Starting phenix.real_space_refine on Sun Sep 13 13:47:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vxx_21452/09_2026/6vxx_21452.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxx_21452/09_2026/6vxx_21452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6vxx_21452/09_2026/6vxx_21452.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vxx_21452/09_2026/6vxx_21452.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vxx_21452/09_2026/6vxx_21452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxx_21452/09_2026/6vxx_21452.map" model { file = "/net/cci-nas-00/data/ceres_data/6vxx_21452/09_2026/6vxx_21452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxx_21452/09_2026/6vxx_21452.cif" } resolution = 2.8 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= 0.083 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 99 5.16 5 C 15087 2.51 5 N 3849 2.21 5 O 4659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 159 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23694 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "B" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "C" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.82, per 1000 atoms: 0.25 Number of scatterers: 23694 At special positions: 0 Unit cell: (131.25, 137.55, 171.15, 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 99 16.00 O 4659 8.00 N 3849 7.00 C 15087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.36 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.06 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.36 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.06 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.36 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.06 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1316 " - " ASN A1074 " " NAG A1321 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1316 " - " ASN B1074 " " NAG B1321 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C 709 " " NAG C1316 " - " ASN C1074 " " NAG C1321 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 990.6 milliseconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 25.4% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.890A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.569A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.228A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 759 removed outlier: 6.976A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.806A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.915A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.799A 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 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.890A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.569A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.229A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 759 removed outlier: 6.975A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.806A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.915A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.799A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.890A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.569A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.228A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 759 removed outlier: 6.975A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.806A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.915A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.799A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.008A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.884A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.802A 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: 7.367A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.728A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.530A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.241A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.802A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.122A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.549A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 453 removed outlier: 5.846A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.631A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.405A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.405A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.496A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.691A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.008A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.367A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.728A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.530A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.241A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.802A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.122A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.550A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.847A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.023A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.631A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.405A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.405A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.497A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.692A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.008A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.367A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.728A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.529A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.240A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.122A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.550A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.847A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.023A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.405A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.405A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.497A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.691A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 2871 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.10 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 7277 1.34 - 1.49: 7418 1.49 - 1.64: 9380 1.64 - 1.79: 54 1.79 - 1.94: 69 Bond restraints: 24198 Sorted by residual: bond pdb=" NE ARG A 454 " pdb=" CZ ARG A 454 " ideal model delta sigma weight residual 1.326 1.388 -0.062 1.10e-02 8.26e+03 3.13e+01 bond pdb=" NE ARG C 454 " pdb=" CZ ARG C 454 " ideal model delta sigma weight residual 1.326 1.387 -0.061 1.10e-02 8.26e+03 3.09e+01 bond pdb=" NE ARG B 454 " pdb=" CZ ARG B 454 " ideal model delta sigma weight residual 1.326 1.387 -0.061 1.10e-02 8.26e+03 3.07e+01 bond pdb=" CB ILE A 468 " pdb=" CG1 ILE A 468 " ideal model delta sigma weight residual 1.530 1.631 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" CB ILE C 468 " pdb=" CG1 ILE C 468 " ideal model delta sigma weight residual 1.530 1.630 -0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 24193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 26865 1.62 - 3.23: 4988 3.23 - 4.85: 771 4.85 - 6.47: 236 6.47 - 8.09: 53 Bond angle restraints: 32913 Sorted by residual: angle pdb=" C PHE B 490 " pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta sigma weight residual 119.87 127.51 -7.64 1.04e+00 9.25e-01 5.40e+01 angle pdb=" C PHE C 490 " pdb=" N PRO C 491 " pdb=" CA PRO C 491 " ideal model delta sigma weight residual 119.87 127.48 -7.61 1.04e+00 9.25e-01 5.35e+01 angle pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.87 127.47 -7.60 1.04e+00 9.25e-01 5.34e+01 angle pdb=" C ASP C 808 " pdb=" N PRO C 809 " pdb=" CA PRO C 809 " ideal model delta sigma weight residual 119.56 127.00 -7.44 1.02e+00 9.61e-01 5.33e+01 angle pdb=" C ASP A 808 " pdb=" N PRO A 809 " pdb=" CA PRO A 809 " ideal model delta sigma weight residual 119.56 126.98 -7.42 1.02e+00 9.61e-01 5.29e+01 ... (remaining 32908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 13326 17.73 - 35.45: 420 35.45 - 53.18: 97 53.18 - 70.91: 36 70.91 - 88.63: 26 Dihedral angle restraints: 13905 sinusoidal: 5415 harmonic: 8490 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -172.97 86.97 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -172.96 86.96 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -172.96 86.96 1 1.00e+01 1.00e-02 9.09e+01 ... (remaining 13902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2687 0.080 - 0.160: 915 0.160 - 0.241: 172 0.241 - 0.321: 145 0.321 - 0.401: 29 Chirality restraints: 3948 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.14e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.09e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.07e+01 ... (remaining 3945 not shown) Planarity restraints: 4212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " -0.056 2.00e-02 2.50e+03 5.76e-02 4.15e+01 pdb=" CG ASN B 122 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " 0.088 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 122 " 0.056 2.00e-02 2.50e+03 5.76e-02 4.14e+01 pdb=" CG ASN A 122 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 122 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 122 " -0.088 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 122 " -0.056 2.00e-02 2.50e+03 5.75e-02 4.13e+01 pdb=" CG ASN C 122 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 122 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 122 " 0.088 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " -0.069 2.00e-02 2.50e+03 ... (remaining 4209 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 9020 2.89 - 3.39: 21467 3.39 - 3.90: 40036 3.90 - 4.40: 46413 4.40 - 4.90: 76182 Nonbonded interactions: 193118 Sorted by model distance: nonbonded pdb=" OD1 ASP C 389 " pdb=" NZ LYS C 528 " model vdw 2.389 3.120 nonbonded pdb=" OD1 ASP B 389 " pdb=" NZ LYS B 528 " model vdw 2.389 3.120 nonbonded pdb=" OD1 ASP A 389 " pdb=" NZ LYS A 528 " model vdw 2.390 3.120 nonbonded pdb=" NZ LYS C 811 " pdb=" OD2 ASP C 820 " model vdw 2.405 3.120 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.406 3.120 ... (remaining 193113 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 8.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.350 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.017 0.331 24297 Z= 0.892 Angle : 1.387 13.775 33174 Z= 0.931 Chirality : 0.098 0.401 3948 Planarity : 0.005 0.026 4164 Dihedral : 10.737 88.633 8313 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.23 % Allowed : 0.82 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 2844 helix: -0.27 (0.17), residues: 693 sheet: 0.54 (0.19), residues: 633 loop : 0.42 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1000 TYR 0.042 0.005 TYR C 451 PHE 0.024 0.004 PHE C 515 TRP 0.016 0.006 TRP B 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01622 / 0.86 (24198) covalent geometry : angle 1.36158 / 0.93 (32913) SS BOND : bond 0.09604 / 6.23 ( 36) SS BOND : angle 4.41224 / 3.01 ( 72) hydrogen bonds : bond 0.17431 / 11.14 ( 993) hydrogen bonds : angle 8.16161 / 5.70 ( 2871) link_BETA1-4 : bond 0.06633 / 3.74 ( 15) link_BETA1-4 : angle 3.44032 / 2.21 ( 45) link_NAG-ASN : bond 0.06952 / 4.32 ( 48) link_NAG-ASN : angle 2.47110 / 1.63 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 461 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 PHE cc_start: 0.6636 (t80) cc_final: 0.6411 (t80) REVERT: B 436 TRP cc_start: 0.6715 (p90) cc_final: 0.6412 (p90) REVERT: B 869 MET cc_start: 0.8059 (mtt) cc_final: 0.7819 (mtp) REVERT: C 201 PHE cc_start: 0.6521 (t80) cc_final: 0.6298 (t80) REVERT: C 436 TRP cc_start: 0.6817 (p90) cc_final: 0.6601 (p90) outliers start: 6 outliers final: 0 residues processed: 467 average time/residue: 0.6199 time to fit residues: 335.2181 Evaluate side-chains 210 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 196 ASN A 207 HIS A 314 GLN A 519 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 606 ASN A 613 GLN A 675 GLN A 784 GLN A 804 GLN A 907 ASN A 935 GLN A1010 GLN B 66 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 519 HIS B 580 GLN B 613 GLN B 675 GLN B 804 GLN B 935 GLN B1142 GLN C 66 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 519 HIS C 580 GLN C 606 ASN C 613 GLN C 675 GLN C 784 GLN C 804 GLN C 907 ASN C 935 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.175581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126409 restraints weight = 29789.397| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.39 r_work: 0.3564 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24297 Z= 0.177 Angle : 0.744 17.099 33174 Z= 0.371 Chirality : 0.050 0.611 3948 Planarity : 0.004 0.029 4164 Dihedral : 4.720 26.508 3099 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.74 % Allowed : 6.81 % Favored : 90.45 % 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: 0.58 (0.15), residues: 2844 helix: 1.15 (0.19), residues: 687 sheet: 0.31 (0.17), residues: 714 loop : 0.17 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 237 TYR 0.018 0.002 TYR B1067 PHE 0.024 0.002 PHE A 32 TRP 0.012 0.001 TRP A 104 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (24198) covalent geometry : angle 0.67250 / 0.35 (32913) SS BOND : bond 0.00560 / 0.35 ( 36) SS BOND : angle 1.58238 / 0.90 ( 72) hydrogen bonds : bond 0.05710 / 3.63 ( 993) hydrogen bonds : angle 6.35288 / 4.43 ( 2871) link_BETA1-4 : bond 0.00560 / 0.31 ( 15) link_BETA1-4 : angle 1.76683 / 1.14 ( 45) link_NAG-ASN : bond 0.00574 / 0.37 ( 48) link_NAG-ASN : angle 4.69034 / 3.19 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 251 time to evaluate : 0.914 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 41 LYS cc_start: 0.8009 (mttp) cc_final: 0.7366 (mmtp) REVERT: A 205 SER cc_start: 0.8536 (p) cc_final: 0.8127 (t) REVERT: A 237 ARG cc_start: 0.6461 (mtm-85) cc_final: 0.6052 (mpp80) REVERT: A 353 TRP cc_start: 0.7741 (p-90) cc_final: 0.7398 (p-90) REVERT: A 389 ASP cc_start: 0.8386 (t70) cc_final: 0.8065 (m-30) REVERT: A 776 LYS cc_start: 0.8305 (tttt) cc_final: 0.7890 (ttpt) REVERT: A 794 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.6960 (mt) REVERT: A 869 MET cc_start: 0.8646 (mtm) cc_final: 0.8445 (mtp) REVERT: A 947 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8212 (mtpt) REVERT: A 950 ASP cc_start: 0.7335 (m-30) cc_final: 0.7050 (m-30) REVERT: B 190 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.5677 (ttp-110) REVERT: B 201 PHE cc_start: 0.6245 (t80) cc_final: 0.5503 (t80) REVERT: B 314 GLN cc_start: 0.8466 (tt0) cc_final: 0.8220 (tm-30) REVERT: B 436 TRP cc_start: 0.6621 (p90) cc_final: 0.6131 (p90) REVERT: B 759 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7860 (t80) REVERT: B 776 LYS cc_start: 0.8305 (tttt) cc_final: 0.8010 (ttpm) REVERT: B 794 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7070 (mt) REVERT: B 869 MET cc_start: 0.8769 (mtt) cc_final: 0.8403 (mtp) REVERT: B 985 ASP cc_start: 0.7314 (m-30) cc_final: 0.7112 (m-30) REVERT: B 1005 GLN cc_start: 0.8467 (mt0) cc_final: 0.7987 (mt0) REVERT: C 32 PHE cc_start: 0.7698 (m-80) cc_final: 0.7474 (m-80) REVERT: C 342 PHE cc_start: 0.7754 (m-80) cc_final: 0.7173 (m-80) REVERT: C 353 TRP cc_start: 0.7653 (p-90) cc_final: 0.7418 (p-90) REVERT: C 436 TRP cc_start: 0.6832 (p90) cc_final: 0.6422 (p90) REVERT: C 540 ASN cc_start: 0.6862 (t0) cc_final: 0.6624 (t0) REVERT: C 776 LYS cc_start: 0.8276 (tttt) cc_final: 0.7986 (ttpm) REVERT: C 794 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7064 (mt) REVERT: C 950 ASP cc_start: 0.7835 (t0) cc_final: 0.7275 (m-30) REVERT: C 1045 LYS cc_start: 0.8458 (ttpp) cc_final: 0.7967 (ttmt) outliers start: 70 outliers final: 30 residues processed: 298 average time/residue: 0.5352 time to fit residues: 189.1637 Evaluate side-chains 231 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 1037 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 248 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 935 GLN B 30 ASN B 66 HIS B 196 ASN B 207 HIS B 580 GLN B 613 GLN B 675 GLN C 66 HIS C 188 ASN C 196 ASN C 207 HIS C 580 GLN C 613 GLN C 675 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.173078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.123519 restraints weight = 29919.237| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.37 r_work: 0.3525 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24297 Z= 0.195 Angle : 0.660 13.404 33174 Z= 0.328 Chirality : 0.048 0.510 3948 Planarity : 0.004 0.032 4164 Dihedral : 4.624 23.353 3099 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.56 % Allowed : 7.71 % Favored : 88.73 % 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: 0.43 (0.15), residues: 2844 helix: 1.38 (0.20), residues: 690 sheet: 0.07 (0.17), residues: 708 loop : -0.04 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 319 TYR 0.020 0.002 TYR B1067 PHE 0.024 0.002 PHE A 342 TRP 0.018 0.001 TRP B 353 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (24198) covalent geometry : angle 0.60880 / 0.32 (32913) SS BOND : bond 0.00532 / 0.34 ( 36) SS BOND : angle 1.29015 / 0.80 ( 72) hydrogen bonds : bond 0.04897 / 3.11 ( 993) hydrogen bonds : angle 5.97539 / 4.16 ( 2871) link_BETA1-4 : bond 0.00481 / 0.31 ( 15) link_BETA1-4 : angle 1.28612 / 0.87 ( 45) link_NAG-ASN : bond 0.00840 / 0.53 ( 48) link_NAG-ASN : angle 3.79127 / 2.54 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 226 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7994 (mttp) cc_final: 0.7465 (mmtp) REVERT: A 205 SER cc_start: 0.8457 (p) cc_final: 0.8181 (t) REVERT: A 229 LEU cc_start: 0.6035 (mt) cc_final: 0.5735 (tt) REVERT: A 237 ARG cc_start: 0.6412 (mtm-85) cc_final: 0.6141 (mpp80) REVERT: A 353 TRP cc_start: 0.7866 (p-90) cc_final: 0.7550 (p-90) REVERT: A 725 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: A 776 LYS cc_start: 0.8288 (tttt) cc_final: 0.7848 (ttpt) REVERT: A 794 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.6988 (mt) REVERT: A 950 ASP cc_start: 0.7373 (m-30) cc_final: 0.7067 (m-30) REVERT: B 121 ASN cc_start: 0.5771 (t0) cc_final: 0.5482 (m-40) REVERT: B 201 PHE cc_start: 0.6292 (t80) cc_final: 0.5585 (t80) REVERT: B 384 PRO cc_start: 0.8150 (Cg_endo) cc_final: 0.7896 (Cg_exo) REVERT: B 389 ASP cc_start: 0.8457 (t0) cc_final: 0.8077 (t70) REVERT: B 436 TRP cc_start: 0.6723 (p90) cc_final: 0.6258 (p90) REVERT: B 558 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.8005 (ptpt) REVERT: B 776 LYS cc_start: 0.8265 (tttt) cc_final: 0.7972 (ttpm) REVERT: B 790 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8081 (ptpt) REVERT: B 794 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7020 (mt) REVERT: B 950 ASP cc_start: 0.7953 (t0) cc_final: 0.7572 (m-30) REVERT: B 988 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: B 1072 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: C 196 ASN cc_start: 0.5388 (OUTLIER) cc_final: 0.5174 (m-40) REVERT: C 400 PHE cc_start: 0.8068 (p90) cc_final: 0.7807 (p90) REVERT: C 436 TRP cc_start: 0.6890 (p90) cc_final: 0.6408 (p90) REVERT: C 558 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8077 (ptpt) REVERT: C 759 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7984 (t80) REVERT: C 776 LYS cc_start: 0.8270 (tttt) cc_final: 0.7995 (tttm) REVERT: C 794 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.6967 (mt) REVERT: C 950 ASP cc_start: 0.7865 (t0) cc_final: 0.7428 (m-30) REVERT: C 1045 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8061 (ttmt) outliers start: 91 outliers final: 35 residues processed: 293 average time/residue: 0.5303 time to fit residues: 184.8082 Evaluate side-chains 236 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1037 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 236 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 268 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 289 optimal weight: 0.5980 chunk 288 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 285 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 207 HIS A 422 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 66 HIS B 196 ASN B 207 HIS B 580 GLN B 784 GLN B1119 ASN C 66 HIS C 196 ASN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 613 GLN C 784 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.173971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.124609 restraints weight = 30020.719| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.38 r_work: 0.3542 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24297 Z= 0.144 Angle : 0.611 12.947 33174 Z= 0.302 Chirality : 0.046 0.459 3948 Planarity : 0.004 0.036 4164 Dihedral : 4.444 22.319 3099 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.82 % Allowed : 9.59 % Favored : 87.60 % 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: 0.43 (0.15), residues: 2844 helix: 1.69 (0.21), residues: 675 sheet: 0.09 (0.18), residues: 678 loop : -0.21 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.020 0.001 TYR A 269 PHE 0.022 0.001 PHE A 32 TRP 0.025 0.001 TRP B 353 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (24198) covalent geometry : angle 0.56041 / 0.29 (32913) SS BOND : bond 0.00558 / 0.36 ( 36) SS BOND : angle 1.60485 / 0.91 ( 72) hydrogen bonds : bond 0.04382 / 2.78 ( 993) hydrogen bonds : angle 5.76803 / 4.00 ( 2871) link_BETA1-4 : bond 0.00400 / 0.22 ( 15) link_BETA1-4 : angle 1.15457 / 0.79 ( 45) link_NAG-ASN : bond 0.00688 / 0.44 ( 48) link_NAG-ASN : angle 3.52665 / 2.35 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 200 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7896 (mttp) cc_final: 0.7421 (mmtp) REVERT: A 229 LEU cc_start: 0.6099 (mt) cc_final: 0.5850 (tt) REVERT: A 237 ARG cc_start: 0.6320 (mtm-85) cc_final: 0.6057 (mpp80) REVERT: A 353 TRP cc_start: 0.7870 (p-90) cc_final: 0.7602 (p-90) REVERT: A 776 LYS cc_start: 0.8257 (tttt) cc_final: 0.7898 (ttpt) REVERT: A 794 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.6965 (mt) REVERT: A 947 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8297 (mtpt) REVERT: A 1119 ASN cc_start: 0.7906 (m-40) cc_final: 0.7691 (m-40) REVERT: B 201 PHE cc_start: 0.6228 (t80) cc_final: 0.5398 (t80) REVERT: B 229 LEU cc_start: 0.6142 (mt) cc_final: 0.5936 (tt) REVERT: B 353 TRP cc_start: 0.7794 (p-90) cc_final: 0.7531 (p-90) REVERT: B 436 TRP cc_start: 0.6717 (p90) cc_final: 0.6245 (p90) REVERT: B 516 GLU cc_start: 0.7464 (tt0) cc_final: 0.6743 (mt-10) REVERT: B 558 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8045 (ptpt) REVERT: B 646 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7567 (ttp80) REVERT: B 776 LYS cc_start: 0.8241 (tttt) cc_final: 0.7843 (ttpt) REVERT: B 794 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.6860 (mt) REVERT: B 869 MET cc_start: 0.8660 (mtt) cc_final: 0.8342 (mtp) REVERT: B 977 LEU cc_start: 0.8345 (mt) cc_final: 0.8131 (tp) REVERT: B 1072 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: C 32 PHE cc_start: 0.7642 (m-80) cc_final: 0.7375 (m-80) REVERT: C 54 LEU cc_start: 0.8158 (mp) cc_final: 0.7940 (mm) REVERT: C 196 ASN cc_start: 0.5623 (OUTLIER) cc_final: 0.4931 (t0) REVERT: C 353 TRP cc_start: 0.7860 (p-90) cc_final: 0.7483 (p-90) REVERT: C 384 PRO cc_start: 0.8013 (Cg_endo) cc_final: 0.7765 (Cg_exo) REVERT: C 436 TRP cc_start: 0.6942 (p90) cc_final: 0.6453 (p90) REVERT: C 516 GLU cc_start: 0.7590 (tt0) cc_final: 0.6799 (mt-10) REVERT: C 613 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8486 (mt0) REVERT: C 776 LYS cc_start: 0.8270 (tttt) cc_final: 0.8000 (tttm) REVERT: C 794 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.6919 (mt) REVERT: C 1045 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8128 (ttmt) outliers start: 72 outliers final: 37 residues processed: 255 average time/residue: 0.5029 time to fit residues: 153.7184 Evaluate side-chains 233 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 253 optimal weight: 1.9990 chunk 282 optimal weight: 0.9980 chunk 134 optimal weight: 20.0000 chunk 266 optimal weight: 0.5980 chunk 281 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 226 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 284 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 196 ASN B 207 HIS B 580 GLN B 613 GLN C 66 HIS C 196 ASN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 762 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.174084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.125075 restraints weight = 29927.906| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.37 r_work: 0.3544 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24297 Z= 0.141 Angle : 0.591 12.535 33174 Z= 0.293 Chirality : 0.046 0.447 3948 Planarity : 0.003 0.036 4164 Dihedral : 4.344 21.473 3099 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.01 % Allowed : 9.78 % Favored : 87.21 % 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: 0.41 (0.15), residues: 2844 helix: 1.80 (0.21), residues: 675 sheet: 0.12 (0.18), residues: 672 loop : -0.30 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.019 0.001 TYR B1067 PHE 0.021 0.001 PHE A 32 TRP 0.018 0.001 TRP B 353 HIS 0.002 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (24198) covalent geometry : angle 0.54358 / 0.28 (32913) SS BOND : bond 0.00525 / 0.34 ( 36) SS BOND : angle 1.72390 / 1.01 ( 72) hydrogen bonds : bond 0.04213 / 2.68 ( 993) hydrogen bonds : angle 5.68182 / 3.94 ( 2871) link_BETA1-4 : bond 0.00371 / 0.20 ( 15) link_BETA1-4 : angle 1.09642 / 0.76 ( 45) link_NAG-ASN : bond 0.00664 / 0.42 ( 48) link_NAG-ASN : angle 3.33819 / 2.22 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 205 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7866 (mttp) cc_final: 0.7363 (mmtp) REVERT: A 229 LEU cc_start: 0.5927 (mt) cc_final: 0.5708 (tt) REVERT: A 237 ARG cc_start: 0.6389 (mtm-85) cc_final: 0.6120 (mpp80) REVERT: A 353 TRP cc_start: 0.7896 (p-90) cc_final: 0.7642 (p-90) REVERT: A 408 ARG cc_start: 0.7792 (mpp-170) cc_final: 0.7521 (mtm110) REVERT: A 740 MET cc_start: 0.8803 (tpp) cc_final: 0.8548 (tpp) REVERT: A 776 LYS cc_start: 0.8269 (tttt) cc_final: 0.7821 (ttpt) REVERT: A 794 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.7030 (mt) REVERT: A 947 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8278 (mtpt) REVERT: A 988 GLU cc_start: 0.8109 (mp0) cc_final: 0.7884 (pm20) REVERT: A 1002 GLN cc_start: 0.7948 (tt0) cc_final: 0.7334 (tt0) REVERT: A 1119 ASN cc_start: 0.7940 (m-40) cc_final: 0.7713 (m-40) REVERT: B 32 PHE cc_start: 0.7863 (m-80) cc_final: 0.7352 (m-10) REVERT: B 45 SER cc_start: 0.8788 (p) cc_final: 0.8406 (t) REVERT: B 201 PHE cc_start: 0.6099 (t80) cc_final: 0.5666 (t80) REVERT: B 229 LEU cc_start: 0.6131 (mt) cc_final: 0.5905 (tt) REVERT: B 353 TRP cc_start: 0.7830 (p-90) cc_final: 0.7626 (p-90) REVERT: B 436 TRP cc_start: 0.6735 (p90) cc_final: 0.6256 (p90) REVERT: B 516 GLU cc_start: 0.7453 (tt0) cc_final: 0.6734 (mt-10) REVERT: B 558 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8002 (ptpt) REVERT: B 646 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7576 (ttp80) REVERT: B 776 LYS cc_start: 0.8218 (tttt) cc_final: 0.7812 (ttpt) REVERT: B 790 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8053 (ptpt) REVERT: B 794 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.6865 (mt) REVERT: B 869 MET cc_start: 0.8694 (mtt) cc_final: 0.8404 (mtp) REVERT: B 977 LEU cc_start: 0.8367 (mt) cc_final: 0.8156 (tp) REVERT: B 1002 GLN cc_start: 0.8107 (tt0) cc_final: 0.7741 (tt0) REVERT: B 1072 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: C 32 PHE cc_start: 0.7651 (m-80) cc_final: 0.7393 (m-80) REVERT: C 54 LEU cc_start: 0.8156 (mp) cc_final: 0.7943 (mm) REVERT: C 196 ASN cc_start: 0.5513 (OUTLIER) cc_final: 0.4933 (t0) REVERT: C 342 PHE cc_start: 0.7761 (m-80) cc_final: 0.7386 (m-80) REVERT: C 434 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7791 (pt) REVERT: C 436 TRP cc_start: 0.6929 (p90) cc_final: 0.6417 (p90) REVERT: C 776 LYS cc_start: 0.8256 (tttt) cc_final: 0.7980 (tttm) REVERT: C 794 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.6910 (mt) REVERT: C 1045 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8108 (ttmt) outliers start: 77 outliers final: 41 residues processed: 266 average time/residue: 0.4690 time to fit residues: 150.8286 Evaluate side-chains 239 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 181 optimal weight: 2.9990 chunk 229 optimal weight: 0.2980 chunk 36 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 235 optimal weight: 0.0060 chunk 138 optimal weight: 0.0020 chunk 86 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 overall best weight: 0.6206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 207 HIS C 66 HIS C 196 ASN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 613 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.174149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.125202 restraints weight = 30100.049| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.37 r_work: 0.3545 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24297 Z= 0.134 Angle : 0.577 12.120 33174 Z= 0.287 Chirality : 0.046 0.435 3948 Planarity : 0.003 0.038 4164 Dihedral : 4.292 20.913 3099 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.86 % Allowed : 10.68 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.15), residues: 2844 helix: 1.89 (0.21), residues: 675 sheet: 0.12 (0.18), residues: 660 loop : -0.32 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 408 TYR 0.018 0.001 TYR C1067 PHE 0.022 0.001 PHE C 168 TRP 0.026 0.001 TRP C 353 HIS 0.002 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (24198) covalent geometry : angle 0.53279 / 0.28 (32913) SS BOND : bond 0.00498 / 0.32 ( 36) SS BOND : angle 1.70546 / 0.97 ( 72) hydrogen bonds : bond 0.04064 / 2.58 ( 993) hydrogen bonds : angle 5.62229 / 3.90 ( 2871) link_BETA1-4 : bond 0.00367 / 0.20 ( 15) link_BETA1-4 : angle 1.05227 / 0.73 ( 45) link_NAG-ASN : bond 0.00675 / 0.42 ( 48) link_NAG-ASN : angle 3.18127 / 2.11 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 203 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.5998 (mt) cc_final: 0.5780 (tt) REVERT: A 237 ARG cc_start: 0.6450 (mtm-85) cc_final: 0.6144 (ttm110) REVERT: A 353 TRP cc_start: 0.7917 (p-90) cc_final: 0.7686 (p-90) REVERT: A 408 ARG cc_start: 0.7812 (mpp-170) cc_final: 0.7481 (mtm110) REVERT: A 776 LYS cc_start: 0.8265 (tttt) cc_final: 0.7816 (ttpt) REVERT: A 794 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7016 (mt) REVERT: A 947 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8275 (mtpt) REVERT: A 988 GLU cc_start: 0.8136 (mp0) cc_final: 0.7913 (pm20) REVERT: A 1002 GLN cc_start: 0.7958 (tt0) cc_final: 0.7356 (tt0) REVERT: A 1119 ASN cc_start: 0.7964 (m-40) cc_final: 0.7738 (m-40) REVERT: B 32 PHE cc_start: 0.7881 (m-80) cc_final: 0.7378 (m-10) REVERT: B 45 SER cc_start: 0.8782 (p) cc_final: 0.8421 (t) REVERT: B 201 PHE cc_start: 0.6347 (t80) cc_final: 0.5434 (t80) REVERT: B 229 LEU cc_start: 0.6180 (mt) cc_final: 0.5861 (tt) REVERT: B 436 TRP cc_start: 0.6817 (p90) cc_final: 0.6345 (p90) REVERT: B 558 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7941 (ptpt) REVERT: B 646 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7583 (ttp80) REVERT: B 776 LYS cc_start: 0.8201 (tttt) cc_final: 0.7815 (ttpt) REVERT: B 790 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8061 (ptpt) REVERT: B 794 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.6844 (mt) REVERT: B 869 MET cc_start: 0.8692 (mtt) cc_final: 0.8387 (mtp) REVERT: B 977 LEU cc_start: 0.8298 (mt) cc_final: 0.8082 (tp) REVERT: B 1002 GLN cc_start: 0.8066 (tt0) cc_final: 0.7724 (tt0) REVERT: B 1072 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: C 32 PHE cc_start: 0.7657 (m-80) cc_final: 0.7170 (m-80) REVERT: C 54 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7970 (mm) REVERT: C 190 ARG cc_start: 0.6809 (ttm110) cc_final: 0.6168 (ttp-110) REVERT: C 237 ARG cc_start: 0.6709 (mpp80) cc_final: 0.6154 (mpp80) REVERT: C 342 PHE cc_start: 0.7747 (m-80) cc_final: 0.7371 (m-80) REVERT: C 434 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7844 (pt) REVERT: C 436 TRP cc_start: 0.6925 (p90) cc_final: 0.6402 (p90) REVERT: C 776 LYS cc_start: 0.8245 (tttt) cc_final: 0.7980 (tttm) REVERT: C 794 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.6888 (mt) REVERT: C 1045 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8120 (ttmt) outliers start: 73 outliers final: 40 residues processed: 260 average time/residue: 0.4545 time to fit residues: 143.2012 Evaluate side-chains 244 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 270 optimal weight: 2.9990 chunk 246 optimal weight: 0.9990 chunk 286 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 180 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 540 ASN C 66 HIS C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 613 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.173440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.124377 restraints weight = 29940.431| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.36 r_work: 0.3532 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24297 Z= 0.155 Angle : 0.581 11.759 33174 Z= 0.288 Chirality : 0.046 0.432 3948 Planarity : 0.004 0.038 4164 Dihedral : 4.283 20.302 3099 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.90 % Allowed : 11.35 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 2844 helix: 1.89 (0.21), residues: 675 sheet: 0.02 (0.18), residues: 696 loop : -0.33 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 408 TYR 0.018 0.001 TYR B1067 PHE 0.027 0.001 PHE A 400 TRP 0.034 0.002 TRP C 353 HIS 0.002 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (24198) covalent geometry : angle 0.54041 / 0.28 (32913) SS BOND : bond 0.00529 / 0.34 ( 36) SS BOND : angle 1.55749 / 0.89 ( 72) hydrogen bonds : bond 0.04129 / 2.62 ( 993) hydrogen bonds : angle 5.60056 / 3.89 ( 2871) link_BETA1-4 : bond 0.00375 / 0.20 ( 15) link_BETA1-4 : angle 1.03443 / 0.72 ( 45) link_NAG-ASN : bond 0.00611 / 0.39 ( 48) link_NAG-ASN : angle 3.09389 / 2.04 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 208 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.6079 (mt) cc_final: 0.5838 (tt) REVERT: A 237 ARG cc_start: 0.6445 (mtm-85) cc_final: 0.6138 (ttm110) REVERT: A 408 ARG cc_start: 0.7801 (mpp-170) cc_final: 0.7492 (ptp-110) REVERT: A 436 TRP cc_start: 0.6689 (p90) cc_final: 0.6488 (p90) REVERT: A 529 LYS cc_start: 0.8697 (mmmt) cc_final: 0.8315 (mppt) REVERT: A 740 MET cc_start: 0.8795 (tpp) cc_final: 0.8488 (mmm) REVERT: A 759 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7939 (t80) REVERT: A 776 LYS cc_start: 0.8286 (tttt) cc_final: 0.7930 (tttm) REVERT: A 794 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7015 (mt) REVERT: A 947 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8308 (mtpt) REVERT: A 988 GLU cc_start: 0.8169 (mp0) cc_final: 0.7908 (pm20) REVERT: A 1002 GLN cc_start: 0.7947 (tt0) cc_final: 0.7376 (tt0) REVERT: B 32 PHE cc_start: 0.7897 (m-80) cc_final: 0.7409 (m-10) REVERT: B 45 SER cc_start: 0.8764 (p) cc_final: 0.8425 (t) REVERT: B 201 PHE cc_start: 0.6413 (t80) cc_final: 0.5462 (t80) REVERT: B 229 LEU cc_start: 0.6310 (mt) cc_final: 0.5891 (tt) REVERT: B 389 ASP cc_start: 0.8359 (t0) cc_final: 0.7972 (t0) REVERT: B 436 TRP cc_start: 0.6840 (p90) cc_final: 0.6362 (p90) REVERT: B 516 GLU cc_start: 0.7387 (tt0) cc_final: 0.6664 (mt-10) REVERT: B 558 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7916 (ptpt) REVERT: B 646 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7520 (mtp85) REVERT: B 776 LYS cc_start: 0.8215 (tttt) cc_final: 0.7924 (tttm) REVERT: B 790 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8111 (ptpt) REVERT: B 794 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.6907 (mt) REVERT: B 869 MET cc_start: 0.8696 (mtt) cc_final: 0.8404 (mtp) REVERT: B 1002 GLN cc_start: 0.8140 (tt0) cc_final: 0.7802 (tt0) REVERT: B 1072 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: C 32 PHE cc_start: 0.7673 (m-80) cc_final: 0.7236 (m-80) REVERT: C 54 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8012 (mm) REVERT: C 201 PHE cc_start: 0.6421 (t80) cc_final: 0.5823 (t80) REVERT: C 241 LEU cc_start: 0.6625 (mp) cc_final: 0.6220 (mp) REVERT: C 342 PHE cc_start: 0.7703 (m-80) cc_final: 0.7284 (m-80) REVERT: C 434 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7871 (pt) REVERT: C 436 TRP cc_start: 0.6954 (p90) cc_final: 0.6477 (p90) REVERT: C 776 LYS cc_start: 0.8272 (tttt) cc_final: 0.8005 (tttm) REVERT: C 794 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.6924 (mt) REVERT: C 1045 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8135 (ttmt) outliers start: 74 outliers final: 42 residues processed: 270 average time/residue: 0.4522 time to fit residues: 147.8974 Evaluate side-chains 245 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 192 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 47 optimal weight: 4.9990 chunk 247 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 804 GLN A1119 ASN B 188 ASN B 207 HIS B 501 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 655 HIS C 66 HIS C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 613 GLN C 655 HIS C 901 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.167597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118051 restraints weight = 30234.048| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.32 r_work: 0.3449 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 24297 Z= 0.388 Angle : 0.778 11.995 33174 Z= 0.388 Chirality : 0.054 0.474 3948 Planarity : 0.005 0.041 4164 Dihedral : 5.006 21.260 3099 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.05 % Allowed : 12.01 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 2844 helix: 1.26 (0.20), residues: 678 sheet: -0.36 (0.17), residues: 747 loop : -0.77 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1014 TYR 0.020 0.002 TYR C 265 PHE 0.027 0.003 PHE C 400 TRP 0.042 0.003 TRP B 353 HIS 0.007 0.002 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00947 / 0.39 (24198) covalent geometry : angle 0.73619 / 0.38 (32913) SS BOND : bond 0.00720 / 0.45 ( 36) SS BOND : angle 2.42923 / 1.32 ( 72) hydrogen bonds : bond 0.05566 / 3.53 ( 993) hydrogen bonds : angle 6.14998 / 4.29 ( 2871) link_BETA1-4 : bond 0.00278 / 0.16 ( 15) link_BETA1-4 : angle 1.20912 / 0.81 ( 45) link_NAG-ASN : bond 0.00702 / 0.45 ( 48) link_NAG-ASN : angle 3.49004 / 2.34 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 211 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6512 (mtm-85) cc_final: 0.6131 (mpp80) REVERT: A 353 TRP cc_start: 0.8012 (p-90) cc_final: 0.7733 (p-90) REVERT: A 574 ASP cc_start: 0.8118 (t70) cc_final: 0.7807 (t0) REVERT: A 661 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7850 (tp30) REVERT: A 759 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7768 (t80) REVERT: A 776 LYS cc_start: 0.8334 (tttt) cc_final: 0.8108 (ttpp) REVERT: A 794 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7062 (mt) REVERT: A 988 GLU cc_start: 0.8231 (mp0) cc_final: 0.7950 (pm20) REVERT: A 1002 GLN cc_start: 0.7970 (tt0) cc_final: 0.7603 (tt0) REVERT: B 45 SER cc_start: 0.8844 (p) cc_final: 0.8505 (t) REVERT: B 201 PHE cc_start: 0.6777 (t80) cc_final: 0.5934 (t80) REVERT: B 436 TRP cc_start: 0.6988 (p90) cc_final: 0.6501 (p90) REVERT: B 516 GLU cc_start: 0.7588 (tt0) cc_final: 0.6768 (mt-10) REVERT: B 558 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8018 (ptpt) REVERT: B 776 LYS cc_start: 0.8348 (tttt) cc_final: 0.8069 (ttpm) REVERT: B 790 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8210 (ptpt) REVERT: B 794 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7127 (mt) REVERT: B 950 ASP cc_start: 0.8009 (t0) cc_final: 0.7725 (m-30) REVERT: B 990 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6997 (tm-30) REVERT: B 1072 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: C 32 PHE cc_start: 0.7774 (m-80) cc_final: 0.7311 (m-80) REVERT: C 201 PHE cc_start: 0.6639 (t80) cc_final: 0.5972 (t80) REVERT: C 241 LEU cc_start: 0.6653 (mp) cc_final: 0.6340 (mp) REVERT: C 436 TRP cc_start: 0.6962 (p90) cc_final: 0.6416 (p90) REVERT: C 776 LYS cc_start: 0.8372 (tttt) cc_final: 0.8125 (tttm) REVERT: C 794 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7055 (mt) REVERT: C 950 ASP cc_start: 0.7930 (t0) cc_final: 0.7554 (m-30) REVERT: C 990 GLU cc_start: 0.7222 (mt-10) cc_final: 0.7018 (tm-30) REVERT: C 1045 LYS cc_start: 0.8474 (ttpp) cc_final: 0.8080 (ttmt) outliers start: 78 outliers final: 46 residues processed: 274 average time/residue: 0.5038 time to fit residues: 165.2421 Evaluate side-chains 246 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 121 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 276 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 281 optimal weight: 0.6980 chunk 242 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 207 HIS B 580 GLN C 66 HIS C 207 HIS C 613 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.171725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.122673 restraints weight = 30095.211| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.36 r_work: 0.3510 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24297 Z= 0.147 Angle : 0.634 18.547 33174 Z= 0.315 Chirality : 0.047 0.408 3948 Planarity : 0.004 0.038 4164 Dihedral : 4.583 36.474 3099 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.46 % Allowed : 13.34 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.04 (0.15), residues: 2844 helix: 1.66 (0.21), residues: 678 sheet: -0.21 (0.17), residues: 714 loop : -0.59 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 237 TYR 0.019 0.001 TYR B1067 PHE 0.021 0.001 PHE A 32 TRP 0.044 0.002 TRP B 353 HIS 0.002 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (24198) covalent geometry : angle 0.59266 / 0.30 (32913) SS BOND : bond 0.00493 / 0.32 ( 36) SS BOND : angle 2.36945 / 1.29 ( 72) hydrogen bonds : bond 0.04263 / 2.71 ( 993) hydrogen bonds : angle 5.75091 / 4.00 ( 2871) link_BETA1-4 : bond 0.00342 / 0.20 ( 15) link_BETA1-4 : angle 0.96038 / 0.67 ( 45) link_NAG-ASN : bond 0.00557 / 0.36 ( 48) link_NAG-ASN : angle 3.02321 / 1.99 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 0.800 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 237 ARG cc_start: 0.6458 (mtm-85) cc_final: 0.6107 (ttm110) REVERT: A 353 TRP cc_start: 0.7900 (p-90) cc_final: 0.7629 (p-90) REVERT: A 574 ASP cc_start: 0.8064 (t70) cc_final: 0.7746 (t0) REVERT: A 661 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7839 (tp30) REVERT: A 740 MET cc_start: 0.8774 (mmm) cc_final: 0.8454 (tpp) REVERT: A 776 LYS cc_start: 0.8263 (tttt) cc_final: 0.7870 (ttpt) REVERT: A 794 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.6966 (mt) REVERT: A 869 MET cc_start: 0.8578 (mtm) cc_final: 0.8317 (mtp) REVERT: A 988 GLU cc_start: 0.8213 (mp0) cc_final: 0.8003 (pm20) REVERT: A 1002 GLN cc_start: 0.7947 (tt0) cc_final: 0.7728 (tt0) REVERT: B 45 SER cc_start: 0.8804 (p) cc_final: 0.8451 (t) REVERT: B 389 ASP cc_start: 0.8285 (t70) cc_final: 0.7947 (t0) REVERT: B 436 TRP cc_start: 0.6893 (p90) cc_final: 0.6399 (p90) REVERT: B 516 GLU cc_start: 0.7450 (tt0) cc_final: 0.6670 (mt-10) REVERT: B 558 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7810 (ptpt) REVERT: B 776 LYS cc_start: 0.8249 (tttt) cc_final: 0.7956 (tttm) REVERT: B 790 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8102 (ptpt) REVERT: B 794 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.6965 (mt) REVERT: B 869 MET cc_start: 0.8690 (mtt) cc_final: 0.8370 (mtp) REVERT: B 1002 GLN cc_start: 0.8221 (tt0) cc_final: 0.7674 (tt0) REVERT: B 1119 ASN cc_start: 0.8171 (m-40) cc_final: 0.7831 (m110) REVERT: C 32 PHE cc_start: 0.7723 (m-80) cc_final: 0.7318 (m-80) REVERT: C 201 PHE cc_start: 0.6579 (t80) cc_final: 0.5893 (t80) REVERT: C 241 LEU cc_start: 0.6656 (mp) cc_final: 0.6349 (mp) REVERT: C 342 PHE cc_start: 0.7788 (m-80) cc_final: 0.7573 (m-80) REVERT: C 434 ILE cc_start: 0.8019 (pt) cc_final: 0.7771 (pt) REVERT: C 436 TRP cc_start: 0.6899 (p90) cc_final: 0.6379 (p90) REVERT: C 571 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6269 (t0) REVERT: C 776 LYS cc_start: 0.8252 (tttt) cc_final: 0.7978 (tttm) REVERT: C 794 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.6926 (mt) REVERT: C 1045 LYS cc_start: 0.8513 (ttpp) cc_final: 0.8103 (tptt) outliers start: 63 outliers final: 35 residues processed: 263 average time/residue: 0.4545 time to fit residues: 144.6082 Evaluate side-chains 234 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 83 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 chunk 135 optimal weight: 0.0010 chunk 184 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 66 HIS C 207 HIS C 613 GLN C 965 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.172587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.123742 restraints weight = 30006.386| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.36 r_work: 0.3526 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24297 Z= 0.140 Angle : 0.619 15.568 33174 Z= 0.308 Chirality : 0.047 0.403 3948 Planarity : 0.004 0.038 4164 Dihedral : 4.450 41.050 3099 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.80 % Allowed : 14.16 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.15 (0.15), residues: 2844 helix: 1.79 (0.21), residues: 672 sheet: -0.12 (0.18), residues: 663 loop : -0.54 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 408 TYR 0.019 0.001 TYR C1067 PHE 0.029 0.001 PHE C 400 TRP 0.043 0.002 TRP B 353 HIS 0.002 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (24198) covalent geometry : angle 0.57998 / 0.30 (32913) SS BOND : bond 0.00556 / 0.38 ( 36) SS BOND : angle 2.48155 / 1.53 ( 72) hydrogen bonds : bond 0.04069 / 2.57 ( 993) hydrogen bonds : angle 5.60469 / 3.89 ( 2871) link_BETA1-4 : bond 0.00340 / 0.19 ( 15) link_BETA1-4 : angle 0.92454 / 0.65 ( 45) link_NAG-ASN : bond 0.00550 / 0.36 ( 48) link_NAG-ASN : angle 2.85195 / 1.87 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.6257 (mt) cc_final: 0.6003 (tt) REVERT: A 237 ARG cc_start: 0.6452 (mtm-85) cc_final: 0.6177 (mpp80) REVERT: A 353 TRP cc_start: 0.7913 (p-90) cc_final: 0.7612 (p-90) REVERT: A 408 ARG cc_start: 0.7837 (mpp-170) cc_final: 0.7603 (ptp-110) REVERT: A 436 TRP cc_start: 0.6619 (p90) cc_final: 0.6419 (p90) REVERT: A 574 ASP cc_start: 0.8082 (t70) cc_final: 0.7794 (t0) REVERT: A 740 MET cc_start: 0.8647 (mmm) cc_final: 0.8333 (tpp) REVERT: A 776 LYS cc_start: 0.8269 (tttt) cc_final: 0.7817 (ttpt) REVERT: A 794 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.6977 (mt) REVERT: A 869 MET cc_start: 0.8584 (mtm) cc_final: 0.8324 (mtp) REVERT: A 988 GLU cc_start: 0.8235 (mp0) cc_final: 0.7931 (pm20) REVERT: B 45 SER cc_start: 0.8706 (p) cc_final: 0.8410 (t) REVERT: B 201 PHE cc_start: 0.7102 (t80) cc_final: 0.6545 (t80) REVERT: B 389 ASP cc_start: 0.8273 (t70) cc_final: 0.7940 (t0) REVERT: B 436 TRP cc_start: 0.6833 (p90) cc_final: 0.6367 (p90) REVERT: B 516 GLU cc_start: 0.7353 (tt0) cc_final: 0.6679 (mt-10) REVERT: B 776 LYS cc_start: 0.8225 (tttt) cc_final: 0.7926 (tttm) REVERT: B 790 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8088 (ptpt) REVERT: B 794 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.6967 (mt) REVERT: B 869 MET cc_start: 0.8680 (mtt) cc_final: 0.8332 (mtp) REVERT: B 1002 GLN cc_start: 0.8142 (tt0) cc_final: 0.7819 (tt0) REVERT: B 1119 ASN cc_start: 0.8124 (m-40) cc_final: 0.7904 (m-40) REVERT: C 32 PHE cc_start: 0.7740 (m-80) cc_final: 0.7373 (m-80) REVERT: C 201 PHE cc_start: 0.6577 (t80) cc_final: 0.6082 (t80) REVERT: C 241 LEU cc_start: 0.6616 (mp) cc_final: 0.6231 (mp) REVERT: C 436 TRP cc_start: 0.6901 (p90) cc_final: 0.6372 (p90) REVERT: C 516 GLU cc_start: 0.7527 (tt0) cc_final: 0.6890 (mt-10) REVERT: C 571 ASP cc_start: 0.6733 (OUTLIER) cc_final: 0.6243 (t0) REVERT: C 776 LYS cc_start: 0.8251 (tttt) cc_final: 0.7969 (tttm) REVERT: C 794 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.6843 (mt) REVERT: C 1045 LYS cc_start: 0.8542 (ttpp) cc_final: 0.8125 (tptt) outliers start: 46 outliers final: 31 residues processed: 250 average time/residue: 0.4769 time to fit residues: 144.0636 Evaluate side-chains 236 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 48 optimal weight: 0.4980 chunk 273 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 251 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 151 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 207 HIS B1088 HIS C 66 HIS C 207 HIS C 613 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.173975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.124519 restraints weight = 31415.161| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.60 r_work: 0.3641 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24297 Z= 0.176 Angle : 0.641 15.856 33174 Z= 0.318 Chirality : 0.048 0.404 3948 Planarity : 0.004 0.039 4164 Dihedral : 4.506 41.037 3099 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.88 % Allowed : 14.24 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 2844 helix: 1.73 (0.21), residues: 675 sheet: -0.27 (0.17), residues: 768 loop : -0.62 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.020 0.001 TYR C 396 PHE 0.022 0.002 PHE A 32 TRP 0.041 0.002 TRP B 353 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (24198) covalent geometry : angle 0.59949 / 0.31 (32913) SS BOND : bond 0.00551 / 0.37 ( 36) SS BOND : angle 2.85524 / 1.87 ( 72) hydrogen bonds : bond 0.04286 / 2.70 ( 993) hydrogen bonds : angle 5.63530 / 3.91 ( 2871) link_BETA1-4 : bond 0.00329 / 0.18 ( 15) link_BETA1-4 : angle 0.94007 / 0.67 ( 45) link_NAG-ASN : bond 0.00548 / 0.35 ( 48) link_NAG-ASN : angle 2.84047 / 1.87 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9119.75 seconds wall clock time: 155 minutes 60.00 seconds (9360.00 seconds total)