.7328 (tp) REVERT: A 759 PHE cc_start: 0.7992 (m-80) cc_final: 0.7762 (m-80) REVERT: B 79 PHE cc_start: 0.6606 (t80) cc_final: 0.6376 (t80) REVERT: B 81 ASN cc_start: 0.7459 (m-40) cc_final: 0.7157 (m-40) REVERT: B 309 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8531 (mp0) REVERT: B 314 GLN cc_start: 0.8914 (tt0) cc_final: 0.8656 (tt0) REVERT: B 752 LEU cc_start: 0.9154 (mp) cc_final: 0.8716 (mp) REVERT: B 755 GLN cc_start: 0.8396 (mp10) cc_final: 0.7927 (mp10) REVERT: B 978 ASN cc_start: 0.7914 (m-40) cc_final: 0.7239 (t0) REVERT: C 320 VAL cc_start: 0.7999 (OUTLIER) cc_final: 0.7771 (m) REVERT: C 983 ARG cc_start: 0.8096 (mtm180) cc_final: 0.7808 (mtp-110) REVERT: D 152 MET cc_start: 0.1542 (pp-130) cc_final: 0.0690 (mmt) REVERT: D 183 TYR cc_start: -0.0510 (OUTLIER) cc_final: -0.0979 (t80) REVERT: D 270 MET cc_start: 0.1597 (ttm) cc_final: 0.0143 (mpp) REVERT: D 292 ASP cc_start: 0.2668 (t0) cc_final: 0.2134 (p0) REVERT: D 297 MET cc_start: -0.1908 (ttt) cc_final: -0.2389 (mtt) REVERT: D 383 MET cc_start: 0.4508 (mtp) cc_final: 0.4188 (tmm) REVERT: D 557 MET cc_start: 0.3499 (ptm) cc_final: 0.2902 (ptm) REVERT: D 566 TRP cc_start: -0.0537 (p-90) cc_final: -0.0811 (p-90) REVERT: D 572 ASN cc_start: 0.3345 (m-40) cc_final: 0.2931 (t0) REVERT: D 579 MET cc_start: 0.0731 (mpp) cc_final: -0.0074 (mpm) REVERT: E 53 ASN cc_start: 0.2798 (t0) cc_final: 0.2315 (t0) REVERT: E 249 MET cc_start: 0.1731 (ttm) cc_final: 0.1267 (tmt) REVERT: E 323 MET cc_start: 0.2161 (mmt) cc_final: 0.1646 (tpt) REVERT: E 325 GLN cc_start: 0.2393 (OUTLIER) cc_final: 0.1868 (mm-40) REVERT: E 366 MET cc_start: 0.2941 (tmm) cc_final: 0.2614 (tpt) REVERT: E 383 MET cc_start: 0.2104 (mtp) cc_final: 0.1824 (tmm) REVERT: E 495 GLU cc_start: 0.3988 (mp0) cc_final: 0.3615 (mt-10) REVERT: E 579 MET cc_start: 0.2040 (ptp) cc_final: 0.1674 (mpp) outliers start: 62 outliers final: 19 residues processed: 253 average time/residue: 0.5701 time to fit residues: 177.3118 Evaluate side-chains 193 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 200 TYR 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 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 327 VAL Chi-restraints excluded: chain C residue 120 VAL 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 939 SER Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 252 TYR 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: 5.9990 chunk 98 optimal weight: 1.9990 chunk 406 optimal weight: 20.0000 chunk 246 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 258 optimal weight: 0.0980 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 824 ASN D 374 HIS D 442 GLN D 535 HIS ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN E 535 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.185126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.114856 restraints weight = 66737.889| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.78 r_work: 0.3181 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34306 Z= 0.183 Angle : 0.571 11.475 46788 Z= 0.286 Chirality : 0.045 0.259 5365 Planarity : 0.004 0.038 5912 Dihedral : 4.249 20.826 4372 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.56 % Allowed : 12.14 % Favored : 86.30 % 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: 1.71 (0.14), residues: 1404 sheet: 0.46 (0.20), residues: 600 loop : -0.39 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 518 TYR 0.023 0.001 TYR C1067 PHE 0.021 0.002 PHE C 168 TRP 0.032 0.001 TRP E 566 HIS 0.005 0.001 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (34196) covalent geometry : angle 0.55204 / 0.28 (46498) SS BOND : bond 0.00219 / 0.15 ( 40) SS BOND : angle 0.69783 / 0.48 ( 80) hydrogen bonds : bond 0.04175 / 2.70 ( 1534) hydrogen bonds : angle 5.21099 / 3.61 ( 4494) link_BETA1-4 : bond 0.00282 / 0.19 ( 18) link_BETA1-4 : angle 1.08081 / 0.71 ( 54) link_NAG-ASN : bond 0.00547 / 0.33 ( 52) link_NAG-ASN : angle 2.51656 / 1.62 ( 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 248 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6670 (t80) cc_final: 0.6444 (t80) REVERT: A 508 TYR cc_start: 0.6036 (m-80) cc_final: 0.5661 (m-10) REVERT: A 532 ASN cc_start: 0.8915 (m-40) cc_final: 0.8564 (t0) REVERT: A 759 PHE cc_start: 0.8157 (m-80) cc_final: 0.7943 (m-80) REVERT: B 200 TYR cc_start: 0.8154 (m-80) cc_final: 0.7449 (t80) REVERT: B 309 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8528 (mp0) REVERT: B 314 GLN cc_start: 0.9062 (tt0) cc_final: 0.8820 (tt0) REVERT: B 433 VAL cc_start: 0.3755 (OUTLIER) cc_final: 0.3470 (t) REVERT: B 752 LEU cc_start: 0.9135 (mt) cc_final: 0.8693 (mp) REVERT: B 755 GLN cc_start: 0.8489 (mp10) cc_final: 0.7944 (mp10) REVERT: B 978 ASN cc_start: 0.8099 (m-40) cc_final: 0.7402 (t0) REVERT: C 51 THR cc_start: 0.8599 (p) cc_final: 0.8371 (p) REVERT: C 983 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7870 (mtp-110) REVERT: D 152 MET cc_start: 0.1532 (pp-130) cc_final: 0.0608 (mtt) REVERT: D 183 TYR cc_start: -0.0420 (OUTLIER) cc_final: -0.0840 (t80) REVERT: D 270 MET cc_start: 0.1541 (ttm) cc_final: -0.0014 (mpp) REVERT: D 292 ASP cc_start: 0.2815 (t0) cc_final: 0.2220 (p0) REVERT: D 297 MET cc_start: -0.1946 (ttt) cc_final: -0.2462 (mtt) REVERT: D 383 MET cc_start: 0.4648 (mtp) cc_final: 0.4346 (tmm) REVERT: D 557 MET cc_start: 0.3640 (ptm) cc_final: 0.3048 (ptm) REVERT: D 572 ASN cc_start: 0.3294 (m-40) cc_final: 0.2904 (t0) REVERT: E 53 ASN cc_start: 0.3112 (t0) cc_final: 0.2633 (t0) REVERT: E 249 MET cc_start: 0.1832 (ttm) cc_final: 0.1318 (tmt) REVERT: E 323 MET cc_start: 0.2036 (mmt) cc_final: 0.1538 (tpt) REVERT: E 325 GLN cc_start: 0.3262 (OUTLIER) cc_final: 0.3010 (mm-40) REVERT: E 366 MET cc_start: 0.3007 (tmm) cc_final: 0.2777 (tpt) REVERT: E 383 MET cc_start: 0.2175 (mtp) cc_final: 0.1820 (tmm) REVERT: E 495 GLU cc_start: 0.3996 (mp0) cc_final: 0.3409 (mt-10) REVERT: E 579 MET cc_start: 0.1794 (ptp) cc_final: 0.1567 (mpp) outliers start: 56 outliers final: 26 residues processed: 233 average time/residue: 0.5208 time to fit residues: 151.4459 Evaluate side-chains 207 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 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 327 VAL 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 540 ASN Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 939 SER 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 E residue 152 MET 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: 3.9990 chunk 231 optimal weight: 6.9990 chunk 368 optimal weight: 9.9990 chunk 373 optimal weight: 20.0000 chunk 214 optimal weight: 0.6980 chunk 212 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 383 optimal weight: 20.0000 chunk 330 optimal weight: 3.9990 chunk 334 optimal weight: 8.9990 chunk 218 optimal weight: 0.0570 overall best weight: 1.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1142 GLN D 154 ASN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS E 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.181499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.106622 restraints weight = 67975.812| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.89 r_work: 0.3214 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 34306 Z= 0.173 Angle : 0.569 10.873 46788 Z= 0.282 Chirality : 0.045 0.263 5365 Planarity : 0.004 0.105 5912 Dihedral : 4.222 21.933 4372 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.78 % Allowed : 12.61 % Favored : 85.61 % 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: 0.74 (0.13), residues: 4027 helix: 1.76 (0.14), residues: 1406 sheet: 0.41 (0.20), residues: 598 loop : -0.35 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.022 0.001 TYR C1067 PHE 0.019 0.001 PHE B 140 TRP 0.032 0.001 TRP E 566 HIS 0.014 0.001 HIS E 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (34196) covalent geometry : angle 0.55036 / 0.28 (46498) SS BOND : bond 0.00200 / 0.14 ( 40) SS BOND : angle 0.66699 / 0.46 ( 80) hydrogen bonds : bond 0.04033 / 2.60 ( 1534) hydrogen bonds : angle 5.14999 / 3.57 ( 4494) link_BETA1-4 : bond 0.00228 / 0.15 ( 18) link_BETA1-4 : angle 1.02433 / 0.68 ( 54) link_NAG-ASN : bond 0.00525 / 0.31 ( 52) link_NAG-ASN : angle 2.46996 / 1.58 ( 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 247 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 183 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.4456 (OUTLIER) cc_final: 0.3865 (tpm170) REVERT: A 79 PHE cc_start: 0.6870 (t80) cc_final: 0.6565 (t80) REVERT: A 508 TYR cc_start: 0.6068 (m-80) cc_final: 0.5820 (m-10) REVERT: A 532 ASN cc_start: 0.8793 (m-40) cc_final: 0.8454 (t0) REVERT: B 200 TYR cc_start: 0.8185 (m-80) cc_final: 0.7647 (t80) REVERT: B 309 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8538 (mp0) REVERT: B 314 GLN cc_start: 0.8969 (tt0) cc_final: 0.8765 (tp40) REVERT: B 433 VAL cc_start: 0.3771 (OUTLIER) cc_final: 0.3392 (t) REVERT: B 752 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8716 (mp) REVERT: B 755 GLN cc_start: 0.8546 (mp10) cc_final: 0.7977 (mp10) REVERT: B 978 ASN cc_start: 0.8067 (m-40) cc_final: 0.7352 (t0) REVERT: C 51 THR cc_start: 0.8643 (p) cc_final: 0.8424 (p) REVERT: C 983 ARG cc_start: 0.8147 (mtm180) cc_final: 0.7859 (mtp-110) REVERT: D 152 MET cc_start: 0.1635 (pp-130) cc_final: 0.0729 (mtt) REVERT: D 183 TYR cc_start: -0.0374 (OUTLIER) cc_final: -0.0757 (t80) REVERT: D 270 MET cc_start: 0.1782 (ttm) cc_final: 0.0179 (mpp) REVERT: D 292 ASP cc_start: 0.2836 (t0) cc_final: 0.2378 (p0) REVERT: D 297 MET cc_start: -0.1986 (ttm) cc_final: -0.2471 (mtt) REVERT: D 383 MET cc_start: 0.4781 (mtp) cc_final: 0.4428 (tmm) REVERT: D 557 MET cc_start: 0.3664 (ptm) cc_final: 0.3145 (ptm) REVERT: D 572 ASN cc_start: 0.3351 (m-40) cc_final: 0.3118 (t0) REVERT: D 579 MET cc_start: 0.1267 (mpp) cc_final: 0.0438 (mpm) REVERT: E 53 ASN cc_start: 0.2867 (t0) cc_final: 0.2359 (t0) REVERT: E 249 MET cc_start: 0.1576 (ttm) cc_final: 0.1070 (tmt) REVERT: E 291 ILE cc_start: 0.0272 (OUTLIER) cc_final: -0.0264 (tp) REVERT: E 323 MET cc_start: 0.1994 (mmt) cc_final: 0.1305 (tpt) REVERT: E 366 MET cc_start: 0.3017 (tmm) cc_final: 0.2752 (tpt) REVERT: E 383 MET cc_start: 0.2069 (mtp) cc_final: 0.1839 (tmm) REVERT: E 495 GLU cc_start: 0.4415 (mp0) cc_final: 0.3920 (mt-10) REVERT: E 579 MET cc_start: 0.1740 (ptp) cc_final: 0.1507 (mpp) outliers start: 64 outliers final: 32 residues processed: 230 average time/residue: 0.5881 time to fit residues: 167.6728 Evaluate side-chains 207 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 200 TYR Chi-restraints excluded: chain A residue 226 LEU 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 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 752 LEU 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 258 TRP Chi-restraints excluded: chain C residue 318 PHE 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 939 SER Chi-restraints excluded: chain C residue 993 ILE 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 E residue 105 SER Chi-restraints excluded: chain E residue 198 ASP 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: 3.9990 chunk 268 optimal weight: 4.9990 chunk 319 optimal weight: 20.0000 chunk 230 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 377 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 94 optimal weight: 0.8980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 314 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 ASN D 442 GLN D 522 GLN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.181306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.111944 restraints weight = 67037.569| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.78 r_work: 0.3140 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 34306 Z= 0.248 Angle : 0.622 11.998 46788 Z= 0.310 Chirality : 0.047 0.264 5365 Planarity : 0.004 0.076 5912 Dihedral : 4.446 22.773 4372 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.14 % Allowed : 12.98 % Favored : 84.88 % 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: 0.50 (0.13), residues: 4027 helix: 1.58 (0.14), residues: 1411 sheet: 0.12 (0.20), residues: 627 loop : -0.47 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.026 0.002 TYR E 50 PHE 0.023 0.002 PHE C 565 TRP 0.036 0.002 TRP E 566 HIS 0.005 0.001 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.25 (34196) covalent geometry : angle 0.60392 / 0.31 (46498) SS BOND : bond 0.00289 / 0.20 ( 40) SS BOND : angle 0.76653 / 0.51 ( 80) hydrogen bonds : bond 0.04422 / 2.85 ( 1534) hydrogen bonds : angle 5.29769 / 3.68 ( 4494) link_BETA1-4 : bond 0.00207 / 0.14 ( 18) link_BETA1-4 : angle 1.17237 / 0.76 ( 54) link_NAG-ASN : bond 0.00586 / 0.36 ( 52) link_NAG-ASN : angle 2.58819 / 1.69 ( 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 260 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 183 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6947 (t80) cc_final: 0.6582 (t80) REVERT: A 118 LEU cc_start: 0.7991 (tm) cc_final: 0.7557 (mt) REVERT: A 532 ASN cc_start: 0.8908 (m-40) cc_final: 0.8563 (t0) REVERT: B 200 TYR cc_start: 0.8140 (m-80) cc_final: 0.7600 (t80) REVERT: B 309 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8512 (mp0) REVERT: B 314 GLN cc_start: 0.9011 (tt0) cc_final: 0.8810 (tp40) REVERT: B 433 VAL cc_start: 0.3793 (OUTLIER) cc_final: 0.3489 (t) REVERT: B 752 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8618 (mp) REVERT: B 755 GLN cc_start: 0.8500 (mp10) cc_final: 0.7934 (mp10) REVERT: C 51 THR cc_start: 0.8606 (p) cc_final: 0.8402 (p) REVERT: C 537 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8434 (mtmm) REVERT: C 983 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7826 (mtp-110) REVERT: D 152 MET cc_start: 0.1517 (pp-130) cc_final: 0.1088 (pp-130) REVERT: D 183 TYR cc_start: -0.0291 (OUTLIER) cc_final: -0.0660 (t80) REVERT: D 270 MET cc_start: 0.1718 (ttm) cc_final: 0.0761 (mpp) REVERT: D 292 ASP cc_start: 0.2768 (t0) cc_final: 0.2325 (p0) REVERT: D 297 MET cc_start: -0.2214 (ttm) cc_final: -0.2650 (mtt) REVERT: D 323 MET cc_start: 0.0302 (OUTLIER) cc_final: -0.0353 (mmt) REVERT: D 383 MET cc_start: 0.4723 (mtp) cc_final: 0.4403 (tmm) REVERT: D 557 MET cc_start: 0.3740 (ptm) cc_final: 0.3205 (ptm) REVERT: D 572 ASN cc_start: 0.3203 (m-40) cc_final: 0.2774 (t0) REVERT: D 579 MET cc_start: 0.1018 (mpp) cc_final: 0.0220 (mpm) REVERT: E 50 TYR cc_start: 0.3364 (t80) cc_final: 0.3147 (t80) REVERT: E 53 ASN cc_start: 0.3243 (t0) cc_final: 0.2768 (t0) REVERT: E 249 MET cc_start: 0.1144 (ttm) cc_final: 0.0626 (tmt) REVERT: E 291 ILE cc_start: 0.0156 (OUTLIER) cc_final: -0.0285 (tp) REVERT: E 323 MET cc_start: 0.1875 (mmt) cc_final: 0.1424 (tpt) REVERT: E 366 MET cc_start: 0.3068 (tmm) cc_final: 0.2840 (tpt) REVERT: E 383 MET cc_start: 0.2044 (mtp) cc_final: 0.1838 (tmm) REVERT: E 495 GLU cc_start: 0.3892 (mp0) cc_final: 0.3185 (mt-10) REVERT: E 579 MET cc_start: 0.1723 (ptp) cc_final: 0.1487 (mpp) outliers start: 77 outliers final: 33 residues processed: 239 average time/residue: 0.5486 time to fit residues: 164.7160 Evaluate side-chains 202 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 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 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 240 THR Chi-restraints excluded: chain C residue 258 TRP 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 794 ILE Chi-restraints excluded: chain C residue 900 MET 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 323 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 244 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 210 optimal weight: 0.5980 chunk 185 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 321 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 GLN B 965 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 42 GLN D 221 GLN D 442 GLN E 76 GLN E 96 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.179270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.111298 restraints weight = 69929.808| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.37 r_work: 0.3256 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34306 Z= 0.117 Angle : 0.556 11.722 46788 Z= 0.274 Chirality : 0.044 0.267 5365 Planarity : 0.004 0.071 5912 Dihedral : 4.146 20.761 4372 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.42 % Allowed : 13.92 % Favored : 84.66 % 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: 0.75 (0.13), residues: 4027 helix: 1.81 (0.14), residues: 1411 sheet: 0.30 (0.20), residues: 594 loop : -0.35 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.024 0.001 TYR B 170 PHE 0.022 0.001 PHE B 140 TRP 0.037 0.001 TRP E 566 HIS 0.008 0.001 HIS E 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (34196) covalent geometry : angle 0.53958 / 0.27 (46498) SS BOND : bond 0.00151 / 0.11 ( 40) SS BOND : angle 0.60665 / 0.42 ( 80) hydrogen bonds : bond 0.03715 / 2.40 ( 1534) hydrogen bonds : angle 5.02700 / 3.49 ( 4494) link_BETA1-4 : bond 0.00342 / 0.22 ( 18) link_BETA1-4 : angle 0.93058 / 0.63 ( 54) link_NAG-ASN : bond 0.00476 / 0.27 ( 52) link_NAG-ASN : angle 2.32684 / 1.49 ( 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 230 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 179 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6880 (t80) cc_final: 0.6592 (t80) REVERT: A 118 LEU cc_start: 0.8004 (tm) cc_final: 0.7565 (mt) REVERT: A 508 TYR cc_start: 0.5895 (m-10) cc_final: 0.5689 (m-10) REVERT: A 532 ASN cc_start: 0.8848 (m-40) cc_final: 0.8513 (t0) REVERT: B 200 TYR cc_start: 0.8118 (m-80) cc_final: 0.7659 (t80) REVERT: B 309 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8576 (mp0) REVERT: B 433 VAL cc_start: 0.3742 (OUTLIER) cc_final: 0.3476 (t) REVERT: C 51 THR cc_start: 0.8660 (p) cc_final: 0.8361 (p) REVERT: C 240 THR cc_start: 0.8725 (t) cc_final: 0.8494 (m) REVERT: D 183 TYR cc_start: -0.0370 (OUTLIER) cc_final: -0.0708 (t80) REVERT: D 297 MET cc_start: -0.2106 (ttm) cc_final: -0.2519 (mtt) REVERT: D 363 LYS cc_start: 0.3768 (mmtm) cc_final: 0.3553 (mppt) REVERT: D 383 MET cc_start: 0.4616 (mtp) cc_final: 0.4381 (tmm) REVERT: D 557 MET cc_start: 0.3522 (ptm) cc_final: 0.3012 (ptm) REVERT: D 572 ASN cc_start: 0.3143 (m-40) cc_final: 0.2850 (t0) REVERT: D 579 MET cc_start: 0.1321 (mpp) cc_final: 0.0440 (mpm) REVERT: E 53 ASN cc_start: 0.2984 (t0) cc_final: 0.2559 (t0) REVERT: E 62 MET cc_start: -0.1089 (OUTLIER) cc_final: -0.2108 (ttt) REVERT: E 249 MET cc_start: 0.1203 (ttm) cc_final: 0.0823 (tmt) REVERT: E 291 ILE cc_start: 0.0242 (OUTLIER) cc_final: -0.0299 (tp) REVERT: E 366 MET cc_start: 0.3002 (tmm) cc_final: 0.2762 (tpt) REVERT: E 495 GLU cc_start: 0.3954 (mp0) cc_final: 0.3571 (mt-10) REVERT: E 579 MET cc_start: 0.2024 (ptp) cc_final: 0.1788 (mpp) outliers start: 51 outliers final: 24 residues processed: 214 average time/residue: 0.6094 time to fit residues: 160.6733 Evaluate side-chains 188 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 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 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 433 VAL 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 318 PHE Chi-restraints excluded: chain C residue 324 GLU 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 463 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 291 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 61 optimal weight: 5.9990 chunk 345 optimal weight: 0.9980 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: 0.0770 chunk 234 optimal weight: 9.9990 chunk 274 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 GLN D 42 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 599 ASN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.178182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.109552 restraints weight = 69856.448| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.35 r_work: 0.3214 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 34306 Z= 0.211 Angle : 0.605 12.684 46788 Z= 0.297 Chirality : 0.046 0.275 5365 Planarity : 0.004 0.075 5912 Dihedral : 4.286 20.737 4372 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.44 % Allowed : 14.06 % Favored : 84.50 % 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: 0.61 (0.13), residues: 4027 helix: 1.69 (0.14), residues: 1415 sheet: 0.07 (0.20), residues: 573 loop : -0.38 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.022 0.001 TYR C1067 PHE 0.024 0.002 PHE B 981 TRP 0.039 0.001 TRP E 566 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (34196) covalent geometry : angle 0.58852 / 0.29 (46498) SS BOND : bond 0.00251 / 0.18 ( 40) SS BOND : angle 0.69354 / 0.47 ( 80) hydrogen bonds : bond 0.04113 / 2.66 ( 1534) hydrogen bonds : angle 5.15617 / 3.58 ( 4494) link_BETA1-4 : bond 0.00239 / 0.16 ( 18) link_BETA1-4 : angle 1.03879 / 0.69 ( 54) link_NAG-ASN : bond 0.00527 / 0.32 ( 52) link_NAG-ASN : angle 2.42225 / 1.57 ( 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 220 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6892 (t80) cc_final: 0.6565 (t80) REVERT: A 118 LEU cc_start: 0.8043 (tm) cc_final: 0.7633 (mt) REVERT: A 508 TYR cc_start: 0.5902 (m-10) cc_final: 0.5698 (m-10) REVERT: A 532 ASN cc_start: 0.8903 (m-40) cc_final: 0.8547 (t0) REVERT: B 200 TYR cc_start: 0.8158 (m-80) cc_final: 0.7807 (t80) REVERT: B 309 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8482 (mp0) REVERT: B 433 VAL cc_start: 0.3742 (OUTLIER) cc_final: 0.3444 (t) REVERT: C 324 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7843 (pm20) REVERT: C 537 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8414 (mtmm) REVERT: D 152 MET cc_start: 0.1671 (pp-130) cc_final: 0.1188 (ptm) REVERT: D 183 TYR cc_start: -0.0244 (OUTLIER) cc_final: -0.0534 (t80) REVERT: D 270 MET cc_start: 0.1919 (ttm) cc_final: 0.1164 (tmm) REVERT: D 297 MET cc_start: -0.2159 (ttm) cc_final: -0.2593 (mtt) REVERT: D 363 LYS cc_start: 0.3660 (mmtm) cc_final: 0.3451 (mppt) REVERT: D 557 MET cc_start: 0.3423 (ptm) cc_final: 0.2804 (ptm) REVERT: D 572 ASN cc_start: 0.3274 (m-40) cc_final: 0.2959 (t0) REVERT: D 579 MET cc_start: 0.1469 (mpp) cc_final: 0.0450 (mpm) REVERT: E 53 ASN cc_start: 0.3153 (t0) cc_final: 0.2581 (t0) REVERT: E 62 MET cc_start: -0.0808 (OUTLIER) cc_final: -0.1746 (ttt) REVERT: E 249 MET cc_start: 0.1283 (ttm) cc_final: 0.0897 (tmt) REVERT: E 291 ILE cc_start: 0.0174 (OUTLIER) cc_final: -0.0314 (tp) REVERT: E 323 MET cc_start: 0.1060 (OUTLIER) cc_final: 0.0032 (tpt) REVERT: E 366 MET cc_start: 0.2884 (tmm) cc_final: 0.2672 (tpt) REVERT: E 495 GLU cc_start: 0.3815 (mp0) cc_final: 0.3351 (mt-10) REVERT: E 579 MET cc_start: 0.2018 (ptp) cc_final: 0.1782 (mpp) outliers start: 52 outliers final: 30 residues processed: 205 average time/residue: 0.5281 time to fit residues: 134.9809 Evaluate side-chains 194 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 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 731 MET 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 226 LEU Chi-restraints excluded: chain B residue 433 VAL 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 258 TRP 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 731 MET 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 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 62 MET Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 323 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 229 optimal weight: 7.9990 chunk 182 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 chunk 326 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 chunk 332 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN D 599 ASN ** 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 = 0.4651 r_free = 0.4651 target = 0.179162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.111180 restraints weight = 70012.779| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.31 r_work: 0.3290 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34306 Z= 0.118 Angle : 0.567 12.700 46788 Z= 0.277 Chirality : 0.044 0.269 5365 Planarity : 0.004 0.079 5912 Dihedral : 4.082 19.832 4372 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.17 % Allowed : 14.67 % Favored : 84.16 % 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: 0.80 (0.13), residues: 4027 helix: 1.84 (0.14), residues: 1411 sheet: 0.19 (0.20), residues: 571 loop : -0.26 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.021 0.001 TYR A1067 PHE 0.026 0.001 PHE B 140 TRP 0.043 0.001 TRP E 566 HIS 0.004 0.001 HIS E 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (34196) covalent geometry : angle 0.55229 / 0.27 (46498) SS BOND : bond 0.00152 / 0.11 ( 40) SS BOND : angle 0.59388 / 0.42 ( 80) hydrogen bonds : bond 0.03637 / 2.36 ( 1534) hydrogen bonds : angle 4.97510 / 3.45 ( 4494) link_BETA1-4 : bond 0.00319 / 0.21 ( 18) link_BETA1-4 : angle 0.91577 / 0.63 ( 54) link_NAG-ASN : bond 0.00472 / 0.27 ( 52) link_NAG-ASN : angle 2.26270 / 1.44 ( 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 217 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 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 79 PHE cc_start: 0.6799 (t80) cc_final: 0.6498 (t80) REVERT: A 118 LEU cc_start: 0.7978 (tm) cc_final: 0.7565 (mt) REVERT: A 508 TYR cc_start: 0.5876 (m-10) cc_final: 0.5634 (m-10) REVERT: A 532 ASN cc_start: 0.8810 (m-40) cc_final: 0.8599 (t0) REVERT: B 140 PHE cc_start: 0.7278 (p90) cc_final: 0.6895 (p90) REVERT: B 141 LEU cc_start: 0.6763 (mp) cc_final: 0.6043 (tp) REVERT: B 200 TYR cc_start: 0.8126 (m-80) cc_final: 0.7798 (t80) REVERT: B 309 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8574 (mp0) REVERT: B 433 VAL cc_start: 0.3755 (OUTLIER) cc_final: 0.3461 (t) REVERT: C 95 ILE cc_start: 0.8127 (mm) cc_final: 0.7512 (tp) REVERT: C 240 THR cc_start: 0.8796 (t) cc_final: 0.8522 (m) REVERT: C 537 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8330 (mtmm) REVERT: D 270 MET cc_start: 0.1733 (ttm) cc_final: 0.0704 (mpp) REVERT: D 297 MET cc_start: -0.2379 (ttm) cc_final: -0.2796 (mtt) REVERT: D 323 MET cc_start: -0.0235 (OUTLIER) cc_final: -0.0639 (mmt) REVERT: D 363 LYS cc_start: 0.3781 (mmtm) cc_final: 0.3546 (mppt) REVERT: D 383 MET cc_start: 0.5556 (tmm) cc_final: 0.5159 (mtt) REVERT: D 557 MET cc_start: 0.3801 (ptm) cc_final: 0.3300 (ptm) REVERT: D 572 ASN cc_start: 0.3225 (m-40) cc_final: 0.2914 (t0) REVERT: D 579 MET cc_start: 0.0997 (mpp) cc_final: 0.0176 (mpm) REVERT: E 53 ASN cc_start: 0.3952 (t0) cc_final: 0.3339 (t0) REVERT: E 62 MET cc_start: -0.1202 (OUTLIER) cc_final: -0.2499 (ttt) REVERT: E 190 MET cc_start: -0.2351 (OUTLIER) cc_final: -0.2551 (ttp) REVERT: E 249 MET cc_start: 0.0822 (ttm) cc_final: 0.0292 (tmt) REVERT: E 291 ILE cc_start: -0.0024 (OUTLIER) cc_final: -0.0389 (tp) REVERT: E 366 MET cc_start: 0.2705 (tmm) cc_final: 0.2445 (tpt) REVERT: E 495 GLU cc_start: 0.4059 (mp0) cc_final: 0.3135 (mt-10) REVERT: E 579 MET cc_start: 0.1390 (ptp) cc_final: 0.1158 (mpp) outliers start: 42 outliers final: 21 residues processed: 204 average time/residue: 0.5288 time to fit residues: 133.6264 Evaluate side-chains 189 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 731 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 84 LEU 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 84 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 794 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 993 ILE 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 190 MET Chi-restraints excluded: chain E residue 212 VAL 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: 3.9990 chunk 303 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 366 optimal weight: 9.9990 chunk 274 optimal weight: 3.9990 chunk 302 optimal weight: 9.9990 chunk 329 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 262 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.178307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.110088 restraints weight = 69922.754| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.44 r_work: 0.3236 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34306 Z= 0.187 Angle : 0.598 13.771 46788 Z= 0.293 Chirality : 0.045 0.278 5365 Planarity : 0.004 0.069 5912 Dihedral : 4.211 20.137 4372 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.00 % Allowed : 14.95 % Favored : 84.05 % 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: 0.71 (0.13), residues: 4027 helix: 1.79 (0.14), residues: 1411 sheet: 0.11 (0.20), residues: 573 loop : -0.31 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 567 TYR 0.021 0.001 TYR A1067 PHE 0.021 0.001 PHE A 400 TRP 0.043 0.001 TRP E 566 HIS 0.004 0.001 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (34196) covalent geometry : angle 0.58242 / 0.29 (46498) SS BOND : bond 0.00224 / 0.16 ( 40) SS BOND : angle 0.66713 / 0.46 ( 80) hydrogen bonds : bond 0.03967 / 2.56 ( 1534) hydrogen bonds : angle 5.10993 / 3.55 ( 4494) link_BETA1-4 : bond 0.00245 / 0.16 ( 18) link_BETA1-4 : angle 1.02467 / 0.68 ( 54) link_NAG-ASN : bond 0.00499 / 0.30 ( 52) link_NAG-ASN : angle 2.36864 / 1.52 ( 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 197 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6787 (t80) cc_final: 0.6440 (t80) REVERT: A 118 LEU cc_start: 0.8029 (tm) cc_final: 0.7632 (mt) REVERT: A 508 TYR cc_start: 0.5910 (m-10) cc_final: 0.5698 (m-10) REVERT: A 532 ASN cc_start: 0.9016 (m-40) cc_final: 0.8746 (t0) REVERT: B 140 PHE cc_start: 0.7343 (p90) cc_final: 0.6964 (p90) REVERT: B 141 LEU cc_start: 0.6668 (mp) cc_final: 0.5944 (tp) REVERT: B 200 TYR cc_start: 0.8197 (m-80) cc_final: 0.7717 (t80) REVERT: B 309 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8484 (mp0) REVERT: B 433 VAL cc_start: 0.3733 (OUTLIER) cc_final: 0.3430 (t) REVERT: C 240 THR cc_start: 0.8739 (t) cc_final: 0.8499 (m) REVERT: C 537 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8405 (mtmm) REVERT: D 152 MET cc_start: 0.1689 (pp-130) cc_final: 0.1265 (ptm) REVERT: D 270 MET cc_start: 0.1931 (ttm) cc_final: 0.1225 (tmm) REVERT: D 297 MET cc_start: -0.2270 (ttm) cc_final: -0.2637 (mtt) REVERT: D 363 LYS cc_start: 0.3584 (mmtm) cc_final: 0.3361 (mppt) REVERT: D 383 MET cc_start: 0.5774 (tmm) cc_final: 0.5425 (mtt) REVERT: D 557 MET cc_start: 0.3469 (ptm) cc_final: 0.2846 (ptm) REVERT: D 572 ASN cc_start: 0.3453 (m-40) cc_final: 0.3123 (t0) REVERT: D 579 MET cc_start: 0.1465 (mpp) cc_final: 0.0486 (mpm) REVERT: E 53 ASN cc_start: 0.3309 (t0) cc_final: 0.2676 (t0) REVERT: E 62 MET cc_start: -0.1558 (OUTLIER) cc_final: -0.2439 (ttt) REVERT: E 190 MET cc_start: -0.2527 (OUTLIER) cc_final: -0.2786 (ttp) REVERT: E 249 MET cc_start: 0.1052 (ttm) cc_final: 0.0616 (tmt) REVERT: E 291 ILE cc_start: 0.0295 (OUTLIER) cc_final: -0.0186 (tp) REVERT: E 366 MET cc_start: 0.2831 (tmm) cc_final: 0.2606 (tpt) REVERT: E 495 GLU cc_start: 0.3998 (mp0) cc_final: 0.3467 (mt-10) REVERT: E 579 MET cc_start: 0.1531 (ptp) cc_final: 0.1272 (mpp) REVERT: E 606 TRP cc_start: 0.2325 (p90) cc_final: 0.1553 (p90) outliers start: 36 outliers final: 24 residues processed: 190 average time/residue: 0.5430 time to fit residues: 129.0950 Evaluate side-chains 184 residues out of total 3599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 582 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 84 LEU 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 84 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 993 ILE 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 E residue 62 MET Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 516 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 57 optimal weight: 1.9990 chunk 354 optimal weight: 20.0000 chunk 403 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 299 optimal weight: 0.9980 chunk 293 optimal weight: 20.0000 chunk 357 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 233 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN B 957 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.177424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.110868 restraints weight = 69776.141| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.85 r_work: 0.3215 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 34306 Z= 0.226 Angle : 0.634 13.776 46788 Z= 0.311 Chirality : 0.046 0.292 5365 Planarity : 0.004 0.075 5912 Dihedral : 4.388 23.460 4372 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.11 % Allowed : 14.92 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.13), residues: 4027 helix: 1.62 (0.14), residues: 1409 sheet: -0.08 (0.20), residues: 556 loop : -0.40 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 567 TYR 0.021 0.002 TYR A1067 PHE 0.022 0.002 PHE B 140 TRP 0.044 0.002 TRP E 566 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 (34196) covalent geometry : angle 0.61727 / 0.31 (46498) SS BOND : bond 0.00261 / 0.19 ( 40) SS BOND : angle 0.71072 / 0.48 ( 80) hydrogen bonds : bond 0.04182 / 2.70 ( 1534) hydrogen bonds : angle 5.24752 / 3.65 ( 4494) link_BETA1-4 : bond 0.00278 / 0.18 ( 18) link_BETA1-4 : angle 1.04277 / 0.68 ( 54) link_NAG-ASN : bond 0.00534 / 0.32 ( 52) link_NAG-ASN : angle 2.51311 / 1.63 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25669.92 seconds wall clock time: 434 minutes 26.28 seconds (26066.28 seconds total)